Toward Switchable Photovoltaic Effect via Tailoring Mobile Oxygen Vacancies in Perovskite Oxide Films.

PubMed

Ge, Chen; Jin, Kui-Juan; Zhang, Qing-Hua; Du, Jian-Yu; Gu, Lin; Guo, Hai-Zhong; Yang, Jing-Ting; Gu, Jun-Xing; He, Meng; Xing, Jie; Wang, Can; Lu, Hui-Bin; Yang, Guo-Zhen

2016-12-21

The defect chemistry of perovskite oxides involves the cause to most of their abundant functional properties, including interface magnetism, charge transport, ionic exchange, and catalytic activity. The possibility to achieve dynamic control over oxygen anion vacancies offers a unique opportunity for the development of appealing switchable devices, which at present are commonly based on ferroelectric materials. Herein, we report the discovery of a switchable photovoltaic effect, that the sign of the open voltage and the short circuit current can be reversed by inverting the polarity of the applied field, upon electrically tailoring the distribution of oxygen vacancies in perovskite oxide films. This phenomenon is demonstrated in lateral photovoltaic devices based on both ferroelectric BiFeO 3 and paraelectric SrTiO 3 films, under a reversed applied field whose magnitude is much smaller than the coercivity value of BiFeO 3 . The migration of oxygen vacancies was directly observed by employing an advanced annular bright-field scanning transmission electron microscopy technique with in situ biasing equipment. We conclude that the band bending induced by the motion of oxygen vacancies is the driving force for the reversible switching between two photovoltaic states. The present work can provide an active path for the design of novel switchable photovoltaic devices with a wide range of transition metal oxides in terms of the ionic degrees of freedom.

DNA-assisted upconversion nanoplatform for imaging-guided synergistic therapy and laser-switchable drug detoxification.

PubMed

Li, Luoyuan; Hao, Panlong; Wei, Peng; Fu, Limin; Ai, Xicheng; Zhang, Jianping; Zhou, Jing

2017-08-01

The side effects of chemotherapy bring significant physical and psychological suffering to patients. To solve this urgent medical problem, Yb 3+ and Er 3+ co-doped NaLuF 4 upconversion nanoparticles (UCNPs) were constructed for upconversion luminescence (UCL)-labeled diagnosis under 980 nm laser irradiation. The UCNPs were then modified layer by layer with polypyrrole and a special programming DNA segment as photothermal conversion agents and controllable drug carriers, respectively. The nanoplatform was successfully used for imaging-guided synergistic therapy (photothermal therapy and chemotherapy) at a safe power density (300 mW cm -2 ), and DNA-assisted detoxification at lower temperature in cancer cells when the laser off. The synergistic therapy of the nanoplatform achieved a higher therapeutic index (∼85%) than chemotherapy only (∼44%) and photothermal therapy only (∼25%) in vitro. In vivo experiments also suggested that the nanoplatform had a higher therapeutic effect and lower side effects. The toxicity study was also evaluated, indicating the nanoplatform is low toxic to living system. This multifunctional upconversion nanoplatform provided an innovative method for imaging-guided photothermal-chemotherapy and laser-switchable drug detoxification. Copyright © 2017 Elsevier Ltd. All rights reserved.

Interface modulated currents in periodically proton exchanged Mg doped lithium niobate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neumayer, Sabine M.; Rodriguez, Brian J., E-mail: brian.rodriguez@ucd.ie, E-mail: gallo@kth.se; Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4

2016-03-21

Conductivity in Mg doped lithium niobate (Mg:LN) plays a key role in the reduction of photorefraction and is therefore widely exploited in optical devices. However, charge transport through Mg:LN and across interfaces such as electrodes also yields potential electronic applications in devices with switchable conductivity states. Furthermore, the introduction of proton exchanged (PE) phases in Mg:LN enhances ionic conductivity, thus providing tailorability of conduction mechanisms and functionality dependent on sample composition. To facilitate the construction and design of such multifunctional electronic devices based on periodically PE Mg:LN or similar ferroelectric semiconductors, fundamental understanding of charge transport in these materials, asmore » well as the impact of internal and external interfaces, is essential. In order to gain insight into polarization and interface dependent conductivity due to band bending, UV illumination, and chemical reactivity, wedge shaped samples consisting of polar oriented Mg:LN and PE phases were investigated using conductive atomic force microscopy. In Mg:LN, three conductivity states (on/off/transient) were observed under UV illumination, controllable by the polarity of the sample and the externally applied electric field. Measurements of currents originating from electrochemical reactions at the metal electrode–PE phase interfaces demonstrate a memresistive and rectifying capability of the PE phase. Furthermore, internal interfaces such as domain walls and Mg:LN–PE phase boundaries were found to play a major role in the accumulation of charge carriers due to polarization gradients, which can lead to increased currents. The insight gained from these findings yield the potential for multifunctional applications such as switchable UV sensitive micro- and nanoelectronic devices and bistable memristors.« less

Switchable Schottky diode characteristics induced by electroforming process in Mn-doped ZnO thin films

NASA Astrophysics Data System (ADS)

Nam, Yoonseung; Hwang, Inrok; Oh, Sungtaek; Lee, Sangik; Lee, Keundong; Hong, Sahwan; Kim, Jinsoo; Choi, Taekjib; Ho Park, Bae

2013-04-01

We investigated the asymmetric current-voltage (I-V) characteristics and accompanying unipolar resistive switching of pure ZnO and Mn(1%)-doped ZnO (Mn:ZnO) films sandwiched between Pt electrodes. After electroforming, a high resistance state of the Mn:ZnO capacitor revealed switchable diode characteristics whose forward direction was determined by the polarity of the electroforming voltage. Linear fitting of the I-V curves highlighted that the rectifying behavior was influenced by a Schottky barrier at the Pt/Mn:ZnO interface. Our results suggest that formation of conducting filaments from the cathode during the electroforming process resulted in a collapse of the Schottky barrier (near the cathode), and rectifying behaviors dominated by a remnant Schottky barrier near the anode.

Dipole pinning effect on photovoltaic characteristics of ferroelectric BiFeO3 films

NASA Astrophysics Data System (ADS)

Biswas, P. P.; Thirmal, Ch.; Pal, S.; Murugavel, P.

2018-01-01

Ferroelectric bismuth ferrite is an attractive candidate for switchable devices. The effect of dipole pinning due to the oxygen vacancy layer on the switching behavior of the BiFeO3 thin film fabricated by the chemical solution deposition method was studied after annealing under air, O2, and N2 environment. The air annealed film showed well defined and dense grains leading to a lower leakage current and superior electrical properties compared to the other two films. The photovoltage and transient photocurrent measured under positive and negative poling elucidated the switching nature of the films. Though the air and O2 annealed films showed a switchable photovoltaic response, the response was severely affected by oxygen vacancies in the N2 annealed film. In addition, the open circuit voltage was found to be mostly dependent on the polarization of BiFeO3 rather than the Schottky barriers at the interface. This work provides an important insight into the effect of dipole pinning caused by oxygen vacancies on the switchable photovoltaic effect of BiFeO3 thin films along with the importance of stoichiometric, defect free, and phase pure samples to facilitate meaningful practical applications.

Achievement of two logical states through a polymer/silicon interface for organic-inorganic hybrid memory

NASA Astrophysics Data System (ADS)

Chen, Jianhui; Chen, Bingbing; Shen, Yanjiao; Guo, Jianxin; Liu, Baoting; Dai, Xiuhong; Xu, Ying; Mai, Yaohua

2017-11-01

A hysteresis loop of minority carrier lifetime vs voltage is found in polystyrenesulfonate (PSS)/Si organic-inorganic hybrid heterojunctions, implying an interfacial memory effect. Capacitance-voltage and conductance-voltage hysteresis loops are observed and reveal a memory window. A switchable interface state, which can be controlled by charge transfer based on an electrochemical oxidation/deoxidation process, is suggested to be responsible for this hysteresis effect. We perform first-principle total-energy calculations on the influence of external electric fields and electrons or holes, which are injected into interface states on the adsorption energy of PSS on Si. It is demonstrated that the dependence of the interface adsorption energy difference on the electric field is the origin of this two-state switching. These results offer a concept of organic-inorganic hybrid interface memory being optically or electrically readable, low-cost, and compatible with the flexible organic electronics.

Stacked Switchable Element and Diode Combination

DOEpatents

Branz, H. M.; Wang, Q.

2006-06-27

A device (10) comprises a semiconductor diode (12) and a switchable element (14) positioned in stacked adjacent relationship so that the semiconductor diode (12) and the switchable element (14) are electrically connected in series with one another. The switchable element (14) is switchable from a low-conductance state to a high-conductance state in response to the application of a forming voltage to the switchable element (14).

Stacked switchable element and diode combination

DOEpatents

Branz, Howard M.; Wang, Qi

2006-06-27

A device (10) comprises a semiconductor diode (12) and a switchable element (14) positioned in stacked adjacent relationship so that the semiconductor diode (12) and the switchable element (14) are electrically connected in series with one another. The switchable element (14) is switchable from a low-conductance state to a high-conductance state in response to the application of a forming voltage to the switchable element (14).

Stacked switchable element and diode combination with a low breakdown switchable element

DOEpatents

Wang, Qi [Littleton, CO; Ward, James Scott [Englewood, CO; Hu, Jian [Englewood, CO; Branz, Howard M [Boulder, CO

2012-06-19

A device (10) comprises a semiconductor diode (12) and a switchable element (14) positioned in stacked adjacent relationship. The semiconductor diode (12) and the switchable element (14) are electrically connected in series with one another. The switchable element (14) is switchable from a low-conductance state to a high-conductance state in response to the application of a low-density forming current and/or a low voltage.

Polarization and interface charge coupling in ferroelectric/AlGaN/GaN heterostructure

NASA Astrophysics Data System (ADS)

Zhang, Min; Kong, Yuechan; Zhou, Jianjun; Xue, Fangshi; Li, Liang; Jiang, Wenhai; Hao, Lanzhong; Luo, Wenbo; Zeng, Huizhong

2012-03-01

Asymmetrical shift behaviors of capacitance-voltage (C-V) curve with opposite direction are observed in two AlGaN/GaN metal-ferroelectric-semiconductor (MFS) heterostructures with Pb(Zr,Ti)O3 and LiNbO3 gate dielectrics. By incorporating the switchable polar nature of the ferroelectric into a self-consistent calculation, the coupling effect between the ferroelectric and the interface charges is disclosed. The opposite initial orientation of ferroelectric dipoles determined by the interface charges is essentially responsible for the different C-V characteristics. A critical fixed charge density of -1.27 × 1013cm-2 is obtained, which plays a key role in the dependence of the C-V characteristic on the ferroelectric polarization. The results pave the way for design of memory devices based on MFS structure with heteropolar interface.

Facilitating mathematics learning for students with upper extremity disabilities using touch-input system.

PubMed

Choi, Kup-Sze; Chan, Tak-Yin

2015-03-01

To investigate the feasibility of using tablet device as user interface for students with upper extremity disabilities to input mathematics efficiently into computer. A touch-input system using tablet device as user interface was proposed to assist these students to write mathematics. User-switchable and context-specific keyboard layouts were designed to streamline the input process. The system could be integrated with conventional computer systems only with minor software setup. A two-week pre-post test study involving five participants was conducted to evaluate the performance of the system and collect user feedback. The mathematics input efficiency of the participants was found to improve during the experiment sessions. In particular, their performance in entering trigonometric expressions by using the touch-input system was significantly better than that by using conventional mathematics editing software with keyboard and mouse. The participants rated the touch-input system positively and were confident that they could operate at ease with more practice. The proposed touch-input system provides a convenient way for the students with hand impairment to write mathematics and has the potential to facilitate their mathematics learning. Implications for Rehabilitation Students with upper extremity disabilities often face barriers to learning mathematics which is largely based on handwriting. Conventional computer user interfaces are inefficient for them to input mathematics into computer. A touch-input system with context-specific and user-switchable keyboard layouts was designed to improve the efficiency of mathematics input. Experimental results and user feedback suggested that the system has the potential to facilitate mathematics learning for the students.

2000 survey of window manufacturers on the subject of switchable glass

NASA Astrophysics Data System (ADS)

LaPointe, Michael R.; Sottile, Gregory M.

2001-11-01

The results of a 2000 survey of United States window manufacturers on the subject of switchable glass are discussed. The areas covered in this paper include awareness of the overall product category of switchable glass and various types of switchable glass, attitudes toward specific features of switchable glass, expectations for manufacturer production of such products, expectations for market penetration rates among end-product consumers, levels of price sensitivity among window manufacturers regarding switchable glass, and expectations for the pace of new product development within the window industry over the next five years.

Switchable DNA wire: deposition-stripping of copper nanoclusters as an "ON-OFF" nanoswitch.

PubMed

Zhu, Xiaoli; Liu, Siyu; Cao, Jiepei; Mao, Xiaoxia; Li, Genxi

2016-01-19

Today, a consensus that DNA working as a molecular wire shows promise in nanoscale electronics is reached. Considering that the "ON-OFF" switch is the basis of a logic circuit, the switch of DNA-mediated charge transport (DNA CT) should be conquered. Here, on the basis of chemical or electrochemical deposition and stripping of DNA-templated copper nanoclusters (CuNCs), we develop an "ON-OFF" nanoswitch for DNA CT. While CuNCs are deposited, the DNA CT is blocked, which can be also recovered after stripping the CuNCs. A switch cycle can be completed in a few seconds and can be repeated for many times. Moreover, by regulating the amount of reagents, deposition/stripping time, applied potential, etc., the switch is adjustable to make the wire at either an "ON-OFF" state or an intermediate state. We believe that this concept and the successful implementation will promote the practical application of DNA wire one step further.

Switchable DNA wire: deposition-stripping of copper nanoclusters as an “ON-OFF” nanoswitch

PubMed Central

Zhu, Xiaoli; Liu, Siyu; Cao, Jiepei; Mao, Xiaoxia; Li, Genxi

2016-01-01

Today, a consensus that DNA working as a molecular wire shows promise in nanoscale electronics is reached. Considering that the “ON-OFF” switch is the basis of a logic circuit, the switch of DNA-mediated charge transport (DNA CT) should be conquered. Here, on the basis of chemical or electrochemical deposition and stripping of DNA-templated copper nanoclusters (CuNCs), we develop an “ON-OFF” nanoswitch for DNA CT. While CuNCs are deposited, the DNA CT is blocked, which can be also recovered after stripping the CuNCs. A switch cycle can be completed in a few seconds and can be repeated for many times. Moreover, by regulating the amount of reagents, deposition/stripping time, applied potential, etc., the switch is adjustable to make the wire at either an “ON-OFF” state or an intermediate state. We believe that this concept and the successful implementation will promote the practical application of DNA wire one step further. PMID:26781761

Charge-switchable gold nanoparticles for enhanced enzymatic thermostability.

PubMed

Shankar, Shiv; Soni, Sarvesh K; Daima, Hemant K; Selvakannan, P R; Khire, Jayant M; Bhargava, Suresh K; Bansal, Vipul

2015-09-07

This study illustrates a facile strategy for efficient immobilization of enzymes on a metal nanoparticle surface. The strategy proposed here enables the enzymatic activity to be retained while increasing the enzyme thermostability. It is demonstrated that the use of a zwitterionic amino acid tyrosine as a reducing and capping agent to synthesise gold nanoparticles allows efficient immobilization of phytase enzyme through charge-switchable electrostatic interactions. The detailed kinetic and thermodynamic studies reveal that the proposed enzyme immobilization strategy improves the overall quality of phytase by reducing the activation energy required for substrate hydrolysis and broadening the temperature window in which immobilized enzyme is able to operate. The outcomes of this study indicate that the underlying zwitterionic nature of 20 natural amino acids along with significant variability in their isoelectric points and hydropathy indices as well the ability of some of the amino acids to reduce metal ions is likely to offer significant opportunities for tailoring nano-bio interfaces in a rational manner for a range of biological applications.

pH-Switchable Interaction of a Carboxybetaine Ester-Based SAM with DNA and Gold Nanoparticles.

PubMed

Filip, Jaroslav; Popelka, Anton; Bertok, Tomas; Holazova, Alena; Osicka, Josef; Kollar, Jozef; Ilcikova, Marketa; Tkac, Jan; Kasak, Peter

2017-07-11

We describe a self-assembled monolayer (SAM) on a gold surface with a carboxybetaine ester functionality to control the interaction between DNA and gold nanoparticles via pH. The negatively charged phosphate backbone of DNA interacts with and adsorbs to the positively charged carboxybetaine esters on the SAM. DNA release can be achieved by the hydrolysis of carboxybetaine ester (CBE) to a zwitterionic carboxybetaine state. Furthermore, the adsorption of negatively charged citrate-capped gold nanoparticles to a SAM-modified plain gold surface can be controlled by the pH. The SAM based on carboxybetaine ester allows for the homogeneous adsorption of particles, whereas the SAM after hydrolysis at high pH repels AuNP adsorption. The antifouling surface properties of the surface modified with carboxybetaine were investigated with protein samples.

Ferroelectrics: A pathway to switchable surface chemistry and catalysis

NASA Astrophysics Data System (ADS)

Kakekhani, Arvin; Ismail-Beigi, Sohrab; Altman, Eric I.

2016-08-01

It has been known for more than six decades that ferroelectricity can affect a material's surface physics and chemistry thereby potentially enhancing its catalytic properties. Ferroelectrics are a class of materials with a switchable electrical polarization that can affect surface stoichiometry and electronic structure and thus adsorption energies and modes; e.g., molecular versus dissociative. Therefore, ferroelectrics may be utilized to achieve switchable surface chemistry whereby surface properties are not fixed but can be dynamically controlled by, for example, applying an external electric field or modulating the temperature. Several important examples of applications of ferroelectric and polar materials in photocatalysis and heterogeneous catalysis are discussed. In photocatalysis, the polarization direction can control band bending at water/ferroelectric and ferroelectric/semiconductor interfaces, thereby facilitating charge separation and transfer to the electrolyte and enhancing photocatalytic activity. For gas-surface interactions, available results suggest that using ferroelectrics to support catalytically active transition metals and oxides is another way to enhance catalytic activity. Finally, the possibility of incorporating ferroelectric switching into the catalytic cycle itself is described. In this scenario, a dynamic collaboration of two polarization states can be used to drive reactions that have been historically challenging to achieve on surfaces with fixed chemical properties (e.g., direct NOx decomposition and the selective partial oxidation of methane). These predictions show that dynamic modulation of the polarization can help overcome some of the fundamental limitations on catalytic activity imposed by the Sabatier principle.

Polymerase/DNA interactions and enzymatic activity: multi-parameter analysis with electro-switchable biosurfaces

NASA Astrophysics Data System (ADS)

Langer, Andreas; Schräml, Michael; Strasser, Ralf; Daub, Herwin; Myers, Thomas; Heindl, Dieter; Rant, Ulrich

2015-07-01

The engineering of high-performance enzymes for future sequencing and PCR technologies as well as the development of many anticancer drugs requires a detailed analysis of DNA/RNA synthesis processes. However, due to the complex molecular interplay involved, real-time methodologies have not been available to obtain comprehensive information on both binding parameters and enzymatic activities. Here we introduce a chip-based method to investigate polymerases and their interactions with nucleic acids, which employs an electrical actuation of DNA templates on microelectrodes. Two measurement modes track both the dynamics of the induced switching process and the DNA extension simultaneously to quantitate binding kinetics, dissociation constants and thermodynamic energies. The high sensitivity of the method reveals previously unidentified tight binding states for Taq and Pol I (KF) DNA polymerases. Furthermore, the incorporation of label-free nucleotides can be followed in real-time and changes in the DNA polymerase conformation (finger closing) during enzymatic activity are observable.

Programmable bioelectronics in a stimuli-encoded 3D graphene interface.

PubMed

Parlak, Onur; Beyazit, Selim; Tse-Sum-Bui, Bernadette; Haupt, Karsten; Turner, Anthony P F; Tiwari, Ashutosh

2016-05-21

The ability to program and mimic the dynamic microenvironment of living organisms is a crucial step towards the engineering of advanced bioelectronics. Here, we report for the first time a design for programmable bioelectronics, with 'built-in' switchable and tunable bio-catalytic performance that responds simultaneously to appropriate stimuli. The designed bio-electrodes comprise light and temperature responsive compartments, which allow the building of Boolean logic gates (i.e."OR" and "AND") based on enzymatic communications to deliver logic operations.

DNA Microcapsule for Photo-Triggered Drug Release Systems.

PubMed

Kamiya, Yukiko; Yamada, Yoshinobu; Muro, Takahiro; Matsuura, Kazunori; Asanuma, Hiroyuki

2017-12-19

In this study we constructed spherical photo-responsive microcapsules composed of three photo-switchable DNA strands. These strands first formed a three-way junction (TWJ) motif that further self-assembled to form microspheres through hybridization of the sticky-end regions of each branch. To serve as the photo-switch, multiple unmodified azobenzene (Azo) or 2,6-dimethyl-4-(methylthio)azobenzene (SDM-Azo) were introduced into the sticky-end regions via a d-threoninol linker. The DNA capsule structure deformed upon trans-to-cis isomerization of Azo or SDM-Azo induced by specific light irradiation. In addition, photo-triggered release of encapsulated small molecules from the DNA microcapsule was successfully achieved. Moreover, we demonstrated that photo-triggered release of doxorubicin caused cytotoxicity to cultured cells. This biocompatible photo-responsive microcapsule has potential application as a photo-controlled drug-release system. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural and optical properties of Mg2 Ni Hx switchable mirrors upon hydrogen loading

NASA Astrophysics Data System (ADS)

Lohstroh, W.; Westerwaal, R. J.; van Mechelen, J. L. M.; Chacon, C.; Johansson, E.; Dam, B.; Griessen, R.

2004-10-01

The structural, thermodynamic and optical properties of Mg2Ni thin films covered with Pd are investigated upon exposure to hydrogen. Similar to bulk, thin films of metallic Mg2Ni take up 4 hydrogen per formula unit and semiconducting transparent Mg2NiH4-δ is formed. The dielectric function γ˜ of Mg2Ni and fully loaded Mg2NiH4-δ is determined from reflection and transmission measurements using a Drude-Lorentz parametrization. Besides the two “normal” optical states of a switchable mirror—metallic reflecting and semiconducting transparent— Mg2NiHx exhibit a third “black” state at intermediate hydrogen concentrations with low reflection and essentially zero transmission. This state originates from a subtle interplay of the optical properties of the constituent materials and a self-organized double layering of the film during loading. Mg2NiH4-δ preferentially nucleates at the film/substrate interface and not—as intuitively expected—close to the catalytic Pd capping layer. Using γ˜Mg2Ni and γ˜Mg2NiH4 and this loading sequence, the optical response at all hydrogen concentrations can be described quantitatively. The uncommon hydrogen loading sequence is confirmed by x-ray diffraction and hydrogen profiling using the resonant nuclear reaction H1(N15,αγ)C12 . Pressure-composition isotherms suggest that the formation of Mg2NiH4-δ at the film/substrate interface is mainly due to locally enhanced kinetics.

Photo-switchable membrane and method

DOEpatents

Marshall, Kenneth L; Glowacki, Eric

2013-05-07

Switchable gas permeation membranes in which a photo-switchable low-molecular-weight liquid crystalline (LC) material acts as the active element, and a method of making such membranes. Different LC eutectic mixtures were doped with mesogenic azo dyes and infused into track-etched porous membranes with regular cylindrical pores. Photo-induced isothermal phase changes in the imbibed mesogenic material afforded large, reversible changes in the permeability of the photo-switchable membrane to nitrogen. For example, membranes imbibed with a photo-switchable cyanobiphenyl LC material demonstrated low permeability in the nematic state, while the photo-generated isotropic state demonstrated a 16.times.-greater sorption coefficient. Both states obey a high linear sorption behavior in accordance with Henry's Law. In contrast, membranes imbibed with a photo-switchable phenyl benzoate LC material showed the opposite permeability behavior to the biphenyl-imbibed membrane, along with nonlinear sorption behavior.

Layered Metal Nanoparticle Structures on Electrodes for Sensing, Switchable Controlled Uptake/Release, and Photo-electrochemical Applications.

PubMed

Tel-Vered, Ran; Kahn, Jason S; Willner, Itamar

2016-01-06

Layered metal nanoparticle (NP) assemblies provide highly porous and conductive composites of unique electrical and optical (plasmonic) properties. Two methods to construct layered metal NP matrices are described, and these include the layer-by-layer deposition of NPs, or the electropolymerization of monolayer-functionalized NPs, specifically thioaniline-modified metal NPs. The layered NP composites are used as sensing matrices through the use of electrochemistry or surface plasmon resonance (SPR) as transduction signals. The crosslinking of the metal NP composites with molecular receptors, or the imprinting of molecular recognition sites into the electropolymerized NP matrices lead to selective and chiroselective sensing interfaces. Furthermore, the electrosynthesis of redox-active, imprinted, bis-aniline bridged Au NP composites yields electrochemically triggered "sponges" for the switchable uptake and release of electron-acceptor substrates, and results in conductive surfaces of electrochemically controlled wettability. Also, photosensitizer-relay-crosslinked Au NP composites, or electrochemically polymerized layered semiconductor quantum dot/metal NP matrices on electrodes, are demonstrated as functional nanostructures for photoelectrochemical applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photo-switchable microbial fuel-cells.

PubMed

Schlesinger, Orr; Dandela, Rambabu; Bhagat, Ashok; Adepu, Raju; Meijler, Michael M; Xia, Lin; Alfonta, Lital

2018-05-01

Regulation of Bio-systems in a clean, simple, and efficient way is important for the design of smart bio-interfaces and bioelectronic devices. Light as a non-invasive mean to control the activity of a protein enables spatial and temporal control far superior to other chemical and physical methods. The ability to regulate the activity of a catalytic enzyme in a biofuel-cell reduces the waste of resources and energy and turns the fuel-cell into a smart and more efficient device for power generation. Here we present a microbial-fuel-cell based on a surface displayed, photo-switchable alcohol dehydrogenase. The enzyme was modified near the active site using non-canonical amino acids and a small photo-reactive molecule, which enables reversible control of enzymatic activity. Depending on the modification site, the enzyme exhibits reversible behavior upon irradiation with UV and visible light, in both biochemical, and electrochemical assays. The change observed in power output of a microbial fuel cell utilizing the modified enzyme was almost five-fold, between inactive and active states. © 2018 Wiley Periodicals, Inc.

Programmable bioelectronics in a stimuli-encoded 3D graphene interface

NASA Astrophysics Data System (ADS)

Parlak, Onur; Beyazit, Selim; Tse-Sum-Bui, Bernadette; Haupt, Karsten; Turner, Anthony P. F.; Tiwari, Ashutosh

2016-05-01

The ability to program and mimic the dynamic microenvironment of living organisms is a crucial step towards the engineering of advanced bioelectronics. Here, we report for the first time a design for programmable bioelectronics, with `built-in' switchable and tunable bio-catalytic performance that responds simultaneously to appropriate stimuli. The designed bio-electrodes comprise light and temperature responsive compartments, which allow the building of Boolean logic gates (i.e. ``OR'' and ``AND'') based on enzymatic communications to deliver logic operations.The ability to program and mimic the dynamic microenvironment of living organisms is a crucial step towards the engineering of advanced bioelectronics. Here, we report for the first time a design for programmable bioelectronics, with `built-in' switchable and tunable bio-catalytic performance that responds simultaneously to appropriate stimuli. The designed bio-electrodes comprise light and temperature responsive compartments, which allow the building of Boolean logic gates (i.e. ``OR'' and ``AND'') based on enzymatic communications to deliver logic operations. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr02355j

Mechanistic Insights on the Photosensitized Chemistry of a Fatty Acid at the Air/Water Interface

PubMed Central

2016-01-01

Interfaces are ubiquitous in the environment and many atmospheric key processes, such as gas deposition, aerosol, and cloud formation are, at one stage or another, strongly impacted by physical and chemical processes occurring at interfaces. Here, the photoinduced chemistry of an air/water interface coated with nonanoic acid—a fatty acid surfactant we use as a proxy for chemically complex natural aqueous surface microlayers—was investigated as a source of volatile and semivolatile reactive organic species. The carboxylic acid coating significantly increased the propensity of photosensitizers, chosen to mimic those observed in real environmental waters, to partition to the interface and enhance reactivity there. Photochemical formation of functionalized and unsaturated compounds was systematically observed upon irradiation of these coated surfaces. The role of a coated interface appears to be critical in providing a concentrated medium allowing radical–radical reactions to occur in parallel with molecular oxygen additions. Mechanistic insights are provided from extensive analysis of products observed in both gas and aqueous phases by online switchable reagent ion-time of flight-mass spectrometry and by off-line ultraperformance liquid chromatography coupled to a Q Exactive high resolution mass spectrometer through heated electrospray ionization, respectively. PMID:27611489

Electrically switchable polymer stabilised broadband infrared reflectors and their potential as smart windows for energy saving in buildings.

PubMed

Khandelwal, Hitesh; Loonen, Roel C G M; Hensen, Jan L M; Debije, Michael G; Schenning, Albertus P H J

2015-07-01

Electrically switchable broadband infrared reflectors that are relatively transparent in the visible region have been fabricated using polymer stabilised cholesteric liquid crystals. The IR reflectors can change their reflection/transmission properties by applying a voltage in response to changes in environmental conditions. Simulations predict that a significant amount of energy can be saved on heating, cooling and lighting of buildings in places such as Madrid by using this switchable IR reflector. We have also fabricated a switchable IR reflector which can also generate electricity. These polymer based switchable IR reflectors are of high potential as windows of automobiles and buildings to control interior temperatures and save energy.

Electrically switchable polymer stabilised broadband infrared reflectors and their potential as smart windows for energy saving in buildings

PubMed Central

Khandelwal, Hitesh; Loonen, Roel C. G. M.; Hensen, Jan L. M.; Debije, Michael G.; Schenning, Albertus P. H. J.

2015-01-01

Electrically switchable broadband infrared reflectors that are relatively transparent in the visible region have been fabricated using polymer stabilised cholesteric liquid crystals. The IR reflectors can change their reflection/transmission properties by applying a voltage in response to changes in environmental conditions. Simulations predict that a significant amount of energy can be saved on heating, cooling and lighting of buildings in places such as Madrid by using this switchable IR reflector. We have also fabricated a switchable IR reflector which can also generate electricity. These polymer based switchable IR reflectors are of high potential as windows of automobiles and buildings to control interior temperatures and save energy. PMID:26132328

HMSIW-based switchable units using super compact loaded shunt stubs and its applications on SIW/HMSIW switches

NASA Astrophysics Data System (ADS)

Chen, Haidong; Che, Wenquan; Zhang, Tianyu; Cao, Yue; Feng, Wenjie

2018-06-01

Half-mode substrate integrated waveguide (HMSIW) switchable unit, built by HMSIW section with loaded single or multi-microstrip shunt stub(s), was proposed in this work. Both shorted and opened stubs were studied, investigated and compared, bandwidth enhancement method for proposed switchable units was proposed and demonstrated. Based on these switchable units, narrowband and broadband HMSIW single-pole-single-through (SPST) switches, SIW SPST switch and SIW/HMSIW-based single-pole-double-through (SPDT) switch were designed, fabricated and measured. Good performances were observed experimentally for these proposed circuits, showing the advantages of proposed concept and an excellent candidate for switchable or reconfigurable SIW/HMSIW circuits or systems.

DNA origami nanorobot fiber optic genosensor to TMV.

PubMed

Torelli, Emanuela; Manzano, Marisa; Srivastava, Sachin K; Marks, Robert S

2018-01-15

In the quest of greater sensitivity and specificity of diagnostic systems, one continually searches for alternative DNA hybridization methods, enabling greater versatility and where possible field-enabled detection of target analytes. We present, herein, a hybrid molecular self-assembled scaffolded DNA origami entity, intimately immobilized via capture probes linked to aminopropyltriethoxysilane, onto a glass optical fiber end-face transducer, thus producing a novel biosensor. Immobilized DNA nanorobots with a switchable flap can then be actuated by a specific target DNA present in a sample, by exposing a hemin/G-quadruplex DNAzyme, which then catalyzes the generation of chemiluminescence, once the specific fiber probes are immersed in a luminol-based solution. Integrating organic nanorobots to inorganic fiber optics creates a hybrid system that we demonstrate as a proof-of-principle can be utilized in specific DNA sequence detection. This system has potential applications in a wide range of fields, including point-of-care diagnostics or cellular in vivo biosensing when using ultrathin fiber optic probes for research purposes. Copyright © 2017 Elsevier B.V. All rights reserved.

Detection and size analysis of proteins with switchable DNA layers.

PubMed

Rant, Ulrich; Pringsheim, Erika; Kaiser, Wolfgang; Arinaga, Kenji; Knezevic, Jelena; Tornow, Marc; Fujita, Shozo; Yokoyama, Naoki; Abstreiter, Gerhard

2009-04-01

We introduce a chip-compatible scheme for the label-free detection of proteins in real-time that is based on the electrically driven conformation switching of DNA oligonucleotides on metal surfaces. The switching behavior is a sensitive indicator for the specific recognition of IgG antibodies and antibody fragments, which can be detected in quantities of less than 10(-18) mol on the sensor surface. Moreover, we show how the dynamics of the induced molecular motion can be monitored by measuring the high-frequency switching response. When proteins bind to the layer, the increase in hydrodynamic drag slows the switching dynamics, which allows us to determine the size of the captured proteins. We demonstrate the identification of different antibody fragments by means of their kinetic fingerprint. The switchDNA method represents a generic approach to simultaneously detect and size target molecules using a single analytical platform.

Reversible Modulation of DNA-Based Hydrogel Shapes by Internal Stress Interactions.

PubMed

Hu, Yuwei; Kahn, Jason S; Guo, Weiwei; Huang, Fujian; Fadeev, Michael; Harries, Daniel; Willner, Itamar

2016-12-14

We present the assembly of asymmetric two-layer hybrid DNA-based hydrogels revealing stimuli-triggered reversibly modulated shape transitions. Asymmetric, linear hydrogels that include layer-selective switchable stimuli-responsive elements that control the hydrogel stiffness are designed. Trigger-induced stress in one of the layers results in the bending of the linear hybrid structure, thereby minimizing the elastic free energy of the systems. The removal of the stress by a counter-trigger restores the original linear bilayer hydrogel. The stiffness of the DNA hydrogel layers is controlled by thermal, pH (i-motif), K + ion/crown ether (G-quadruplexes), chemical (pH-doped polyaniline), or biocatalytic (glucose oxidase/urease) triggers. A theoretical model relating the experimental bending radius of curvatures of the hydrogels with the Young's moduli and geometrical parameters of the hydrogels is provided. Promising applications of shape-regulated stimuli-responsive asymmetric hydrogels include their use as valves, actuators, sensors, and drug delivery devices.

CO2-Triggered Switchable Solvents, Surfactants, and Other Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jessop, Philip G.; Mercer, Sean; Heldebrant, David J.

2012-06-14

Waste CO2 at atmospheric pressure can be used to trigger dramatic changes in the properties of certain switchable materials. Compared to other triggers such as light, acids, oxidants, CO2 has the advantages that it is inexpensive, nonhazardous, non-accumulating in the system, easily removed, and it does not require the material to be transparent. Known CO2-triggered switchable materials 10 now include solvents, surfactants, solutes, catalysts, particles, polymers, and gels. The added flexibility of switchable materials represents a new strategy for minimizing energy and material consumption in process and product design.

Charge reversible gold nanoparticles for high efficient absorption and desorption of DNA

NASA Astrophysics Data System (ADS)

Wang, Can; Zhuang, Jiaqi; Jiang, Shan; Li, Jun; Yang, Wensheng

2012-10-01

Mercaptoundecylamine and mercaptoundecanoic acid co-modified Au nanoparticles were prepared by two-step ligand exchange of 6-mercaptohexanoic acid modified gold nanoparticles. Such particles terminated by appropriate ratios of the amine and carboxyl groups ( R N/C) were identified to show reversible charge on their surface, which were switchable by pH of the solution. The isoelectric point (IEP) of the particles is tunable by changing the ratios of the amine and carboxyl groups on the particle surfaces. The particles can absorb DNA effectively at pH lower than the IEP driven by the direct electrostatic interactions between DNA and the particle surface. When pH of the solutions was elevated to be higher than the IEP, the absorbed DNA can be released almost completely due to the electrostatic repulsion between the particle surface and DNA. With appropriate R N/C ratios of 0.8, the absorption and desorption efficiencies of DNA were 97 and 98 %, respectively, corresponding an extraction efficiency of 95 %. Such particles with reversible surface charges allow the high efficient extraction of DNA by simply changing pH instead of by changing salt concentration in the conventional salt bridge method.

Switchable Polymer Based Thin Film Coils as a Power Module for Wireless Neural Interfaces.

PubMed

Kim, S; Zoschke, K; Klein, M; Black, D; Buschick, K; Toepper, M; Tathireddy, P; Harrison, R; Solzbacher, F

2007-05-01

Reliable chronic operation of implantable medical devices such as the Utah Electrode Array (UEA) for neural interface requires elimination of transcutaneous wire connections for signal processing, powering and communication of the device. A wireless power source that allows integration with the UEA is therefore necessary. While (rechargeable) micro batteries as well as biological micro fuel cells are yet far from meeting the power density and lifetime requirements of an implantable neural interface device, inductive coupling between two coils is a promising approach to power such a device with highly restricted dimensions. The power receiving coils presented in this paper were designed to maximize the inductance and quality factor of the coils and microfabricated using polymer based thin film technologies. A flexible configuration of stacked thin film coils allows parallel and serial switching, thereby allowing to tune the coil's resonance frequency. The electrical properties of the fabricated coils were characterized and their power transmission performance was investigated in laboratory condition.

The origin of two-dimensional electron gases at oxide interfaces: insights from theory.

PubMed

Bristowe, N C; Ghosez, Philippe; Littlewood, P B; Artacho, Emilio

2014-04-09

The response of oxide thin films to polar discontinuities at interfaces and surfaces has generated enormous activity due to the variety of interesting effects that it gives rise to. A case in point is the discovery of the electron gas at the interface between LaAlO3 and SrTiO3, which has since been shown to be quasi-two-dimensional, switchable, magnetic and/or superconducting. Despite these findings, the origin of the two-dimensional electron gas is highly debated and several possible mechanisms remain. Here we review the main proposed mechanisms and attempt to model expected effects in a quantitative way with the ambition of better constraining what effects can/cannot explain the observed phenomenology. We do it in the framework of a phenomenological model constructed to provide an understanding of the electronic and/or redox screening of the chemical charge in oxide heterostructures. We also discuss the effect of intermixing, both conserving and not conserving the total stoichiometry.

Origin of Two-Dimensional Electron Gases at Oxide Interfaces: Insights from Theory

DOE PAGES

Bristowe, N. C.; Ghosez, Philippe; Littlewood, Peter B.; ...

2014-03-18

The response of oxide thin films to polar discontinuities at interfaces and surfaces has generated enormous activity due to the variety of interesting effects that it gives rise to. A case in point is the discovery of the electron gas at the interface between LaAlO3 and SrTiO3, which has since been shown to be quasitwodimensional, switchable, magnetic and/or superconducting. Despite these findings, the origin of the twodimensional electron gas is highly debated and several possible mechanisms remain. Here we review the main proposed mechanisms and attempt to model expected effects in a quantitative way with the ambition of better constrainingmore » what effects can/cannot explain the observed phenomenology. We do it in the framework of a phenomenological model constructed to provide an understanding of the electronic and/or redox screening of the chemical charge in oxide heterostructures. We also discuss the effect of intermixing, both conserving and not conserving the total stoichiometry« less

Pixel switching of epitaxial Pd/YHx/CaF2 switchable mirrors

PubMed

Kerssemakers; van der Molen SJ; Koeman; Gunther; Griessen

2000-08-03

Exposure of rare-earth films to hydrogen can induce a metal-insulator transition, accompanied by pronounced optical changes. This 'switchable mirror' effect has received considerable attention from theoretical, experimental and technological points of view. Most systems use polycrystalline films, but the synthesis of yttrium-based epitaxial switchable mirrors has also been reported. The latter form an extended self-organized ridge network during initial hydrogen loading, which results in the creation of micrometre-sized triangular domains. Here we observe homogeneous and essentially independent optical switching of individual domains in epitaxial switchable mirrors during hydrogen absorption. The optical switching is accompanied by topographical changes as the domains sequentially expand and contract; the ridges block lateral hydrogen diffusion and serve as a microscopic lubricant for the domain oscillations. We observe the correlated changes in topology and optical properties using in situ atomic force and optical microscopy. Single-domain phase switching is not observed in polycrystalline films, which are optically homogeneous. The ability to generate a tunable, dense pattern of switchable pixels is of technological relevance for solid-state displays based on switchable mirrors.

Internal stresses and formation of switchable nanowires at thin silica film edges

NASA Astrophysics Data System (ADS)

Phillips, J. C.

2011-02-01

At vertical edges, thin films of silicon oxide (SiO2-x) can contain defect-free semiconductive c-Si layered nanocrystals (Si NC) embedded in and supported by an insulating g-SiO2 matrix. Yaoet al. [Appl. Phys. A (in press)] have shown that a trenched thin film geometry enables the NC to form switchable nanowires (SNW) when trained by an applied field. The field required to form SNW decreases rapidly within a few cycles, or by annealing at 600 °C in even fewer cycles, and is stable to 700 °C. Here we describe the intrinsic evolution of Si NC and SNW in terms of the competition between internal stresses and electro-osmosis. The analysis relies heavily on experimental data from a wide range of thin film studies, and it explains why a vertical edge across the planar polySi-SiO2-x interface is necessary to form SNW. The discussion also shows that the formation mechanisms of Si NC and polySi/SiO2-x SNW are intrinsic and result from optimization of nanowire connectivity in the presence of residual host misfit stresses.

Light-induced protein degradation in human-derived cells.

PubMed

Sun, Wansheng; Zhang, Wenyao; Zhang, Chao; Mao, Miaowei; Zhao, Yuzheng; Chen, Xianjun; Yang, Yi

2017-05-27

Controlling protein degradation can be a valuable tool for posttranslational regulation of protein abundance to study complex biological systems. In the present study, we designed a light-switchable degron consisting of a light oxygen voltage (LOV) domain of Avena sativa phototropin 1 (AsLOV2) and a C-terminal degron. Our results showed that the light-switchable degron could be used for rapid and specific induction of protein degradation in HEK293 cells by light in a proteasome-dependent manner. Further studies showed that the light-switchable degron could also be utilized to mediate the degradation of secreted Gaussia princeps luciferase (GLuc), demonstrating the adaptability of the light-switchable degron in different types of protein. We suggest that the light-switchable degron offers a robust tool to control protein levels and may serves as a new and significant method for gene- and cell-based therapies. Copyright © 2017 Elsevier Inc. All rights reserved.

A microfluidic study of liquid-liquid extraction mediated by carbon dioxide.

PubMed

Lestari, Gabriella; Salari, Alinaghi; Abolhasani, Milad; Kumacheva, Eugenia

2016-07-05

Liquid-liquid extraction is an important separation and purification method; however, it faces a challenge in reducing the energy consumption and the environmental impact of solvent (extractant) recovery. The reversible chemical reactions of switchable solvents (nitrogenous bases) with carbon dioxide (CO2) can be implemented in reactive liquid-liquid extraction to significantly reduce the cost and energy requirements of solvent recovery. The development of new effective switchable solvents reacting with CO2 and the optimization of extraction conditions rely on the ability to evaluate and screen the performance of switchable solvents in extraction processes. We report a microfluidic strategy for time- and labour-efficient studies of CO2-mediated solvent extraction. The platform utilizes a liquid segment containing an aqueous extractant droplet and a droplet of a solution of a switchable solvent in a non-polar liquid, with gaseous CO2 supplied to the segment from both sides. Following the reaction of the switchable solvent with CO2, the solvent becomes hydrophilic and transfers from the non-polar solvent to the aqueous droplet. By monitoring the time-dependent variation in droplet volumes, we determined the efficiency and extraction time for the CO2-mediated extraction of different nitrogenous bases in a broad experimental parameter space. The platform enables a significant reduction in the amount of switchable solvents used in these studies, provides accurate temporal characterization of the liquid-liquid extraction process, and offers the capability of high-throughput screening of switchable solvents.

Physical aspects of ferroelectric semiconductors for photovoltaic solar energy conversion

NASA Astrophysics Data System (ADS)

Lopez-Varo, Pilar; Bertoluzzi, Luca; Bisquert, Juan; Alexe, Marin; Coll, Mariona; Huang, Jinsong; Jimenez-Tejada, Juan Antonio; Kirchartz, Thomas; Nechache, Riad; Rosei, Federico; Yuan, Yongbo

2016-10-01

Solar energy conversion using semiconductors to fabricate photovoltaic devices relies on efficient light absorption, charge separation of electron-hole pair carriers or excitons, and fast transport and charge extraction to counter recombination processes. Ferroelectric materials are able to host a permanent electrical polarization which provides control over electrical field distribution in bulk and interfacial regions. In this review, we provide a critical overview of the physical principles and mechanisms of solar energy conversion using ferroelectric semiconductors and contact layers, as well as the main achievements reported so far. In a ferroelectric semiconductor film with ideal contacts, the polarization charge would be totally screened by the metal layers and no charge collection field would exist. However, real materials show a depolarization field, smooth termination of polarization, and interfacial energy barriers that do provide the control of interface and bulk electric field by switchable spontaneous polarization. We explore different phenomena as the polarization-modulated Schottky-like barriers at metal/ferroelectric interfaces, depolarization fields, vacancy migration, and the switchable rectifying behavior of ferroelectric thin films. Using a basic physical model of a solar cell, our analysis provides a general picture of the influence of ferroelectric effects on the actual power conversion efficiency of the solar cell device, and we are able to assess whether these effects or their combinations are beneficial or counterproductive. We describe in detail the bulk photovoltaic effect and the contact layers that modify the built-in field and the charge injection and separation in bulk heterojunction organic cells as well as in photocatalytic and water splitting devices. We also review the dominant families of ferroelectric materials that have been most extensively investigated and have provided the best photovoltaic performance.

An Intrinsically Switchable Ladder-Type Ferroelectric BST-on-Si Composite FBAR Filter.

PubMed

Lee, Seungku; Mortazawi, Amir

2016-03-01

This paper presents a ladder-type bulk acoustic wave (BAW) intrinsically switchable filter based on ferroelectric thin-film bulk acoustic resonators (FBARs). The switchable filter can be turned on and off by the application of an external bias voltage due to the electrostrictive effect in thin-film ferroelectrics. In this paper, Barium Strontium Titanate (BST) is used as the ferroelectric material. A systematic design approach for switchable ladder-type ferroelectric filters is provided based on required filter specifications. A switchable filter is implemented in the form of a BST-on-Si composite structure to control the effective electromechanical coupling coefficient of FBARs. As an experimental verification, a 2.5-stage intrinsically switchable BST-on-Si composite FBAR filter is designed, fabricated, and measured. Measurement results for a typical BST-on-Si composite FBAR show a resonator mechanical quality factor (Q(m)) of 971, as well as a (Q(m)) × f of 2423 GHz. The filter presented here provides a measured insertion loss of 7.8 dB, out-of-band rejection of 26 dB, and fractional bandwidth of 0.33% at 2.5827 GHz when the filter is in the on state at a dc bias of 40 V. In its off state, the filter exhibits an isolation of 31 dB.

A Synthetic DNA-Binding Domain Guides Distinct Chromatin-Modifying Small Molecules to Activate an Identical Gene Network.

PubMed

Han, Le; Pandian, Ganesh N; Chandran, Anandhakumar; Sato, Shinsuke; Taniguchi, Junichi; Kashiwazaki, Gengo; Sawatani, Yoshito; Hashiya, Kaori; Bando, Toshikazu; Xu, Yufang; Qian, Xuhong; Sugiyama, Hiroshi

2015-07-20

Synthetic dual-function ligands targeting specific DNA sequences and histone-modifying enzymes were applied to achieve regulatory control over multi-gene networks in living cells. Unlike the broad array of targeting small molecules for histone deacetylases (HDACs), few modulators are known for histone acetyltransferases (HATs), which play a central role in transcriptional control. As a novel chemical approach to induce selective HAT-regulated genes, we conjugated a DNA-binding domain (DBD) "I" to N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-benzamide (CTB), an artificial HAT activator. In vitro enzyme activity assays and microarray studies were used to demonstrate that distinct functional small molecules could be transformed to have identical bioactivity when conjugated with a targeting DBD. This proof-of-concept synthetic strategy validates the switchable functions of HDACs and HATs in gene regulation and provides a molecular basis for developing versatile bioactive ligands. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Differential p53 engagement in response to oxidative and oncogenic stresses in Fanconi anemia mice.

PubMed

Rani, Reena; Li, Jie; Pang, Qishen

2008-12-01

Members of the Fanconi anemia (FA) protein family are involved in repair of genetic damage caused by DNA cross-linkers. It is not clear whether the FA proteins function in oxidative DNA damage and oncogenic stress response. Here, we report that deficiency in the Fanca gene in mice elicits a p53-dependent growth arrest and DNA damage response to oxidative DNA damage and oncogenic stress. Using a Fanca-/-Trp53-/- double knockout model and a functionally switchable p53 retrovirus, we define the kinetics, dependence, and persistence of p53-mediated response to oxidative and oncogenic stresses in Fanca-/- cells. Notably, oxidative stress induces persistent p53 response in Fanca-/- cells, likely due to accumulation of unrepaired DNA damage. On the other hand, whereas wild-type cells exhibit prolonged response to oncogene activation, the p53-activating signals induced by oncogenic ras are short-lived in Fanca-/- cells, suggesting that Fanca may be required for the cell to engage p53 during constitutive ras activation. We propose that the FA proteins protect cells from stress-induced proliferative arrest and tumor evolution by acting as a modulator of the signaling pathways that link FA to p53.

Differential p53 engagement in response to oxidative and oncogenic stresses in Fanconi anemia mice

PubMed Central

Rani, Reena; Li, Jie; Pang, Qishen

2008-01-01

Members of the Fanconi anemia (FA) protein family are involved in repair of genetic damage caused by DNA cross-linkers. It is not clear whether the FA proteins function in oxidative DNA damage and oncogenic stress response. Here we report that deficiency in the Fanca gene in mice elicits a p53-dependent growth arrest and DNA damage response to oxidative DNA damage and oncogenic stress. Using a Fanca-/- Trp53-/- double knockout model and a functionally switchable p53 retrovirus, we define the kinetics, dependence, and persistence of p53-mediated response to oxidative and oncogenic stresses in Fanca-/- cells. Notably, oxidative stress induces persistent p53 response in Fanca-/- cells, likely due to accumulation of unrepaired DNA damage. On the other hand, whereas WT cells exhibit prolonged response to oncogene activation, the p53-activating signals induced by oncogenic ras are short-lived in Fanca-/- cells, suggesting that Fanca may be required for the cell to engage p53 during constitutive ras activation. We propose that the FA proteins protect cells from stress-induced proliferative arrest and tumor evolution by acting as a modulator of the signaling pathways that link FA to p53. PMID:19047147

Light-switchable polymer from cationic to zwitterionic form: synthesis, characterization, and interactions with DNA and bacterial cells.

PubMed

Sobolčiak, Patrik; Spírek, Mário; Katrlík, Jaroslav; Gemeiner, Peter; Lacík, Igor; Kasák, Peter

2013-04-25

A novel cationic polymer poly(N,N-dimethyl-N-[3-(methacroylamino) propyl]-N-[2-[(2-nitrophenyl)methoxy]-2-oxo-ethyl]ammonium chloride) is synthesized by free-radical polymerization of N-[3-(dimethylamino)propyl] methacrylamide and subsequent quaternization with o-nitrobenzyl 2-chloroacetate. The photolabile o-nitrobenzyl carboxymethyl pendant moiety is transformed to the zwitterionic carboxybetaine form upon the irradiation at 365 nm. This feature is used to condense and, upon the light irradiation, to release double-strand DNA tested by gel electrophoresis and surface plasmon resonance experiments as well as to switch the antibacterial activity to non-toxic character demonstrated for Escherichia coli bacterial cells in solution and at the surface using the self-assembled monolayers. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tunable and switchable all-fiber comb filter using a PBS-based two-stage cascaded Mach-Zehnder interferometer

NASA Astrophysics Data System (ADS)

Luo, Zhi-Chao; Luo, Ai-Ping; Xu, Wen-Cheng

2011-08-01

We propose and demonstrate a novel tunable and switchable all-fiber comb filter by employing a polarization beam splitter (PBS)-based two-stage cascaded Mach-Zehnder (M-Z) interferometer. The proposed comb filter consists of a rotatable polarizer, a fiber PBS, a non-3-dB coupler and a 3-dB coupler. By simply adjusting the polarization state of the input light, the dual-function of channel spacing tunable and wavelength switchable (interleaving) operations can be efficiently obtained. The theoretical analysis is verified by the experimental results. A comb filter with both the channel spacing tunable from 0.18 nm to 0.36 nm and the wavelength switchable functions is experimentally demonstrated.

Scaling of structure and electrical properties in ultrathin epitaxial ferroelectric heterostructures

NASA Astrophysics Data System (ADS)

Nagarajan, V.; Junquera, J.; He, J. Q.; Jia, C. L.; Waser, R.; Lee, K.; Kim, Y. K.; Baik, S.; Zhao, T.; Ramesh, R.; Ghosez, Ph.; Rabe, K. M.

2006-09-01

Scaling of the structural order parameter, polarization, and electrical properties was investigated in model ultrathin epitaxial SrRuO3/PbZr0.2Ti0.8O3/SrRuO3/SrTiO3 heterostructures. High-resolution transmission electron microscopy images revealed the interfaces to be sharp and fully coherent. Synchrotron x-ray studies show that a high tetragonality (c /a˜1.058) is maintained down to 50Å thick films, suggesting indirectly that ferroelectricity is fully preserved at such small thicknesses. However, measurement of the switchable polarization (ΔP) using a pulsed probe setup and the out-of-plane piezoelectric response (d33) revealed a systematic drop from ˜140μC/cm2 and 60pm/V for a 150Å thick film to 11μC/cm2 and 7pm/V for a 50Å thick film. This apparent contradiction between the structural measurements and the measured switchable polarization is explained by an increasing presence of a strong depolarization field, which creates a pinned 180° polydomain state for the thinnest films. Existence of a polydomain state is demonstrated by piezoresponse force microscopy images of the ultrathin films. These results suggest that the limit for a ferroelectric memory device may be much larger than the fundamental limit for ferroelectricity.

Wavelength-switchable C-band erbium-doped fibre laser incorporating all-fibre Fabry-Perot interferometer fabricated by chemical etching

NASA Astrophysics Data System (ADS)

He, Wei; Zhu, Lianqing; Dong, Mingli; Lou, Xiaoping; Luo, Fei

2018-04-01

A switchable and stable triple-wavelength, ring-cavity, erbium-doped fibre laser incorporating an all-fibre Fabry-Perot interferometer (FPI) is designed and experimentally demonstrated. In the proposed fibre laser, the all-fibre FPI is fabricated using the chemical etching method and is used to generate the filter effect. The laser threshold is 88 mW. Switchable single-wavelength lasing at 1529.9, 1545.1 and 1560.2 nm can be realized with a power fluctuation less than 0.64 dB under 20 min of scanning time at room temperature. In addition, the wavelength-switchable dual-wavelength lasers can be tuned by changing the polarization state in the experiment, and the maximum power fluctuations for the 1545.1 and 1560.2 nm lasers are less than 1.19 and 1.57 dB at 26 °C, respectively. Furthermore, a triple-wavelength laser is obtained by adjusting the polarization controller. The results demonstrate that switchable single-, dual-, or triple-wavelength lasers can be generated through the proposed fibre laser.

Switchable polarization in an unzipped graphene oxide monolayer.

PubMed

Noor-A-Alam, Mohammad; Shin, Young-Han

2016-08-14

Ferroelectricity in low-dimensional oxide materials is generally suppressed at the scale of a few nanometers, and has attracted considerable attention from both fundamental and technological aspects. Graphene is one of the thinnest materials (one atom thick). Therefore, engineering switchable polarization in non-polar pristine graphene could potentially lead to two-dimensional (2D) ferroelectric materials. In the present study, based on density functional theory, we show that an unzipped graphene oxide (UGO) monolayer can exhibit switchable polarization due to its foldable bonds between the oxygen atom and two carbon atoms underneath the oxygen. We find that a free standing UGO monolayer exhibits antiferroelectric switchable polarization. A UGO monolayer can be obtained as an intermediate product during the chemical exfoliation process of graphene. Interestingly, despite its dimensionality, our estimated polarization in a UGO monolayer is comparable to that in bulk ferroelectric materials (e.g., ferroelectric polymers). Our calculations could help realize antiferroelectric switchable polarization in 2D materials, which could find various potential applications in nanoscale devices such as sensors, actuators, and capacitors with high energy-storage density.

Switchable and non-switchable zero backscattering of dielectric nano-resonators

DOE PAGES

Wang, Feng; Wei, Qi -Huo; Htoon, Han

2015-02-27

Previous studies have shown that two-dimensional (2D) arrays of high-permittivity dielectric nanoparticles are capable of fully suppressing backward light scattering when the resonant frequencies of electrical and magnetic dipolar modes are coincident. In this paper, we numerically demonstrate that the zero-backscattering of 2D Si nanocuboid arrays can be engineered to be switchable or non-switchable in response to a variation in the environmental refractive index. For each cuboid width/length, there exist certain cuboid heights and orthogonal periodicity ratio for which the electrical and magnetic resonances exhibit similar spectra widths and equivalent sensitivities to the environmental index changes, so that the zero-backscatteringmore » is non-switchable upon environmental change. For some other cuboid heights and certain anisotropic periodicity ratios, the electric and magnetic modes exhibit different sensitivities to environmental index changes, making the zero-backscattering sensitive to environmental changes. We also show that by using two different types of nano-resonators in the unit cell, Fano resonances can be introduced to greatly enhance the switching sensitivity of zero-backscattering.« less

Surface shapes and surrounding environment analysis of single- and double-stranded DNA-binding proteins in protein-DNA interface.

PubMed

Wang, Wei; Liu, Juan; Sun, Lin

2016-07-01

Protein-DNA bindings are critical to many biological processes. However, the structural mechanisms underlying these interactions are not fully understood. Here, we analyzed the residues shape (peak, flat, or valley) and the surrounding environment of double-stranded DNA-binding proteins (DSBs) and single-stranded DNA-binding proteins (SSBs) in protein-DNA interfaces. In the results, we found that the interface shapes, hydrogen bonds, and the surrounding environment present significant differences between the two kinds of proteins. Built on the investigation results, we constructed a random forest (RF) classifier to distinguish DSBs and SSBs with satisfying performance. In conclusion, we present a novel methodology to characterize protein interfaces, which will deepen our understanding of the specificity of proteins binding to ssDNA (single-stranded DNA) or dsDNA (double-stranded DNA). Proteins 2016; 84:979-989. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface.

PubMed

Ma, Buyong; Pan, Yongping; Gunasekaran, K; Venkataraghavan, R Babu; Levine, Arnold J; Nussinov, Ruth

2005-03-15

p53, the tumor suppressor protein, functions as a dimer of dimers. However, how the tetramer binds to the DNA is still an open question. In the crystal structure, three copies of the p53 monomers (containing chains A, B, and C) were crystallized with the DNA-consensus element. Although the structure provides crucial data on the p53-DNA contacts, the active oligomeric state is unclear because the two dimeric (A-B and B-C) interfaces present in the crystal cannot both exist in the tetramer. Here, we address the question of which of these two dimeric interfaces may be more biologically relevant. We analyze the sequence and structural properties of the p53-p53 dimeric interfaces and carry out extensive molecular dynamics simulations of the crystal structures of the human and mouse p53 dimers. We find that the A-B interface residues are more conserved than those of the B-C. Molecular dynamics simulations show that the A-B interface can provide a stable DNA-binding motif in the dimeric state, unlike B-C. Our results indicate that the interface between chains A-B in the p53-DNA complex constitutes a better candidate for a stable biological interface, whereas the B-C interface is more likely to be due to crystal packing. Thus, they have significant implications toward our understanding of DNA binding by p53 as well as p53-mediated interactions with other proteins.

Switchable wavelength-selective and diffuse metamaterial absorber/emitter with a phase transition spacer layer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hao; Yang, Yue; Wang, Liping, E-mail: liping.wang@asu.edu

2014-08-18

We numerically demonstrate a switchable metamaterial absorber/emitter by thermally turning on or off the excitation of magnetic resonance upon the phase transition of vanadium dioxide (VO{sub 2}). Perfect absorption peak exists around the wavelength of 5 μm when the excitation of magnetic resonance is supported with the insulating VO{sub 2} spacer layer. The wavelength-selective absorption is switched off when the magnetic resonance is disabled with metallic VO{sub 2} that shorts the top and bottom metallic structures. The resonance wavelength can be tuned with different geometry, and the switchable metamaterial exhibits diffuse behaviors at oblique angles. The results would facilitate the designmore » of switchable metamaterials for active control in energy and sensing applications.« less

In situ Charge Density Imaging of Metamaterials made with Switchable Two dimensionalElectron Gas at Oxide Heterointerfaces

DTIC Science & Technology

2017-11-28

AFRL-AFOSR-JP-TR-2018-0028 In-situ Charge-Density Imaging of Metamaterials from Switchable 2D electron gas CHANG BEOM EOM UNIVERSITY OF WISCONSIN...Imaging of Metamaterials made with Switchable Two-dimensional Electron Gas at Oxide Heterointerfaces 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA2386-16-1...using pulsed laser deposition atomic with in-situ reflection high-energy electron diffraction (RHEED). We have also demonstrated that the inline

Effect of hydrogen-switchable mirrors on the Casimir force.

PubMed

Iannuzzi, Davide; Lisanti, Mariangela; Capasso, Federico

2004-03-23

We present systematic measurements of the Casimir force between a gold-coated plate and a sphere coated with a hydrogen-switchable mirror. Hydrogen-switchable mirrors are shiny metals that can become transparent upon hydrogenation. Despite such a dramatic change of the optical properties of the sphere, we did not observe any significant decrease of the Casimir force after filling the experimental apparatus with hydrogen. This counterintuitive result can be explained by the Lifshitz theory that describes the Casimir attraction between metallic and dielectric materials.

Effect of hydrogen-switchable mirrors on the Casimir force

PubMed Central

Iannuzzi, Davide; Lisanti, Mariangela; Capasso, Federico

2004-01-01

We present systematic measurements of the Casimir force between a gold-coated plate and a sphere coated with a hydrogen-switchable mirror. Hydrogen-switchable mirrors are shiny metals that can become transparent upon hydrogenation. Despite such a dramatic change of the optical properties of the sphere, we did not observe any significant decrease of the Casimir force after filling the experimental apparatus with hydrogen. This counterintuitive result can be explained by the Lifshitz theory that describes the Casimir attraction between metallic and dielectric materials. PMID:15024111

Transition Metal Switchable Mirror

ScienceCinema

None

2017-12-09

The switchable-mirrors technology was developed by Tom Richardson and Jonathan Slack of Berkeley Lab's Environmental Energy Technologies Division. By using transition metals rather than the rare earth metals used in the first metal-hydride switchable mirrors, Richardson and Slack were able to lower the cost and simplify the manufacturing process. Energy performance is improved as well, because the new windows can reflect or transmit both visible and infrared light. Besides windows for offices and homes, possible applications include automobile sunroofs, signs and displays, aircraft windows, and spacecraft.

Transition Metal Switchable Mirror

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2009-08-21

The switchable-mirrors technology was developed by Tom Richardson and Jonathan Slack of Berkeley Lab's Environmental Energy Technologies Division. By using transition metals rather than the rare earth metals used in the first metal-hydride switchable mirrors, Richardson and Slack were able to lower the cost and simplify the manufacturing process. Energy performance is improved as well, because the new windows can reflect or transmit both visible and infrared light. Besides windows for offices and homes, possible applications include automobile sunroofs, signs and displays, aircraft windows, and spacecraft.

Allosteric analysis of glucocorticoid receptor-DNA interface induced by cyclic Py-Im polyamide: a molecular dynamics simulation study.

PubMed

Wang, Yaru; Ma, Na; Wang, Yan; Chen, Guangju

2012-01-01

It has been extensively developed in recent years that cell-permeable small molecules, such as polyamide, can be programmed to disrupt transcription factor-DNA interfaces and can silence aberrant gene expression. For example, cyclic pyrrole-imidazole polyamide that competes with glucocorticoid receptor (GR) for binding to glucocorticoid response elements could be expected to affect the DNA dependent binding by interfering with the protein-DNA interface. However, how such small molecules affect the transcription factor-DNA interfaces and gene regulatory pathways through DNA structure distortion is not fully understood so far. In the present work, we have constructed some models, especially the ternary model of polyamides+DNA+GR DNA-binding domain (GRDBD) dimer, and carried out molecular dynamics simulations and free energy calculations for them to address how polyamide molecules disrupt the GRDBD and DNA interface when polyamide and protein bind at the same sites on opposite grooves of DNA. We found that the cyclic polyamide binding in minor groove of DNA can induce a large structural perturbation of DNA, i.e. a >4 Å widening of the DNA minor groove and a compression of the major groove by more than 4 Å as compared with the DNA molecule in the GRDBD dimer+DNA complex. Further investigations for the ternary system of polyamides+DNA+GRDBD dimer and the binary system of allosteric DNA+GRDBD dimer revealed that the compression of DNA major groove surface causes GRDBD to move away from the DNA major groove with the initial average distance of ∼4 Å to the final average distance of ∼10 Å during 40 ns simulation course. Therefore, this study straightforward explores how small molecule targeting specific sites in the DNA minor groove disrupts the transcription factor-DNA interface in DNA major groove, and consequently modulates gene expression.

Transition metal redox switches for reversible "on/off" and "slow/fast" single-molecule magnet behaviour in dysprosium and erbium bis-diamidoferrocene complexes.

PubMed

Dickie, Courtney M; Laughlin, Alexander L; Wofford, Joshua D; Bhuvanesh, Nattamai S; Nippe, Michael

2017-12-01

Single-molecule magnets (SMMs) are considered viable candidates for next-generation data storage and quantum computing. Systems featuring switchability of their magnetization dynamics are particularly interesting with respect to accessing more complex logic gates and device architectures. Here we show that transition metal based redox events can be exploited to enable reversible switchability of slow magnetic relaxation of magnetically anisotropic lanthanide ions. Specifically, we report anionic homoleptic bis-diamidoferrocene complexes of Dy 3+ (oblate) and Er 3+ (prolate) which can be reversibly oxidized by one electron to yield their respective charge neutral redox partners (Dy: [1] - , 1 ; Er: [2] - , 2 ). Importantly, compounds 1 and 2 are thermally stable which allowed for detailed studies of their magnetization dynamics. We show that the Dy 3+ [1] - / 1 system can function as an "on"/"off" or a "slow"/"fast" redox switchable SMM system in the absence or presence of applied dc fields, respectively. The Er 3+ based [2] - / 2 system features "on"/"off" switchability of SMM properties in the presence of applied fields. Results from electrochemical investigations, UV-vis-NIR spectroscopy, and 57 Fe Mössbauer spectroscopy indicate the presence of significant electronic communication between the mixed-valent Fe ions in 1 and 2 in both solution and solid state. This comparative evaluation of redox-switchable magnetization dynamics in low coordinate lanthanide complexes may be used as a potential blueprint toward the development of future switchable magnetic materials.

Single-Cell in Situ RNA Analysis With Switchable Fluorescent Oligonucleotides.

PubMed

Xiao, Lu; Guo, Jia

2018-01-01

Comprehensive RNA analyses in individual cells in their native spatial contexts promise to transform our understanding of normal physiology and disease pathogenesis. Here we report a single-cell in situ RNA analysis approach using switchable fluorescent oligonucleotides (SFO). In this method, transcripts are first hybridized by pre-decoding oligonucleotides. These oligonucleotides subsequently recruit SFO to stain their corresponding RNA targets. After fluorescence imaging, all the SFO in the whole specimen are simultaneously removed by DNA strand displacement reactions. Through continuous cycles of target staining, fluorescence imaging, and SFO removal, a large number of different transcripts can be identified by unique fluorophore sequences and visualized at the optical resolution. To demonstrate the feasibility of this approach, we show that the hybridized SFO can be efficiently stripped by strand displacement reactions within 30 min. We also demonstrate that this SFO removal process maintains the integrity of the RNA targets and the pre-decoding oligonucleotides, and keeps them hybridized. Applying this approach, we show that transcripts can be restained in at least eight hybridization cycles with high analysis accuracy, which theoretically would enable the whole transcriptome to be quantified at the single molecule sensitivity in individual cells. This in situ RNA analysis technology will have wide applications in systems biology, molecular diagnosis, and targeted therapies.

Molecular architecture of protein-RNA recognition sites.

PubMed

Barik, Amita; C, Nithin; Pilla, Smita P; Bahadur, Ranjit Prasad

2015-01-01

The molecular architecture of protein-RNA interfaces are analyzed using a non-redundant dataset of 152 protein-RNA complexes. We find that an average protein-RNA interface is smaller than an average protein-DNA interface but larger than an average protein-protein interface. Among the different classes of protein-RNA complexes, interfaces with tRNA are the largest, while the interfaces with the single-stranded RNA are the smallest. Significantly, RNA contributes more to the interface area than its partner protein. Moreover, unlike protein-protein interfaces where the side chain contributes less to the interface area compared to the main chain, the main chain and side chain contributions flipped in protein-RNA interfaces. We find that the protein surface in contact with the RNA in protein-RNA complexes is better packed than that in contact with the DNA in protein-DNA complexes, but loosely packed than that in contact with the protein in protein-protein complexes. Shape complementarity and electrostatic potential are the two major factors that determine the specificity of the protein-RNA interaction. We find that the H-bond density at the protein-RNA interfaces is similar with that of protein-DNA interfaces but higher than the protein-protein interfaces. Unlike protein-DNA interfaces where the deoxyribose has little role in intermolecular H-bonds, due to the presence of an oxygen atom at the 2' position, the ribose in RNA plays significant role in protein-RNA H-bonds. We find that besides H-bonds, salt bridges and stacking interactions also play significant role in stabilizing protein-nucleic acids interfaces; however, their contribution at the protein-protein interfaces is insignificant.

Transition Metal Switchable Mirror

ScienceCinema

None

2017-12-29

The switchable-mirrors technology was developed by Tom Richardson and Jonathan Slack of Berkeley Lab's Environmental Energy Technologies Division. By using transition metals rather than the rare earth metals used in the first metal-hydride switchable mirrors, Richardson and Slack were able to lower the cost and simplify the manufacturing process. Energy performance is improved as well, because the new windows can reflect or transmit both visible and infrared light. Besides windows for offices and homes, possible applications include automobile sunroofs, signs and displays, aircraft windows, and spacecraft. More information at: http://windows.lbl.gov/materials/chromogenics/default.htm

Transition Metal Switchable Mirror

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2009-08-21

The switchable-mirrors technology was developed by Tom Richardson and Jonathan Slack of Berkeley Lab's Environmental Energy Technologies Division. By using transition metals rather than the rare earth metals used in the first metal-hydride switchable mirrors, Richardson and Slack were able to lower the cost and simplify the manufacturing process. Energy performance is improved as well, because the new windows can reflect or transmit both visible and infrared light. Besides windows for offices and homes, possible applications include automobile sunroofs, signs and displays, aircraft windows, and spacecraft. More information at: http://windows.lbl.gov/materials/chromogenics/default.htm

Standard atomic volumes in double-stranded DNA and packing in protein–DNA interfaces

PubMed Central

Nadassy, Katalin; Tomás-Oliveira, Isabel; Alberts, Ian; Janin, Joël; Wodak, Shoshana J.

2001-01-01

Standard volumes for atoms in double-stranded B-DNA are derived using high resolution crystal structures from the Nucleic Acid Database (NDB) and compared with corresponding values derived from crystal structures of small organic compounds in the Cambridge Structural Database (CSD). Two different methods are used to compute these volumes: the classical Voronoi method, which does not depend on the size of atoms, and the related Radical Planes method which does. Results show that atomic groups buried in the interior of double-stranded DNA are, on average, more tightly packed than in related small molecules in the CSD. The packing efficiency of DNA atoms at the interfaces of 25 high resolution protein–DNA complexes is determined by computing the ratios between the volumes of interfacial DNA atoms and the corresponding standard volumes. These ratios are found to be close to unity, indicating that the DNA atoms at protein–DNA interfaces are as closely packed as in crystals of B-DNA. Analogous volume ratios, computed for buried protein atoms, are also near unity, confirming our earlier conclusions that the packing efficiency of these atoms is similar to that in the protein interior. In addition, we examine the number, volume and solvent occupation of cavities located at the protein–DNA interfaces and compared them with those in the protein interior. Cavities are found to be ubiquitous in the interfaces as well as inside the protein moieties. The frequency of solvent occupation of cavities is however higher in the interfaces, indicating that those are more hydrated than protein interiors. Lastly, we compare our results with those obtained using two different measures of shape complementarity of the analysed interfaces, and find that the correlation between our volume ratios and these measures, as well as between the measures themselves, is weak. Our results indicate that a tightly packed environment made up of DNA, protein and solvent atoms plays a significant role in protein–DNA recognition. PMID:11504874

Low-Energy Water Recovery from Subsurface Brines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choi, Young Chul; Kim, Gyu Dong; Hendren, Zachary

A novel non-aqueous phase solvent (NAS) desalination process was proposed and developed in this research project. The NAS desalination process uses less energy than thermal processes, doesn’t require any additional chemicals for precipitation, and can be utilized to treat high TDS brine. In this project, our experimental work determined that water solubility changes and selective absorption are the key characteristics of NAS technology for successful desalination. Three NAS desalination mechanisms were investigated: (1) CO2 switchable, (2) high-temp absorption to low-temp desorption (thermally switchable), and (3) low-temp absorption to high-temp desorption (thermally switchable). Among these mechanisms, thermally switchable (low-temp absorption tomore » high-temp desorption) showed the highest water recovery and relatively high salt rejection. A test procedure for semi-continuous, bench scale NAS desalination process was also developed and used to assess performance under a range of conditions.« less

Insights into the relationship between CO₂ switchability and basicity: examples of melamine and its derivatives.

PubMed

Yin, Hongyao; Feng, Yujun; Liu, Hanbin; Mu, Meng; Fei, Chenhong

2014-08-26

Owing to its wide availability, nontoxicity, and low cost, CO2 working as a trigger to reversibly switch material properties, including polarity, ionic strength, hydrophilicity, viscosity, surface charge, and degree of polymerization or cross-linking, has attracted an increasing attention in recent years. However, a quantitative correlation between basicity of these materials and their CO2 switchability has been less documented though it is of great importance for fabricating switchable system. In this work, the "switch-on" and "switch-off" abilities of melamine and its amino-substituted derivatives by introducing and removing CO2 are studied, and then their quantitative relationship with basicity is established, so that performances of other organobases can be quantitatively predicted. These findings are beneficial for forecasting the CO2 stimuli-responsive behavior of other organobases and the design of CO2-switchable materials.

Controllable light filters using an all-solid-state switchable mirror with a Mg-Ir thin film for preterm infant incubators

NASA Astrophysics Data System (ADS)

Tajima, Kazuki; Shimoike, Mika; Li, Heng; Inagaki, Masumi; Izumi, Hitomi; Akiyama, Misaki; Matsushima, Yukiko; Ohta, Hidenobu

2013-04-01

We have fabricated a controllable light filter using an all-solid-state switchable mirror incorporating a Mg-Ir thin film for use in preterm infant incubators. The solid-state switchable mirror device was fabricated by depositing a multilayer on a glass substrate. The mixed hydride of MgH2 and Mg6Ir2H11 created from the Mg-Ir thin film is red in the transparent state. The optical switching speeds between the reflective and transparent red states depended on applied voltage. The device showed three states, namely, reflective, black, and transparent red, due to the properties of the switchable mirror material. These results suggest that the material could be used as a controllable light filter for preterm infant incubators, since it eliminates the light wavelength that disturbs regular sleep-wake cycles of preterm infants.

Giant switchable photovoltaic effect in organometal trihalide perovskite devices

NASA Astrophysics Data System (ADS)

Xiao, Zhengguo; Yuan, Yongbo; Shao, Yuchuan; Wang, Qi; Dong, Qingfeng; Bi, Cheng; Sharma, Pankaj; Gruverman, Alexei; Huang, Jinsong

2015-02-01

Organolead trihalide perovskite (OTP) materials are emerging as naturally abundant materials for low-cost, solution-processed and highly efficient solar cells. Here, we show that, in OTP-based photovoltaic devices with vertical and lateral cell configurations, the photocurrent direction can be switched repeatedly by applying a small electric field of <1 V μm-1. The switchable photocurrent, generally observed in devices based on ferroelectric materials, reached 20.1 mA cm-2 under one sun illumination in OTP devices with a vertical architecture, which is four orders of magnitude larger than that measured in other ferroelectric photovoltaic devices. This field-switchable photovoltaic effect can be explained by the formation of reversible p-i-n structures induced by ion drift in the perovskite layer. The demonstration of switchable OTP photovoltaics and electric-field-manipulated doping paves the way for innovative solar cell designs and for the exploitation of OTP materials in electrically and optically readable memristors and circuits.

Interfacial electrofluidics in confined systems

PubMed Central

Tang, Biao; Groenewold, Jan; Zhou, Min; Hayes, Robert A.; Zhou, Guofu (G.F.)

2016-01-01

Electrofluidics is a versatile principle that can be used for high speed actuation of liquid interfaces. In most of the applications, the fundamental mechanism of electro-capillary instability plays a crucial role, yet it’s potential richness in confined fluidic layers has not been well addressed. Electrofluidic displays which are comprised of thin pixelated colored films in a range of architectures are excellent systems for studying such phenomena. In this study we show theoretically and experimentally that confinement leads to the generation of a cascade of voltage dependent modes as a result of the electro-capillary instability. In the course of reconciling theory with our experimental data we have observed a number of previously unreported phenomena such as a significant induction time (several milliseconds) prior to film rupture as well as a rupture location not corresponding to the minimum electric field strength in the case of the standard convex water/oil interface used in working devices. These findings are broadly applicable to a wide range of switchable electrofluidic applications and devices having confined liquid films. PMID:27221211

Carrier Density Modulation in Ge Heterostructure by Ferroelectric Switching

DOE PAGES

Ponath, Patrick; Fredrickson, Kurt; Posadas, Agham B.; ...

2015-01-14

The development of nonvolatile logic through direct coupling of spontaneous ferroelectric polarization with semiconductor charge carriers is nontrivial, with many issues, including epitaxial ferroelectric growth, demonstration of ferroelectric switching, and measurable semiconductor modulation. Here we report a true ferroelectric field effect carrier density modulation in an underlying Ge(001) substrate by switching of the ferroelectric polarization in the epitaxial c-axis-oriented BaTiO3 (BTO) grown by molecular beam epitaxy (MBE) on Ge. Using density functional theory, we demonstrate that switching of BTO polarization results in a large electric potential change in Ge. Aberration-corrected electron microscopy confirms the interface sharpness, and BTO tetragonality. Electron-energy-lossmore » spectroscopy (EELS) indicates the absence of any low permittivity interlayer at the interface with Ge. Using piezoelectric force microscopy (PFM), we confirm the presence of fully switchable, stable ferroelectric polarization in BTO that appears to be single domain. Using microwave impedance microscopy (MIM), we clearly demonstrate a ferroelectric field effect.« less

Evidence for oxygen vacancy or ferroelectric polarization induced switchable diode and photovoltaic effects in BiFeO3 based thin films.

PubMed

Guo, Yiping; Guo, Bing; Dong, Wen; Li, Hua; Liu, Hezhou

2013-07-12

The diode and photovoltaic effects of BiFeO3 and Bi0.9Sr0.1FeO(3-δ) polycrystalline thin films were investigated by poling the films with increased magnitude and alternating direction. It was found that both electromigration of oxygen vacancies and polarization flipping are able to induce switchable diode and photovoltaic effects. For the Bi0.9Sr0.1FeO(3-δ) thin films with high oxygen vacancy concentration, reversibly switchable diode and photovoltaic effects can be observed due to the electromigration of oxygen vacancies under an electric field much lower than its coercive field. However, for the pure BiFeO3 thin films with lower oxygen vacancy concentration, the reversibly switchable diode and photovoltaic effect is hard to detect until the occurrence of polarization flipping. The switchable diode and photovoltaic effects can be explained well using the concepts of Schottky-like barrier-to-Ohmic contacts resulting from the combination of oxygen vacancies and polarization. The sign of photocurrent could be independent of the direction of polarization when the modulation of the energy band induced by oxygen vacancies is large enough to offset that induced by polarization. The photovoltaic effect induced by the electromigration of oxygen vacancies is unstable due to the diffusion of oxygen vacancies or the recombination of oxygen vacancies with hopping electrons. Our work provides deep insights into the nature of diode and photovoltaic effects in ferroelectric films, and will facilitate the advanced design of switchable devices combining spintronic, electronic, and optical functionalities.

Antagonistic Enzymes in a Biocatalytic pH Feedback System Program Autonomous DNA Hydrogel Life Cycles.

PubMed

Heinen, Laura; Heuser, Thomas; Steinschulte, Alexander; Walther, Andreas

2017-08-09

Enzymes regulate complex functions and active behavior in natural systems and have shown increasing prospect for developing self-regulating soft matter systems. Striving for advanced autonomous hydrogel materials with fully programmable, self-regulated life cycles, we combine two enzymes with an antagonistic pH-modulating effect in a feedback-controlled biocatalytic reaction network (BRN) and couple it to pH-responsive DNA hydrogels to realize hydrogel systems with distinct preprogrammable lag times and lifetimes in closed systems. The BRN enables precise and orthogonal internal temporal control of the "ON" and "OFF" switching times of the temporary gel state by modulation of programmable, nonlinear pH changes. The time scales are tunable by variation of the enzyme concentrations and additional buffer substances. The resulting material system operates in full autonomy after injection of the chemical fuels driving the BRN. The concept may open new applications inherent to DNA hydrogels, for instance, autonomous shape memory behavior for soft robotics. We further foresee general applicability to achieve autonomous life cycles in other pH switchable systems.

Improving the Molecular Ion Signal Intensity for In Situ Liquid SIMS Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Yufan; Yao, Juan; Ding, Yuanzhao

In situ liquid secondary ion mass spectrometry (SIMS) enabled by system for analysis at the liquid vacuum interface (SALVI) has proven to be a promising new tool to provide molecular information at solid–liquid and liquid–vacuum interfaces. However, the initial data showed that useful signals in positive ion spectra are too weak to be meaningful in most cases. In addition, it is difficult to obtain strong negative molecular ion signals when m/z>200. These two drawbacks have been the biggest obstacle towards practical use of this new analytical approach. In this study, we report that strong and reliable positive and negative molecularmore » signals are achievable after optimizing the SIMS experimental conditions. Four model systems, including a 1,8-diazabicycloundec-7-ene (DBU)-base switchable ionic liquid, a live Shewanella oneidensis biofilm, a hydrated mammalian epithelia cell, and an electrolyte popularly used in Li ion batteries were studied. A signal enhancement of about two orders of magnitude was obtained in comparison with non-optimized conditions. Therefore, molecular ion signal intensity has become very acceptable to use for in situ liquid SIMS to study solid–liquid and liquid–vacuum interfaces.« less

Improving the Molecular Ion Signal Intensity for In Situ Liquid SIMS Analysis.

PubMed

Zhou, Yufan; Yao, Juan; Ding, Yuanzhao; Yu, Jiachao; Hua, Xin; Evans, James E; Yu, Xiaofei; Lao, David B; Heldebrant, David J; Nune, Satish K; Cao, Bin; Bowden, Mark E; Yu, Xiao-Ying; Wang, Xue-Lin; Zhu, Zihua

2016-12-01

In situ liquid secondary ion mass spectrometry (SIMS) enabled by system for analysis at the liquid vacuum interface (SALVI) has proven to be a promising new tool to provide molecular information at solid-liquid and liquid-vacuum interfaces. However, the initial data showed that useful signals in positive ion spectra are too weak to be meaningful in most cases. In addition, it is difficult to obtain strong negative molecular ion signals when m/z>200. These two drawbacks have been the biggest obstacle towards practical use of this new analytical approach. In this study, we report that strong and reliable positive and negative molecular signals are achievable after optimizing the SIMS experimental conditions. Four model systems, including a 1,8-diazabicycloundec-7-ene (DBU)-base switchable ionic liquid, a live Shewanella oneidensis biofilm, a hydrated mammalian epithelia cell, and an electrolyte popularly used in Li ion batteries were studied. A signal enhancement of about two orders of magnitude was obtained in comparison with non-optimized conditions. Therefore, molecular ion signal intensity has become very acceptable for use of in situ liquid SIMS to study solid-liquid and liquid-vacuum interfaces. Graphical Abstract ᅟ.

Block copolymer micelles as switchable templates for nanofabrication.

PubMed

Krishnamoorthy, Sivashankar; Pugin, Raphaël; Brugger, Juergen; Heinzelmann, Harry; Hoogerwerf, Arno C; Hinderling, Christian

2006-04-11

Block copolymer inverse micelles from polystyrene-block-poly-2-vinylpyridine (PS-b-P2VP) deposited as monolayer films onto surfaces show responsive behavior and are reversibly switchable between two states of different topography and surface chemistry. The as-coated films are in the form of arrays of nanoscale bumps, which can be transformed into arrays of nanoscale holes by switching through exposure to methanol. The use of these micellar films to act as switchable etch masks for the structuring of the underlying material to form either pillars or holes depending on the switching state is demonstrated.

Use of a conformational switching aptamer for rapid and specific ex vivo identification of central nervous system lymphoma in a xenograft model

NASA Astrophysics Data System (ADS)

Georges, Joseph F.; Liu, Xiaowei; Eschbacher, Jennifer; Nichols, Joshua; Mooney, Michael A.; Joy, Anna; Spetzler, Robert F.; Feuerstein, Burt G.; Anderson, Trent; Preul, Mark C.; Yan, Hao; Nakaji, Peter

2018-02-01

Improved tools for providing specific intraoperative diagnoses could improve patient care. In neurosurgery, intraoperatively differentiating non-operative lesions can be challenging, often necessitating immunohistochemical (IHC) procedures which require up to 24-48 hours. Here, we evaluate the feasibility of generating rapid ex vivo specific labeling using a novel lymphoma-specific fluorescent switchable aptamer. Our B-cell lymphoma-specific switchable aptamer produced only low-level fluorescence in its unbound conformation and generated an 8-fold increase in fluorescence once bound to its target on CD20-positive lymphoma cells. The aptamer demonstrated strong binding to B-cell lymphoma cells within 10 minutes of incubation. We applied the switchable aptamer to ex vivo xenograft tissue harboring B-cell lymphoma and astrocytoma, and within one hour specific visual identification of lymphoma was routinely possible. In this proof-of-concept study in human cell culture and orthotopic xenografts, we conclude that a fluorescent switchable aptamer can provide rapid and specific labeling of B-cell lymphoma, and that developing aptamer-based labeling approaches could simplify tissue staining and drastically reduce time to histopathological diagnoses compared with IHC-based methods. We propose that switchable aptamers could enhance expeditious, accurate intraoperative decision-making.

Gadolinium nanoparticle based switchable mirrors: quenching of hydrogenation-dehydrogenation hysteresis.

PubMed

Aruna, I; Mehta, B R; Malhotra, L K

2007-06-01

A continuous and reversible 'structural, optical, and electronic' transition between the reflecting metallic dihydride and transparent semiconducting trihydride states observed in rare earth metals on hydrogenation make these materials and their hydrides suitable for switchable mirror, sensing, and other technological applications. Recently Pd capped Gd nanoparticle based 'new generation' switchable mirrors have been fabricated with extended color neutrality, better optical contrast, and faster kinetics in comparison to the polycrystalline, epitaxial, alloy, and multilayer films. The present report aims at investigating the effect of nanoparticle nature on the hydrogenation-dehydrogenation hysteresis in switchable mirrors by carrying out in situ measurement of optical transmittance and electrode potentials during electrochemical hydrogen loading-deloading of Gd nanoparticle samples. Interestingly, Gd nanoparticle samples were observed to exhibit quenched hysteresis. The quenching of hysteresis in hydrogen-induced properties has been attributed to the absence of structural transition upon hydrogenation, reduction in topographical interlocking of the grains and elimination of lateral clamping of the slack nanoparticle layer to the substrate.

Giant switchable photovoltaic effect in organometal trihalide perovskite devices

DOE PAGES

Xiao, Zhengguo; Yuan, Yongbo; Shao, Yuchuan; ...

2014-12-08

Organolead trihalide perovskite (OTP) materials are emerging as naturally abundant materials for low-cost, solution-processed and highly efficient solar cells. Here, we show that, in OTP-based photovoltaic devices with vertical and lateral cell configurations, the photocurrent direction can be switched repeatedly by applying a small electric field of <1 V μm –1. The switchable photocurrent, generally observed in devices based on ferroelectric materials, reached 20.1 mA cm –2 under one sun illumination in OTP devices with a vertical architecture, which is four orders of magnitude larger than that measured in other ferroelectric photovoltaic devices. This field-switchable photovoltaic effect can be explainedmore » by the formation of reversible p–i–n structures induced by ion drift in the perovskite layer. Furthermore, the demonstration of switchable OTP photovoltaics and electric-field-manipulated doping paves the way for innovative solar cell designs and for the exploitation of OTP materials in electrically and optically readable memristors and circuits.« less

Mechanics of responsive polymers via conformationally switchable molecules

NASA Astrophysics Data System (ADS)

Brighenti, Roberto; Artoni, Federico; Vernerey, Franck; Torelli, Martina; Pedrini, Alessandro; Domenichelli, Ilaria; Dalcanale, Enrico

2018-04-01

Active materials are those capable of giving some physical reaction under external stimuli coming from the environment such as temperature, pH, light, mechanical stress, etc. Reactive polymeric materials can be obtained through the introduction of switchable molecules in their network, i.e. molecules having two distinct stable conformations: if properly linked to the hosting polymer chains, the switching from one state to the other can promote a mechanical reaction of the material, detectable at the macroscale, and thus enables us to tune the response according to a desired functionality. In the present paper, the main aspects of the mechanical behavior of polymeric materials with embedded switchable molecules-properly linked to the polymer's chains-are presented and discussed. Starting from the micro mechanisms occurring in such active material, a continuum model is developed, providing a straightforward implementation in computational approaches. Finally, some experimental outcomes related to a switchable molecules (known as quinoxaline cavitands) added to an elastomeric PDMS under chemical stimuli, are presented and quantitatively discussed through the use of the developed mechanical framework.

Universal light-switchable gene promoter system

DOEpatents

Quail, Peter H.; Huq, Enamul; Tepperman, James; Sato, Sae

2005-02-22

An artificial promoter system that can be fused upstream of any desired gene enabling reversible induction or repression of the expression of the gene at will in any suitable host cell or organisms by light is described. The design of the system is such that a molecule of the plant photoreceptor phytochrome is targeted to the specific DNA binding site in the promoter by a protein domain that is fused to the phytochrome and that specifically recognizes this binding site. This bound phytochrome, upon activation by light, recruits a second fusion protein consisting of a protein that binds to phytochrome only upon light activation and a transcriptional activation domain that activates expression of the gene downstream of the promoter.

Integrated, nonvolatile, high-speed analog random access memory

NASA Technical Reports Server (NTRS)

Katti, Romney R. (Inventor); Wu, Jiin-Chuan (Inventor); Stadler, Henry L. (Inventor)

1994-01-01

This invention provides an integrated, non-volatile, high-speed random access memory. A magnetically switchable ferromagnetic or ferrimagnetic layer is sandwiched between an electrical conductor which provides the ability to magnetize the magnetically switchable layer and a magneto resistive or Hall effect material which allows sensing the magnetic field which emanates from the magnetization of the magnetically switchable layer. By using this integrated three-layer form, the writing process, which is controlled by the conductor, is separated from the storage medium in the magnetic layer and from the readback process which is controlled by the magnetoresistive layer. A circuit for implementing the memory in CMOS or the like is disclosed.

Choice-Based Segmentation as an Enrollment Management Tool

ERIC Educational Resources Information Center

Young, Mark R.

2002-01-01

This article presents an approach to enrollment management based on target marketing strategies developed from a choice-based segmentation methodology. Students are classified into "switchable" or "non-switchable" segments based on their probability of selecting specific majors. A modified multinomial logit choice model is used to identify…

Use of a conformational switching aptamer for rapid and specific ex vivo identification of central nervous system lymphoma in a xenograft model.

PubMed

Georges, Joseph F; Liu, Xiaowei; Eschbacher, Jennifer; Nichols, Joshua; Mooney, Michael A; Joy, Anna; Spetzler, Robert F; Feuerstein, Burt G; Preul, Mark C; Anderson, Trent; Yan, Hao; Nakaji, Peter

2015-01-01

Improved tools for providing specific intraoperative diagnoses could improve patient care. In neurosurgery, intraoperatively differentiating non-operative lesions such as CNS B-cell lymphoma from operative lesions can be challenging, often necessitating immunohistochemical (IHC) procedures which require up to 24-48 hours. Here, we evaluate the feasibility of generating rapid ex vivo specific labeling using a novel lymphoma-specific fluorescent switchable aptamer. Our B-cell lymphoma-specific switchable aptamer produced only low-level fluorescence in its unbound conformation and generated an 8-fold increase in fluorescence once bound to its target on CD20-positive lymphoma cells. The aptamer demonstrated strong binding to B-cell lymphoma cells within 15 minutes of incubation as observed by flow cytometry. We applied the switchable aptamer to ex vivo xenograft tissue harboring B-cell lymphoma and astrocytoma, and within one hour specific visual identification of lymphoma was routinely possible. In this proof-of-concept study in human cell culture and orthotopic xenografts, we conclude that a fluorescent switchable aptamer can provide rapid and specific labeling of B-cell lymphoma, and that developing aptamer-based labeling approaches could simplify tissue staining and drastically reduce time to histopathological diagnoses compared with IHC-based methods. We propose that switchable aptamers could enhance expeditious, accurate intraoperative decision-making.

Light-switchable systems for remotely controlled drug delivery.

PubMed

Shim, Gayong; Ko, Seungbeom; Kim, Dongyoon; Le, Quoc-Viet; Park, Gyu Thae; Lee, Jaiwoo; Kwon, Taekhyun; Choi, Han-Gon; Kim, Young Bong; Oh, Yu-Kyoung

2017-12-10

Light-switchable systems have recently received attention as a new mode of remotely controlled drug delivery. In the past, a multitude of nanomedicine studies have sought to enhance the specificity of drug delivery to target sites by focusing on receptors overexpressed on malignant cells or environmental features of diseases sites. Despite these immense efforts, however, there are few clinically available nanomedicines. We need a paradigm shift in drug delivery. One strategy that may overcome the limitations of pathophysiology-based drug delivery is the use of remotely controlled delivery technology. Unlike pathophysiology-based active drug targeting strategies, light-switchable systems are not affected by the heterogeneity of cells, tissue types, and/or microenvironments. Instead, they are triggered by remote light (i.e., near-infrared) stimuli, which are absorbed by photoresponsive molecules or three-dimensional nanostructures. The sequential conversion of light to heat or reactive oxygen species can activate drug release and allow it to be spatio-temporally controlled. Light-switchable systems have been used to activate endosomal drug escape, modulate the release of chemical and biological drugs, and alter nanoparticle structures to control the release rates of drugs. This review will address the limitations of pathophysiology-based drug delivery systems, the current status of light-based remote-switch systems, and future directions in the application of light-switchable systems for remotely controlled drug delivery. Copyright © 2017 Elsevier B.V. All rights reserved.

Virtual screening on an α-helix to β-strand switchable region of the FGFR2 extracellular domain revealed positive and negative modulators.

PubMed

Diaz, Constantino; Corentin, Herbert; Thierry, Vermat; Chantal, Alcouffe; Tanguy, Bozec; David, Sibrac; Jean-Marc, Herbert; Pascual, Ferrara; Françoise, Bono; Edgardo, Ferran

2014-11-01

The secondary structure of some protein segments may vary between α-helix and β-strand. To predict these switchable segments, we have developed an algorithm, Switch-P, based solely on the protein sequence. This algorithm was used on the extracellular parts of FGF receptors. For FGFR2, it predicted that β4 and β5 strands of the third Ig-like domain were highly switchable. These two strands possess a high number of somatic mutations associated with cancer. Analysis of PDB structures of FGF receptors confirmed the switchability prediction for β5. We thus evaluated if compound-driven α-helix/β-strand switching of β5 could modulate FGFR2 signaling. We performed the virtual screening of a library containing 1.4 million of chemical compounds with two models of the third Ig-like domain of FGFR2 showing different secondary structures for β5, and we selected 32 compounds. Experimental testing using proliferation assays with FGF7-stimulated SNU-16 cells and a FGFR2-dependent Erk1/2 phosphorylation assay with FGFR2-transfected L6 cells, revealed activators and inhibitors of FGFR2. Our method for the identification of switchable proteinic regions, associated with our virtual screening approach, provides an opportunity to discover new generation of drugs with under-explored mechanism of action. © 2014 Wiley Periodicals, Inc.

Passive electrically switchable circuit element having improved tunability and method for its manufacture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mickel, Patrick R; James, Conrad D

2014-09-16

A resistive switching device and methods for making the same are disclosed. In the above said device, a resistive switching layer is interposed between opposing electrodes. The resistive switching layer comprises at least two sub-layers of switchable insulative material characterized by different ionic mobilities.

Protein analysis by time-resolved measurements with an electro-switchable DNA chip

PubMed Central

Langer, Andreas; Hampel, Paul A.; Kaiser, Wolfgang; Knezevic, Jelena; Welte, Thomas; Villa, Valentina; Maruyama, Makiko; Svejda, Matej; Jähner, Simone; Fischer, Frank; Strasser, Ralf; Rant, Ulrich

2013-01-01

Measurements in stationary or mobile phases are fundamental principles in protein analysis. Although the immobilization of molecules on solid supports allows for the parallel analysis of interactions, properties like size or shape are usually inferred from the molecular mobility under the influence of external forces. However, as these principles are mutually exclusive, a comprehensive characterization of proteins usually involves a multi-step workflow. Here we show how these measurement modalities can be reconciled by tethering proteins to a surface via dynamically actuated nanolevers. Short DNA strands, which are switched by alternating electric fields, are employed as capture probes to bind target proteins. By swaying the proteins over nanometre amplitudes and comparing their motional dynamics to a theoretical model, the protein diameter can be quantified with Angström accuracy. Alterations in the tertiary protein structure (folding) and conformational changes are readily detected, and even post-translational modifications are revealed by time-resolved molecular dynamics measurements. PMID:23839273

Encoded libraries of chemically modified peptides.

PubMed

Heinis, Christian; Winter, Greg

2015-06-01

The use of powerful technologies for generating and screening DNA-encoded protein libraries has helped drive the development of proteins as pharmaceutical ligands. However the development of peptides as pharmaceutical ligands has been more limited. Although encoded peptide libraries are typically several orders of magnitude larger than classical chemical libraries, can be more readily screened, and can give rise to higher affinity ligands, their use as pharmaceutical ligands is limited by their intrinsic properties. Two of the intrinsic limitations include the rotational flexibility of the peptide backbone and the limited number (20) of natural amino acids. However these limitations can be overcome by use of chemical modification. For example, the libraries can be modified to introduce topological constraints such as cyclization linkers, or to introduce new chemical entities such as small molecule ligands, fluorophores and photo-switchable compounds. This article reviews the chemistry involved, the properties of the peptide ligands, and the new opportunities offered by chemical modification of DNA-encoded peptide libraries. Copyright © 2015. Published by Elsevier Ltd.

The Protein-DNA Interface database

PubMed Central

2010-01-01

The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 Å or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface. We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes. PMID:20482798

The Protein-DNA Interface database.

PubMed

Norambuena, Tomás; Melo, Francisco

2010-05-18

The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 A or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface.We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes.

Biphasic Synergistic Gel Materials with Switchable Mechanics and Self-Healing Capacity.

PubMed

Zhao, Ziguang; Liu, Yuxia; Zhang, Kangjun; Zhuo, Shuyun; Fang, Ruochen; Zhang, Jianqi; Jiang, Lei; Liu, Mingjie

2017-10-16

A fabrication strategy for biphasic gels is reported, which incorporates high-internal-phase emulsions. Closely packed micro-inclusions within the elastic hydrogel matrix greatly improve the mechanical properties of the materials. The materials exhibit excellent switchable mechanics and shape-memory performance because of the switchable micro- inclusions that are incorporated into the hydrogel matrix. The produced materials demonstrated a self-healing capacity that originates from the noncovalent effect of the biphasic heteronetwork. The aforementioned characteristics suggest that the biphasic gels may serve as ideal composite gel materials with validity in a variety of applications, such as soft actuators, flexible devices, and biological materials. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of semiempirical electronic structure theory to compute the force generated by a single surface-mounted switchable rotaxane.

PubMed

Sohlberg, Karl; Bazargan, Gloria; Angelo, Joseph P; Lee, Choongkeun

2017-01-01

Herein we report a study of the switchable [3]rotaxane reported by Huang et al. (Appl Phys Lett 85(22):5391-5393, 1) that can be mounted to a surface to form a nanomechanical, linear, molecular motor. We demonstrate the application of semiempirical electronic structure theory to predict the average and instantaneous force generated by redox-induced ring shuttling. Detailed analysis of the geometric and electronic structure of the system reveals technical considerations essential to success of the approach. The force is found to be in the 100-200 pN range, consistent with published experimental estimates. Graphical Abstract A single surface-mounted switchable rotaxane.

Holding the Nucleosome Together: A Quantitative Description of the DNA-Histone Interface in Solution.

PubMed

Elbahnsi, Ahmad; Retureau, Romain; Baaden, Marc; Hartmann, Brigitte; Oguey, Christophe

2018-02-13

The nucleosome is the fundamental unit of eukaryotic genome packaging in the chromatin. In this complex, the DNA wraps around eight histone proteins to form a superhelical double helix. The resulting bending, stronger than anything observed in free DNA, raises the question of how such a distortion is stabilized by the proteic and solvent environments. In this work, the DNA-histone interface in solution was exhaustively analyzed from nucleosome structures generated by molecular dynamics. An original Voronoi tessellation technique, measuring the topology of interacting elements without any empirical or subjective adjustment, was used to characterize the interface in terms of contact area and occurrence. Our results revealed an interface more robust than previously known, combining extensive, long-lived nonelectrostatic and electrostatic interactions between DNA and both structured and unstructured histone regions. Cation accumulation makes the proximity of juxtaposed DNA gyres in the superhelix possible by shielding the strong electrostatic repulsion of the charged phosphate groups. Overall, this study provides new insights on the nucleosome cohesion, explaining how DNA distortions can be maintained in a nucleoprotein complex.

Enhanced optical discrimination system based on switchable retroreflective films

NASA Astrophysics Data System (ADS)

Schultz, Phillip; Heikenfeld, Jason

2016-04-01

Reported herein is the design, characterization, and demonstration of a laser interrogation and response optical discrimination system based on large-area corner-cube retroreflective films. The switchable retroreflective films use light-scattering liquid crystal to modulate retroreflected intensity. The system can operate with multiple wavelengths (visible to infrared) and includes variable divergence optics for irradiance adjustments and ease of system alignment. The electronic receiver and switchable retroreflector offer low-power operation (<4 mW standby) on coin cell batteries with rapid interrogation to retroreflected signal reception response times (<15 ms). The entire switchable retroreflector film is <1 mm thick and is flexible for optimal placement and increased angular response. The system was demonstrated in high ambient lighting conditions (daylight, 18k lux) with a visible 10-mW output 635-nm source out to a distance of 400 m (naked eye detection). Nighttime demonstrations were performed using a 1.5-mW, 850-nm infrared laser diode out to a distance of 400 m using a night vision camera. This system could have tagging and conspicuity applications in commercial or military settings.

Phase-field modeling of switchable diode-like current-voltage characteristics in ferroelectric BaTiO{sub 3}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Y., E-mail: yxc238@psu.edu; Randall, C. A.; Chen, L. Q.

2014-05-05

A self-consistent model has been proposed to study the switchable current-voltage (I-V) characteristics in Cu/BaTiO{sub 3}/Cu sandwiched structure combining the phase-field model of ferroelectric domains and diffusion equations for ionic/electronic transport. The electrochemical transport equations and Ginzburg-Landau equations are solved using the Chebyshev collocation algorithm. We considered a single parallel plate capacitor configuration which consists of a single layer BaTiO{sub 3} containing a single tetragonal domain orientated normal to the plate electrodes (Cu) and is subject to a sweep of ac bias from −1.0 to 1.0 V at 25 °C. Our simulation clearly shows rectifying I-V response with rectification ratios amount tomore » 10{sup 2}. The diode characteristics are switchable with an even larger rectification ratio after the polarization direction is flipped. The effects of interfacial polarization charge, dopant concentration, and dielectric constant on current responses were investigated. The switchable I-V behavior is attributed to the polarization bound charges that modulate the bulk conduction.« less

The effect of switchable water additives on clay settling.

PubMed

Chen, Chien-Shun; Lau, Ying Yin; Mercer, Sean M; Robert, Tobias; Horton, J Hugh; Jessop, Philip G

2013-01-01

The recycling of process water from strip mining extractions is a very relevant task both industrially and environmentally. The sedimentation of fine tailings during such processes, however, can often require long periods of time and/or the addition of flocculants which make later water recycling difficult. We propose the use of switchable water additives as reversible flocculants for clay/water suspensions. Switchable water additives are compounds such as diamines that make it possible to reversibly control the ionic strength of an aqueous solution. Addition of CO(2) to such an aqueous solution causes the ionic strength to rise dramatically, and the change is reversed upon removal of the CO(2). These additives, while in the presence of CO(2), promote the aggregation of clay tailings, reduce settling times, and greatly increase the clarity of the liberated water. The removal of CO(2) from the liberated water regenerates a low ionic strength solution that does not promote clay aggregation and settling until CO(2) is added again. Such reversible behavior would be useful in applications such as oil sands separations in which the recycled water must not promote aggregation. When added to kaolinite and montmorillonite clay suspensions, switchable water provided process waters of lower turbidity than those additives from inorganic salts or by CO(2)-treatment alone. When recollected, the switchable water supernatant was shown to be recyclable over three cycles for enhanced settling of kaolinite. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Binding regularities in complexes of transcription factors with operator DNA: homeodomain family.

PubMed

Chirgadze, Yu N; Zheltukhin, E I; Polozov, R V; Sivozhelezov, V S; Ivanov, V V

2009-06-01

In order to disclose general regularities of binding in homeodomain-DNA complexes we considered five of them and extended the observed regularities over the entire homeodomain family. The five complexes have been selected by similarity of protein structures and patterns of contacting residues. Their long range interactions and interfaces were compared. The long-range stage of the recognition process was characterized by electrostatic potentials about 5 Angstrom away from molecular surfaces of protein or DNA. For proteins, clear positive potential is displayed only at the side contacting the DNA. The double-chained DNA molecule displays a rather strong negative potential, especially in their grooves. Thus, a functional role of electrostatics is a guiding of the protein into the DNA major groove, so the protein and DNA could form a loose non-specific complex. At the close-range stage, neutralization of the phosphate charges by positively charged residues is necessary for decreasing the strong electrostatic potential of DNA, allowing nucleotide bases to participate in the formation of protein-DNA atomic contacts in the interface. The recognizing alpha-helix of protein was shown to form both invariant and variable groups of contacts with DNA by means of certain specific side groups. The invariant contacts included highly specific protein-DNA hydrogen bonds between asparagine and adenine, nonpolar contacts of hydrophobic amino acids serving as a stereochemical barrier for fixing the protein factor on DNA, and an interface cluster of water molecules providing local conformational mobility necessary for the dissociation process. There is a unique water molecule within the interface that is conservative and located at the interface center. Invariant contacts of the proteins are mostly formed with the TAAT motif of the promoter DNA forward strand. While the invariant contacts specify the family of homeodomains, the variable contacts that are formed with the reverse strand of DNA provide specificity of individual complexes within the homeodomain family.

Simulations of molecular self-assembled monolayers on surfaces: packing structures, formation processes and functions tuned by intermolecular and interfacial interactions.

PubMed

Wen, Jin; Li, Wei; Chen, Shuang; Ma, Jing

2016-08-17

Surfaces modified with a functional molecular monolayer are essential for the fabrication of nano-scale electronics or machines with novel physical, chemical, and/or biological properties. Theoretical simulation based on advanced quantum chemical and classical models is at present a necessary tool in the development, design, and understanding of the interfacial nanostructure. The nanoscale surface morphology, growth processes, and functions are controlled by not only the electronic structures (molecular energy levels, dipole moments, polarizabilities, and optical properties) of building units but also the subtle balance between intermolecular and interfacial interactions. The switchable surfaces are also constructed by introducing stimuli-responsive units like azobenzene derivatives. To bridge the gap between experiments and theoretical models, opportunities and challenges for future development of modelling of ferroelectricity, entropy, and chemical reactions of surface-supported monolayers are also addressed. Theoretical simulations will allow us to obtain important and detailed information about the structure and dynamics of monolayer modified interfaces, which will guide the rational design and optimization of dynamic interfaces to meet challenges of controlling optical, electrical, and biological functions.

Destabilization of the MutSα's protein-protein interface due to binding to the DNA adduct induced by anticancer agent carboplatin via molecular dynamics simulations.

PubMed

Negureanu, Lacramioara; Salsbury, Freddie R

2013-11-01

DNA mismatch repair (MMR) proteins maintain genetic integrity in all organisms by recognizing and repairing DNA errors. Such alteration of hereditary information can lead to various diseases, including cancer. Besides their role in DNA repair, MMR proteins detect and initiate cellular responses to certain type of DNA damage. Its response to the damaged DNA has made the human MMR pathway a useful target for anticancer agents such as carboplatin. This study indicates that strong, specific interactions at the interface of MutSα in response to the mismatched DNA recognition are replaced by weak, non-specific interactions in response to the damaged DNA recognition. Data suggest a severe impairment of the dimerization of MutSα in response to the damaged DNA recognition. While the core of MutSα is preserved in response to the damaged DNA recognition, the loss of contact surface and the rearrangement of contacts at the protein interface suggest a different packing in response to the damaged DNA recognition. Coupled in response to the mismatched DNA recognition, interaction energies, hydrogen bonds, salt bridges, and solvent accessible surface areas at the interface of MutSα and within the subunits are uncoupled or asynchronously coupled in response to the damaged DNA recognition. These pieces of evidence suggest that the loss of a synchronous mode of response in the MutSα's surveillance for DNA errors would possibly be one of the mechanism(s) of signaling the MMR-dependent programed cell death much wanted in anticancer therapies. The analysis was drawn from dynamics simulations.

Nanopore-CMOS Interfaces for DNA Sequencing

PubMed Central

Magierowski, Sebastian; Huang, Yiyun; Wang, Chengjie; Ghafar-Zadeh, Ebrahim

2016-01-01

DNA sequencers based on nanopore sensors present an opportunity for a significant break from the template-based incumbents of the last forty years. Key advantages ushered by nanopore technology include a simplified chemistry and the ability to interface to CMOS technology. The latter opportunity offers substantial promise for improvement in sequencing speed, size and cost. This paper reviews existing and emerging means of interfacing nanopores to CMOS technology with an emphasis on massively-arrayed structures. It presents this in the context of incumbent DNA sequencing techniques, reviews and quantifies nanopore characteristics and models and presents CMOS circuit methods for the amplification of low-current nanopore signals in such interfaces. PMID:27509529

Nanopore-CMOS Interfaces for DNA Sequencing.

PubMed

Magierowski, Sebastian; Huang, Yiyun; Wang, Chengjie; Ghafar-Zadeh, Ebrahim

2016-08-06

DNA sequencers based on nanopore sensors present an opportunity for a significant break from the template-based incumbents of the last forty years. Key advantages ushered by nanopore technology include a simplified chemistry and the ability to interface to CMOS technology. The latter opportunity offers substantial promise for improvement in sequencing speed, size and cost. This paper reviews existing and emerging means of interfacing nanopores to CMOS technology with an emphasis on massively-arrayed structures. It presents this in the context of incumbent DNA sequencing techniques, reviews and quantifies nanopore characteristics and models and presents CMOS circuit methods for the amplification of low-current nanopore signals in such interfaces.

Resistive Switching Memory Phenomena in PEDOT PSS: Coexistence of Switchable Diode Effect and Write Once Read Many Memory

PubMed Central

Nguyen, Viet Cuong; Lee, Pooi See

2016-01-01

We study resistive switching memory phenomena in conducting polymer PEDOT PSS. In the same film, there are two types of memory behavior coexisting; namely, the switchable diode effect and write once read many memory. This is the first report on switchable diode phenomenon based on conducting organic materials. The effect was explained as charge trapping of PEDOT PSS film and movement of proton. The same PEDOT PSS device also exhibits write once read many memory (WORM) phenomenon which arises due to redox reaction that reduces PEDOT PSS and renders it non-conducting. The revelation of these two types of memory phenomena in PEDOT PSS highlights the remarkable versatility of this conducting conjugated polymer. PMID:26806868

Enhanced spectral efficiency using bandwidth switchable SAW filtering for mobile satellite communications systems

NASA Technical Reports Server (NTRS)

Peach, Robert; Malarky, Alastair

1990-01-01

Currently proposed mobile satellite communications systems require a high degree of flexibility in assignment of spectral capacity to different geographic locations. Conventionally this results in poor spectral efficiency which may be overcome by the use of bandwidth switchable filtering. Surface acoustic wave (SAW) technology makes it possible to provide banks of filters whose responses may be contiguously combined to form variable bandwidth filters with constant amplitude and phase responses across the entire band. The high selectivity possible with SAW filters, combined with the variable bandwidth capability, makes it possible to achieve spectral efficiencies over the allocated bandwidths of greater than 90 percent, while retaining full system flexibility. Bandwidth switchable SAW filtering (BSSF) achieves these gains with a negligible increase in hardware complexity.

Electronic devices containing switchably conductive silicon oxides as a switching element and methods for production and use thereof

DOEpatents

Tour, James M.; Yao, Jun; Natelson, Douglas; Zhong, Lin; He, Tao

2015-09-08

In various embodiments, electronic devices containing switchably conductive silicon oxide as a switching element are described herein. The electronic devices are two-terminal devices containing a first electrical contact and a second electrical contact in which at least one of the first electrical contact or the second electrical contact is deposed on a substrate to define a gap region therebetween. A switching layer containing a switchably conductive silicon oxide resides in the gap region between the first electrical contact and the second electrical contact. The electronic devices exhibit hysteretic current versus voltage properties, enabling their use in switching and memory applications. Methods for configuring, operating and constructing the electronic devices are also presented herein.

Electronic devices containing switchably conductive silicon oxides as a switching element and methods for production and use thereof

DOEpatents

Tour, James M; Yao, Jun; Natelson, Douglas; Zhong, Lin; He, Tao

2013-11-26

In various embodiments, electronic devices containing switchably conductive silicon oxide as a switching element are described herein. The electronic devices are two-terminal devices containing a first electrical contact and a second electrical contact in which at least one of the first electrical contact or the second electrical contact is deposed on a substrate to define a gap region therebetween. A switching layer containing a switchably conductive silicon oxide resides in the the gap region between the first electical contact and the second electrical contact. The electronic devices exhibit hysteretic current versus voltage properties, enabling their use in switching and memory applications. Methods for configuring, operating and constructing the electronic devices are also presented herein.

The substrate binding interface of alkylpurine DNA glycosylase AlkD.

PubMed

Mullins, Elwood A; Rubinson, Emily H; Eichman, Brandt F

2014-01-01

Tandem helical repeats have emerged as an important DNA binding architecture. DNA glycosylase AlkD, which excises N3- and N7-alkylated nucleobases, uses repeating helical motifs to bind duplex DNA and to selectively pause at non-Watson-Crick base pairs. Remodeling of the DNA backbone promotes nucleotide flipping of the lesion and the complementary base into the solvent and toward the protein surface, respectively. The important features of this new DNA binding architecture that allow AlkD to distinguish between damaged and normal DNA without contacting the lesion are poorly understood. Here, we show through extensive mutational analysis that DNA binding and N3-methyladenine (3mA) and N7-methylguanine (7mG) excision are dependent upon each residue lining the DNA binding interface. Disrupting electrostatic or hydrophobic interactions with the DNA backbone substantially reduced binding affinity and catalytic activity. These results demonstrate that residues seemingly only involved in general DNA binding are important for catalytic activity and imply that base excision is driven by binding energy provided by the entire substrate interface of this novel DNA binding architecture. Copyright © 2013 Elsevier B.V. All rights reserved.

Destabilization of the MutSα’s protein-protein interface due to binding to the DNA adduct induced by anticancer agent Carboplatin via molecular dynamics simulations

PubMed Central

Negureanu, Lacramioara; Salsbury, Freddie R

2013-01-01

DNA mismatch repair (MMR) proteins maintain genetic integrity in all organisms by recognizing and repairing DNA errors. Such alteration of hereditary information can lead to various diseases, including cancer. Besides their role in DNA repair, MMR proteins detect and initiate cellular responses to certain type of DNA damage. Its response to the damaged DNA has made the human MMR pathway a useful target for anticancer agents such as carboplatin. This study indicates that strong, specific interactions at the interface of MutSα in response to the mismatched DNA recognition are replaced by weak, non-specific interactions in response to the damaged DNA recognition. Data suggest a severe impairment of the dimerization of MutSα in response to the damaged DNA recognition. While the core of MutSα is preserved in response to the damaged DNA recognition, the loss of contact surface and the rearrangement of contacts at the protein interface suggest a different packing in response to the damaged DNA recognition. Coupled in response to the mismatched DNA recognition, interaction energies, hydrogen bonds, salt bridges, and solvent accessible surface areas at the interface of MutSα and within the subunits are uncoupled or asynchronously coupled in response to the damaged DNA recognition. These pieces of evidence suggest that the loss of a synchronous mode of response in the MutSα’s surveillance for DNA errors would possible be one of the mechanism(s) of signaling the MMR-dependent programed cell death much wanted in anticancer therapies. The analysis was drawn from dynamics simulations. PMID:24061854

Switchable dual-wavelength fiber laser based on PCF Sagnac loop and broadband FBG

NASA Astrophysics Data System (ADS)

Chen, Weiguo; Lou, Shuqin; Feng, Suchun; Wang, Liwen; Li, Honglei; Guo, Tieying; Jian, Shuisheng

2009-11-01

Switchable dual-wavelength fiber laser with photonic crystal fiber (PCF) Sagnac loop and broadband fiber Bragg grating (BFBG) at room temperature is demonstrated. By adjusting the polarization controller (PC) appropriately, the laser can be switched between the stable single- and dual-wavelength lasing operations by exploiting polarization hole burning (PHB) and spectral hole burning effects (SHB).

Switchable Shape Memory Alloys (SMA) Thermal Materials Project

NASA Technical Reports Server (NTRS)

Falker, John; Zeitlin, Nancy; Williams, Martha; Fesmire, James

2014-01-01

Develop 2-way switchable thermal systems for use in systems that function in cold to hot temperature ranges using different alloy designs for SMA system concepts. In this project, KSC will specifically address designs of two proof of concept SMA systems with transition temperatures in the 65-95 C range and investigate cycle fatigue and "memory loss" due to thermal cycling.

Improved performance of Mg-Y alloy thin film switchable mirrors after coating with a superhydrophobic surface

NASA Astrophysics Data System (ADS)

La, Mao; Zhou, Huaijuan; Li, Ning; Xin, Yunchuan; Sha, Ren; Bao, Shanhu; Jin, Ping

2017-05-01

The magnesium based switchable mirrors can reversibly change their optical properties between the transparent and the reflective state as a result of hydrogenation and dehydrogenation. These films can potentially be applied as new energy-saving windows, by controlling the transmittance of solar radiation through the regulation of their reflective state. In this study, magnesium-yttrium (Mg-Y) alloy thin films were prepared using a DC magnetron sputtering method. However, the luminous transmittance in the transparent state and the switching durability of switchable mirrors are too poor to satisfy practical demands. In order to improve the films switching durability, luminous transmittance and the surface functionalization, polytetrafluoroethylene (PTFE) was coated with thermal vacuum deposition for use as the top layer of Mg-Y/Pd switchable mirrors. The PTFE layer had a porous network structure and exhibited a superhydrophobic surface with a water contact angle of approximately 152°. By characterization, PTFE thin films shows the excellent protection role against the oxidization of Mg, the switching durability of the films were improved 3 times, and also shows the antireflection role the luminous transmission of films was enhanced by 7% through the top covered with PTFE.

Switchable polarity solvent for liquid phase microextraction of Cd(II) as pyrrolidinedithiocarbamate chelates from environmental samples.

PubMed

Yilmaz, Erkan; Soylak, Mustafa

2015-07-30

A switchable polarity solvent was synthesized from triethylamine (TEA)/water/CO2 (Dry ice) via proton transfer reaction has been used for the microextraction of cadmium(II) as pyrrolidinedithiocarbamate (APDC) chelate. Cd(II)-APDC chelate was extracted into the switchable polarity solvent drops by adding 2 mL 10 M sodium hydroxide solution. Analytical parameters affecting the complex formation and microextraction efficiency such as pH, amount of ligand, volume of switchable polarity solvent and NaOH, sample volume were optimized. The effects of foreign ions were found tolerably. Under optimum conditions, the detection limit was 0.16 μg L(-1) (3Sb/m, n = 7) and the relative standard deviation was 5.4% (n = 7). The method was validated by the analysis of certified reference materials (TMDA-51.3 fortified water, TMDA-53.3 fortified water and SPS-WW2 waste water, 1573a Tomato Leaves and Oriental Basma Tobacco Leaves (INCT-OBTL-5)) and addition/recovery tests. The method was successfully applied to determination of cadmium contents of water, vegetable, fruit and cigarette samples. Copyright © 2015 Elsevier B.V. All rights reserved.

DNA Data Visualization (DDV): Software for Generating Web-Based Interfaces Supporting Navigation and Analysis of DNA Sequence Data of Entire Genomes.

PubMed

Neugebauer, Tomasz; Bordeleau, Eric; Burrus, Vincent; Brzezinski, Ryszard

2015-01-01

Data visualization methods are necessary during the exploration and analysis activities of an increasingly data-intensive scientific process. There are few existing visualization methods for raw nucleotide sequences of a whole genome or chromosome. Software for data visualization should allow the researchers to create accessible data visualization interfaces that can be exported and shared with others on the web. Herein, novel software developed for generating DNA data visualization interfaces is described. The software converts DNA data sets into images that are further processed as multi-scale images to be accessed through a web-based interface that supports zooming, panning and sequence fragment selection. Nucleotide composition frequencies and GC skew of a selected sequence segment can be obtained through the interface. The software was used to generate DNA data visualization of human and bacterial chromosomes. Examples of visually detectable features such as short and long direct repeats, long terminal repeats, mobile genetic elements, heterochromatic segments in microbial and human chromosomes, are presented. The software and its source code are available for download and further development. The visualization interfaces generated with the software allow for the immediate identification and observation of several types of sequence patterns in genomes of various sizes and origins. The visualization interfaces generated with the software are readily accessible through a web browser. This software is a useful research and teaching tool for genetics and structural genomics.

Hydration of protein–RNA recognition sites

PubMed Central

Barik, Amita; Bahadur, Ranjit Prasad

2014-01-01

We investigate the role of water molecules in 89 protein–RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein–RNA interfaces are hydrated less than protein–DNA interfaces, but more than protein–protein interfaces. Majority of the waters at protein–RNA interfaces makes multiple H-bonds; however, a fraction do not make any. Those making H-bonds have preferences for the polar groups of RNA than its partner protein. The spatial distribution of waters makes interfaces with ribosomal proteins and single-stranded RNA relatively ‘dry’ than interfaces with tRNA and duplex RNA. In contrast to protein–DNA interfaces, mainly due to the presence of the 2′OH, the ribose in protein–RNA interfaces is hydrated more than the phosphate or the bases. The minor groove in protein–RNA interfaces is hydrated more than the major groove, while in protein–DNA interfaces it is reverse. The strands make the highest number of water-mediated H-bonds per unit interface area followed by the helices and the non-regular structures. The preserved waters at protein–RNA interfaces make higher number of H-bonds than the other waters. Preserved waters contribute toward the affinity in protein–RNA recognition and should be carefully treated while engineering protein–RNA interfaces. PMID:25114050

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matsuo, Hiroki; Kitanaka, Yuuki; Inoue, Ryotaro

We investigate the mechanism of a switchable diode behavior observed in ferroelectric SrRuO{sub 3}/BiFeO{sub 3} (BFO)/SrRuO{sub 3} capacitors. We experimentally demonstrate that the switchable diode effect observed in the capacitors is induced by the polarization reversal in the BFO film. The conductivity in an Ohmic region in different oxidation states provides direct evidence that electron hole acts as the majority carrier, delivering p-type conduction. Density functional theory (DFT) calculations show that the p-type conduction arises from an unoccupied gap state of Fe{sup 4+} in an FeO{sub 5} pyramid which is derived from Bi vacancy. Our experimental and DFT study leadsmore » to the conclusion that the switchable diode effect originates from an asymmetric band bending in the top and bottom depletion layers modulated by ferroelectric polarization and oxygen vacancies.« less

Programmable in vivo selection of arbitrary DNA sequences.

PubMed

Ben Yehezkel, Tuval; Biezuner, Tamir; Linshiz, Gregory; Mazor, Yair; Shapiro, Ehud

2012-01-01

The extraordinary fidelity, sensory and regulatory capacity of natural intracellular machinery is generally confined to their endogenous environment. Nevertheless, synthetic bio-molecular components have been engineered to interface with the cellular transcription, splicing and translation machinery in vivo by embedding functional features such as promoters, introns and ribosome binding sites, respectively, into their design. Tapping and directing the power of intracellular molecular processing towards synthetic bio-molecular inputs is potentially a powerful approach, albeit limited by our ability to streamline the interface of synthetic components with the intracellular machinery in vivo. Here we show how a library of synthetic DNA devices, each bearing an input DNA sequence and a logical selection module, can be designed to direct its own probing and processing by interfacing with the bacterial DNA mismatch repair (MMR) system in vivo and selecting for the most abundant variant, regardless of its function. The device provides proof of concept for programmable, function-independent DNA selection in vivo and provides a unique example of a logical-functional interface of an engineered synthetic component with a complex endogenous cellular system. Further research into the design, construction and operation of synthetic devices in vivo may lead to other functional devices that interface with other complex cellular processes for both research and applied purposes.

High power ferrite microwave switch

NASA Technical Reports Server (NTRS)

Bardash, I.; Roschak, N. K.

1975-01-01

A high power ferrite microwave switch was developed along with associated electronic driver circuits for operation in a spaceborne high power microwave transmitter in geostationary orbit. Three units were built and tested in a space environment to demonstrate conformance to the required performance characteristics. Each unit consisted of an input magic-tee hybrid, two non-reciprocal latching ferrite phase shifters, an out short-slot 3 db quadrature coupler, a dual driver electronic circuit, and input logic interface circuitry. The basic mode of operation of the high power ferrite microwave switch is identical to that of a four-port, differential phase shift, switchable circulator. By appropriately designing the phase shifters and electronic driver circuits to operate in the flux-transfer magnetization mode, power and temperature insensitive operation was achieved. A list of the realized characteristics of the developed units is given.

Electrically switchable photonic liquid crystal devices for routing of a polarized light wave

NASA Astrophysics Data System (ADS)

Rushnova, Irina I.; Melnikova, Elena A.; Tolstik, Alexei L.; Muravsky, Alexander A.

2018-04-01

The new mode of LC alignment based on photoalignment AtA-2 azo dye where the refractive interface between orthogonal orientations of the LC director exists without voltage and disappeared or changed with critical voltage has been proposed. The technology to fabricate electrically controlled liquid crystal elements for spatial separation and switching of linearly polarized light beams on the basis of the total internal reflection effect has been significantly improved. Its distinctive feature is the application of a composite alignment material comprising two sublayers of Nylon-6 and AtA-2 photoalignment azo dye offering patterned liquid crystal director orientation with high alignment quality value q = 0 . 998. The fabricated electrically controlled spatially structured liquid crystal devices enable implementation of propagation directions separation for orthogonally polarized light beams and their switching with minimal crosstalk.

Robust Quantum Computing using Molecules with Switchable Dipole

DTIC Science & Technology

2010-06-15

REPORT Robust quantum computing using molecules with switchable dipole 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: Of the many systems studied to...Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 15. SUBJECT TERMS Ultracold polar molecules, quantum computing , phase gates...From - To) 30-Aug-2006 Standard Form 298 (Rev 8/98) Prescribed by ANSI Std. Z39.18 - 31-Aug-2009 Robust quantum computing using molecules with

Switchable antifouling coatings and uses thereof

DOEpatents

Denton, Michele L. Baca; Dirk, Shawn M.; Johnson, Ross Stefan

2017-02-28

The present invention relates to antifouling coatings capable of being switched by using heat or ultraviolet light. Prior to switching, the coating includes an onium cation component having antimicrobial and antibacterial properties. Upon switching, the coating is converted to a conjugated polymer state, and the cationic component is released with any adsorbed biofilm layer. Thus, the coatings herein have switchable and releasable properties. Methods of making and using such coatings are also described.

All-Silicon Switchable Magnetoelectric Effect through Interlayer Exchange Coupling.

PubMed

Liu, Hang; Sun, Jia-Tao; Fu, Hui-Xia; Sun, Pei-Jie; Feng, Y P; Meng, Sheng

2017-07-19

The magnetoelectric (ME) effect originating from the effective coupling between electric field and magnetism is an exciting frontier in nanoscale science such as magnetic tunneling junction (MTJ), ferroelectric/piezoelectric heterojunctions etc. The realization of switchable ME effect under external electric field in d0 semiconducting materials of single composition is needed especially for all-silicon spintronics applications because of its natural compatibility with current industry. We employ density functional theory (DFT) to reveal that the pristine Si(111)-3×3 R30° (Si3 hereafter) reconstructed surfaces of thin films with a thickness smaller than eleven bilayers support a sizeable linear ME effect with switchable direction of magnetic moment under external electric field. This is achieved through the interlayer exchange coupling effect in the antiferromagnetic regime, where the spin-up and spin-down magnetized density is located on opposite surfaces of Si3 thin films. The obtained coefficient for the linear ME effect can be four times larger than that of ferromagnetic Fe films, which fail to have the reversal switching capabilities. The larger ME effect originates from the spin-dependent screening of the spin-polarized Dirac fermion. The prediction will promote the realization of well-controlled and switchable data storage in all-silicon electronics. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Zipper-like magnetic molecularly imprinted microspheres for on/off-switchable recognition and extraction of 17β-estradiol from food samples.

PubMed

Zhu, Wenting; Peng, Hailong; Luo, Mei; Yu, Ningxiang; Xiong, Hua; Wang, Ronghui; Li, Yanbin

2018-09-30

Zipper-like on/off-switchable and magnetic molecularly imprinted microspheres (SM-MIMs) were constructed using acrylamide (AAm) and 2-acrylamide-2-methyl propanesulfonic acid (AMPS) as functional monomers for 17β-estradiol (17β-E 2 ) recognition and extraction. The imprinted polymer interactions between poly(AAm) (PAAm) and poly(AMPS) (PAMPS) with on/off-switchable property to temperature, exhibited dissociation at relatively higher temperatures (such as 30 °C) and helped 17β-E 2 enter into imprinted sites, leading to higher binding capability. Conversely, the interpolymer complexes between PAAm and PAMPS formed and blocked 17β-E 2 access to imprinted sites at lower temperature (such as 20 °C). SM-MIMs were used as dispersive solid phase extraction (SPE) adsorbent with HPLC for 17β-E 2 pretreatment and detection in food samples, and low limit detection (2.52 µg L -1 ) and quantification (10.76 µg L -1 ) with higher recovery were obtained. Therefore, SM-MIMs may be a promising adsorbent for 17β-E 2 pretreatment in food samples owing to its advantages of on/off-switchable recognition, eco-friendly elution, and efficient separation. Copyright © 2018. Published by Elsevier Ltd.

Investigating the potential of multiwalled carbon nanotubes based zinc nanocomposite as a recognition interface towards plant pathogen detection.

PubMed

Tahir, Muhammad Ali; Hameed, Sadaf; Munawar, Anam; Amin, Imran; Mansoor, Shahid; Khan, Waheed S; Bajwa, Sadia Zafar

2017-11-01

The emergence of nanotechnology has opened new horizons for constructing efficient recognition interfaces. This is the first report where the potential of a multiwalled carbon nanotube based zinc nanocomposite (MWCNTs-Zn NPs) investigated for the detection of an agricultural pathogen i.e. Chili leaf curl betasatellite (ChLCB). Atomic force microscope analyses revealed the presence of multiwalled carbon nanotubes (MWCNTs) having a diameter of 50-100nm with zinc nanoparticles (Zn-NPs) of 25-500nm. In this system, these bunches of Zn-NPs anchored along the whole lengths of MWCNTs were used for the immobilization of probe DNA strands. The electrochemical performance of DNA biosensor was assessed in the absence and presence of the complementary DNA during cyclic and differential pulse voltammetry scans. Target binding events occurring on the interface surface patterned with single-stranded DNA was quantitatively translated into electrochemical signals due to hybridization process. In the presence of complementary target DNA, as the result of duplex formation, there was a decrease in the peak current from 1.89×10 -04 to 5.84×10 -05 A. The specificity of this electrochemical DNA biosensor was found to be three times as compared to non-complementary DNA. This material structuring technique can be extended to design interfaces for the recognition of the other plant viruses and biomolecules. Copyright © 2017 Elsevier B.V. All rights reserved.

Light and redox switchable molecular components for molecular electronics.

PubMed

Browne, Wesley R; Feringa, Ben L

2010-01-01

The field of molecular and organic electronics has seen rapid progress in recent years, developing from concept and design to actual demonstration devices in which both single molecules and self-assembled monolayers are employed as light-responsive components. Research in this field has seen numerous unexpected challenges that have slowed progress and the initial promise of complex molecular-based computers has not yet been realised. Primarily this has been due to the realisation at an early stage that molecular-based nano-electronics brings with it the interface between the hard (semiconductor) and soft (molecular) worlds and the challenges which accompany working in such an environment. Issues such as addressability, cross-talk, molecular stability and perturbation of molecular properties (e.g., inhibition of photochemistry) have nevertheless driven development in molecular design and synthesis as well as our ability to interface molecular components with bulk metal contacts to a very high level of sophistication. Numerous groups have played key roles in progressing this field not least teams such as those led by Whitesides, Aviram, Ratner, Stoddart and Heath. In this short review we will however focus on the contributions from our own group and those of our collaborators, in employing diarylethene based molecular components.

Programmable ion-sensitive transistor interfaces. III. Design considerations, signal generation, and sensitivity enhancement

NASA Astrophysics Data System (ADS)

Jayant, Krishna; Auluck, Kshitij; Rodriguez, Sergio; Cao, Yingqiu; Kan, Edwin C.

2014-05-01

We report on factors that affect DNA hybridization detection using ion-sensitive field-effect transistors (ISFETs). Signal generation at the interface between the transistor and immobilized biomolecules is widely ascribed to unscreened molecular charges causing a shift in surface potential and hence the transistor output current. Traditionally, the interaction between DNA and the dielectric or metal sensing interface is modeled by treating the molecular layer as a sheet charge and the ionic profile with a Poisson-Boltzmann distribution. The surface potential under this scenario is described by the Graham equation. This approximation, however, often fails to explain large hybridization signals on the order of tens of mV. More realistic descriptions of the DNA-transistor interface which include factors such as ion permeation, exclusion, and packing constraints have been proposed with little or no corroboration against experimental findings. In this study, we examine such physical models by their assumptions, range of validity, and limitations. We compare simulations against experiments performed on electrolyte-oxide-semiconductor capacitors and foundry-ready floating-gate ISFETs. We find that with weakly charged interfaces (i.e., low intrinsic interface charge), pertinent to the surfaces used in this study, the best agreement between theory and experiment exists when ions are completely excluded from the DNA layer. The influence of various factors such as bulk pH, background salinity, chemical reactivity of surface groups, target molecule concentration, and surface coatings on signal generation is studied. Furthermore, in order to overcome Debye screening limited detection, we suggest two signal enhancement strategies. We first describe frequency domain biosensing, highlighting the ability to sort short DNA strands based on molecular length, and then describe DNA biosensing in multielectrolytes comprising trace amounts of higher-valency salt in a background of monovalent saline. Our study provides guidelines for optimized interface design, signal enhancement, and the interpretation of FET-based biosensor signals.

From face to interface recognition: a differential geometric approach to distinguish DNA from RNA binding surfaces.

PubMed

Shazman, Shula; Elber, Gershon; Mandel-Gutfreund, Yael

2011-09-01

Protein nucleic acid interactions play a critical role in all steps of the gene expression pathway. Nucleic acid (NA) binding proteins interact with their partners, DNA or RNA, via distinct regions on their surface that are characterized by an ensemble of chemical, physical and geometrical properties. In this study, we introduce a novel methodology based on differential geometry, commonly used in face recognition, to characterize and predict NA binding surfaces on proteins. Applying the method on experimentally solved three-dimensional structures of proteins we successfully classify double-stranded DNA (dsDNA) from single-stranded RNA (ssRNA) binding proteins, with 83% accuracy. We show that the method is insensitive to conformational changes that occur upon binding and can be applicable for de novo protein-function prediction. Remarkably, when concentrating on the zinc finger motif, we distinguish successfully between RNA and DNA binding interfaces possessing the same binding motif even within the same protein, as demonstrated for the RNA polymerase transcription-factor, TFIIIA. In conclusion, we present a novel methodology to characterize protein surfaces, which can accurately tell apart dsDNA from an ssRNA binding interfaces. The strength of our method in recognizing fine-tuned differences on NA binding interfaces make it applicable for many other molecular recognition problems, with potential implications for drug design.

Optically switchable photonic metasurfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Waters, R. F.; MacDonald, K. F.; Hobson, P. A.

2015-08-24

We experimentally demonstrate an optically switchable gallium-based metasurface, in which a reversible light-induced transition between solid and liquid phases occurring in a confined nanoscale surface layer of the metal drives significant changes in reflectivity and absorption. The metasurface architecture resonantly enhances the metal's “active plasmonic” phase-change nonlinearity by an order of magnitude, offering high contrast all-optical switching in the near-infrared range at low, μW μm{sup −2}, excitation intensities.

Smart Mirrors for Photorefractive Control of Light with Tim Bunning, RX - Agile Filters Application

DTIC Science & Technology

2016-11-08

AFRL-AFOSR-UK-TR-2017-0008 Smart Mirrors for photorefractive control of light with Tim Bunning, RX-- Agile filters application Luciano De Sio...photorefractive control of light with Tim Bunning, RX-- Agile filters application 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-14-1-0050 5c.  PROGRAM...photorefractive, switchable optical filters , liquide crystalline composite materials, Switchable reflective holographic gratings, polymer-dispersed liquid

Switchable radioactive neutron source device

DOEpatents

Boyar, Robert E.; DeVolpi, Alexander; Stanford, George S.; Rhodes, Edgar A.

1989-01-01

This invention is a switchable neutron generating apparatus comprised of a pair of plates, the first plate having an alpha emitter section on it and the second plate having a target material portion on it which generates neutrons when its nuclei absorb an alpha particle. In operation, the alpha portion of the first plate is aligned with the neutron portion of the second plate to produce neutrons and brought out of alignment to cease production of neutrons.

Novel Material Systems and Methodologies for Transient Thermal Management

NASA Technical Reports Server (NTRS)

Oliva-Buisson, Yvette J.

2014-01-01

Development of multifunctional and thermally switchable systems to address reduced mass and components, and tailored for both structural and transient thermal applications. Active, passive, and novel combinations of the two functional approaches are being developed along two lines of research investigation: switchable systems and transient heat spreading. The approach is to build in thermal functionality to structural elements to lay the foundation for a revolution in the way high energy space systems are designed.

Sunlight-switchable light shutter fabricated using liquid crystals doped with push-pull azobenzene.

PubMed

Oh, Seung-Won; Baek, Jong-Min; Yoon, Tae-Hoon

2016-11-14

We propose a sunlight-switchable light shutter using liquid crystal/polymer composite doped with push-pull azobenzene. The proposed light shutter is switchable between the translucent and transparent states by application of an electric field or by UV irradiation. Switching by UV irradiation is based on the change of the liquid crystal (LC) clearing point by the photo-isomerization effect of push-pull azobenzene. Under sunlight, the light shutter can be switched from the translucent to the transparent state by the nematic-isotropic phase transition of the LC domains triggered by trans-cis photo-isomerization of the push-pull azobenzene molecules. When the amount of sunlight is low because of cloud cover or when there is no sunlight at sunset, the light shutter rapidly relaxes from its transparent state back to its initial translucent state by the isotropic-nematic phase transition induced by cis-trans back-isomerization of the push-pull azobenzene molecules.

Fast switchable ferroelectric liquid crystal gratings with two electro-optical modes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Ying; Srivastava, A. K., E-mail: abhishek-srivastava-lu@yahoo.co.in; Chigrinov, V. G.

In this article, we reveal a theoretical and experimental illustration of the Ferroelectric liquid crystal (FLC) grating fabricated by mean of patterned alignment based on photo-alignment. The complexity related to the mismatching of the predefined alignment domains on the top and bottom substrate has been avoided by incorporating only one side photo aligned substrate while the other substrate does not have any alignment layer. Depending on the easy axis in the said alignment domains and the azimuth plane of the impinging polarized light, the diffracting element can be tuned in two modes i.e. DIFF/OFF switchable and DIFF/TRANS switchable modes, whichmore » can be applied to different applications. The diffraction profile has been illustrated theoretically that fits well with the experimental finding and thus the proposed diffraction elements with fast response time and high diffraction efficiency could find application in many modern devices.« less

Switchable silver mirrors with long memory effects.

PubMed

Park, Chihyun; Seo, Seogjae; Shin, Haijin; Sarwade, Bhimrao D; Na, Jongbeom; Kim, Eunkyoung

2015-01-01

An electrochemically stable and bistable switchable mirror was achieved for the first time by introducing (1) a thiol-modified indium tin oxide (ITO) electrode for the stabilization of the metallic film and (2) ionic liquids as an anion-blocking layer, to achieve a long memory effect. The growth of the metallic film was denser and faster at the thiol-modified ITO electrode than at a bare ITO electrode. The electrochemical stability of the metallic film on the thiol-modified ITO was enhanced, maintaining the metallic state without rupture. In the voltage-off state, the metal film maintained bistability for a long period (>2 h) when ionic liquids were introduced as electrolytes for the switchable mirror. The electrical double layer in the highly viscous ionic liquid electrolyte seemed to effectively form a barrier to the bromide ions, to protect the metal thin film from them when in the voltage-off state.

Liquid-crystal-based switchable polarizers for sensor protection.

PubMed

Wu, C S; Wu, S T

1995-11-01

Linear polarizers are generally employed in conjunction with advanced liquid-crystal filters for the protection of human eyes and optical sensors. For detection sensitivity under a no-threat condition to be maximized, the polarizer should remain in a clear state with a minimum insertion loss. When threats are present, it should be quickly switched to function as a linear polarizer with a high extinction ratio. Two types of switchable polarizer for sensor protection are demonstrated. The polarization conversion type exhibits a high optical efficiency in its clear state, a high extinction ratio in the linear polarizer state, and a fast switching speed, except that its field of view is limited to approximately ±10°. In contrast, an improved switchable dichroic polarizer functions effectively over a much wider field of view. However, its extinction ratio and optical efficiency in its clear state are lower than those of the polarization conversion type.

Switchable cucurbituril-bipyridine beacons.

PubMed

Sinha, Mantosh K; Reany, Ofer; Parvari, Galit; Karmakar, Ananta; Keinan, Ehud

2010-08-09

4-Aminobipyridine derivatives form strong inclusion complexes with cucurbit[6]uril, exhibiting remarkably large enhancements in fluorescence intensity and quantum yields. The remarkable complexation-induced pK(a) shift (DeltapK(a)=3.3) highlights the strong charge-dipole interaction upon binding. The reversible binding phenomenon can be used for the design of switchable beacons that can be incorporated into cascades of binding networks. This concept is demonstrated herein by three different applications: 1) a switchable fluorescent beacon for chemical sensing of transition metals and other ligands; 2) direct measurement of binding constants between cucurbit[6]uril and various nonfluorescent guest molecules; and 3) quantitative monitoring of biocatalytic reactions and determination of their kinetic parameters. The latter application is illustrated by the hydrolysis of an amide catalyzed by penicillin G acylase and by the elimination reaction of a beta-cabamoyloxy ketone catalyzed by aldolase antibody 38C2.

Liquid-crystal-based switchable polarizers for sensor protection

NASA Astrophysics Data System (ADS)

Wu, Chiung-Sheng; Wu, Shin-Tson

1995-11-01

Linear polarizers are generally employed in conjunction with advanced liquid-crystal filters for the protection of human eyes and optical sensors. For detection sensitivity under a no-threat condition to be maximized, the polarizer should remain in a clear state with a minimum insertion loss. When threats are present, it should be quickly switched to function as a linear polarizer with a high extinction ratio. Two types of switchable polarizer for sensor protection are demonstrated. The polarization conversion type exhibits a high optical efficiency in its clear state, a high extinction ratio in the linear polarizer state, and a fast switching speed, except that its field of view is limited to approximately +/-10 deg In contrast, an improved switchable dichroic polarizer functions effectively over a much wider field of view. However, its extinction ratio and optical efficiency in its clear state are lower than those of the polarization conversion type.

Electrical potential-assisted DNA hybridization. How to mitigate electrostatics for surface DNA hybridization.

PubMed

Tymoczko, Jakub; Schuhmann, Wolfgang; Gebala, Magdalena

2014-12-24

Surface-confined DNA hybridization reactions are sensitive to the number and identity of DNA capture probes and experimental conditions such as the nature and the ionic strength of the electrolyte solution. When the surface probe density is high or the concentration of bulk ions is much lower than the concentration of ions within the DNA layer, hybridization is significantly slowed down or does not proceed at all. However, high-density DNA monolayers are attractive for designing high-sensitivity DNA sensors. Thus, circumventing sluggish DNA hybridization on such interfaces allows a high surface concentration of target DNA and improved signal/noise ratio. We present potential-assisted hybridization as a strategy in which an external voltage is applied to the ssDNA-modified interface during the hybridization process. Results show that a significant enhancement of hybridization can be achieved using this approach.

Electrostatic Interactions at the Dimer Interface Stabilize the E. coli β Sliding Clamp.

PubMed

Purohit, Anirban; England, Jennifer K; Douma, Lauren G; Tondnevis, Farzaneh; Bloom, Linda B; Levitus, Marcia

2017-08-22

Sliding clamps are ring-shaped oligomeric proteins that encircle DNA and associate with DNA polymerases for processive DNA replication. The dimeric Escherichia coli β-clamp is closed in solution but must adopt an open conformation to be assembled onto DNA by a clamp loader. To determine what factors contribute to the stability of the dimer interfaces in the closed conformation and how clamp dynamics contribute to formation of the open conformation, we identified conditions that destabilized the dimer and measured the effects of these conditions on clamp dynamics. We characterized the role of electrostatic interactions in stabilizing the β-clamp interface. Increasing salt concentration results in decreased dimer stability and faster subunit dissociation kinetics. The equilibrium dissociation constant of the dimeric clamp varies with salt concentration as predicted by simple charge-screening models, indicating that charged amino acids contribute to the remarkable stability of the interface at physiological salt concentrations. Mutation of a charged residue at the interface (Arg-103) weakens the interface significantly, whereas effects are negligible when a hydrophilic (Ser-109) or a hydrophobic (Ile-305) amino acid is mutated instead. It has been suggested that clamp opening by the clamp loader takes advantage of spontaneous opening-closing fluctuations at the clamp's interface, but our time-resolved fluorescence and fluorescence correlation experiments rule out conformational fluctuations that lead to a significant fraction of open states. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

On the electron affinity of cytosine in bulk water and at hydrophobic aqueous interfaces.

PubMed

Vöhringer-Martinez, Esteban; Dörner, Ciro; Abel, Bernd

2014-10-01

In the past one possible mechanism of DNA damage in bulk water has been attributed to the presence of hydrated electrons in water. Recently, one important property of hydrated electrons, namely their binding energy, was reported to be smaller at hydrophobic interfaces than in bulk aqueous solution. This possibly opens up new reaction possibilities with different solutes such as the DNA at hydrophobic, aqueous interfaces. Here, we use QM/MM molecular dynamics simulation to study how the molecular environment at the vacuum-water interface and in the bulk alters the electron affinity of cytosine being a characteristic part of the DNA. The electron affinity at the interface is closer to the corresponding binding energy of the partially hydrated electron. The increased energy resonance makes the electron capture process more probable and suggests that hydrated electrons at hydrophobic interfaces may be more reactive than the fully hydrated ones. Additionally, we found that the relaxation of the anionic form after electron attachment also induces a proton transfer from the surrounding solvent that was confirmed by comparison with the experimental reduction potential.

Photo-switchable Donor-Acceptor (D-A) Dyad Interfacial Self-Assembled Monolayers for Organic Photovoltaic Cells

DTIC Science & Technology

2015-11-05

AFRL-AFOSR-VA-TR-2015-0396 (HBCU) Photo-switchable Donor-Acceptor for Organic Photovoltaic Cells Luis Echegoyen UNIVERSITY OF TEXAS AT EL PASO Final...Acceptor (D-A) Dyad Interfacial Self-Assembled Monolayers for Organic Photovoltaic Cells 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-12-1-0053 5c...demonstrated using impedance spectroscopy for several triphenylamine-fullerene dyads, but their performance in photovoltaic devices was not remarkable, likely

Switchable radioactive neutron source device

DOEpatents

Stanford, G.S.; Rhodes, E.A.; Devolpi, A.; Boyar, R.E.

1987-11-06

This invention is a switchable neutron generating apparatus comprised of a pair of plates, the first plate having an alpha emitter section on it and the second plate having a target material portion on it which generates neutrons when its nuclei absorb an alpha particle. In operation, the alpha portion of the first plate is aligned with the neutron portion of the second plate to produce neutrons and brought out of alignment to cease production of neutrons. 3 figs.

Reversible conversion of valence-tautomeric copper metal-organic frameworks dependent single-crystal-to-single-crystal oxidation/reduction: a redox-switchable catalyst for C-H bonds activation reaction.

PubMed

Huang, Chao; Wu, Jie; Song, Chuanjun; Ding, Ran; Qiao, Yan; Hou, Hongwei; Chang, Junbiao; Fan, Yaoting

2015-06-28

Upon single-crystal-to-single-crystal (SCSC) oxidation/reduction, reversible structural transformations take place between the anionic porous zeolite-like Cu(I) framework and a topologically equivalent neutral Cu(I)Cu(II) mixed-valent framework. The unique conversion behavior of the Cu(I) framework endowed it as a redox-switchable catalyst for the direct arylation of heterocycle C-H bonds.

Layer by layer assembled films between hemoglobin and multiwall carbon nanotubes for pH-switchable biosensing.

PubMed

Pan, Zhongqin; Liu, Xiaojun; Xie, Jing; Bao, Ning; He, Hong; Li, Xiaodong; Zeng, Jiang; Gu, Haiying

2015-05-01

Although pH-switchable behaviors have been reported based on multilayer films modified electrodes, their pH-switchable biosensing is still difficult due to the existence of the electroactive mediator. In this study, we report the pH-dependable determination of hydrogen peroxide (H2O2) based on a four-bilayer film fabricated through layer by layer assembly between hemoglobin (Hb) and multiwall carbon nanotubes (MWCNTs). We observed that response of electroactive probe Fe(CN)6(3-) at the multilayer films was very sensitive and reversible to pH values of phosphate buffer solutions phosphate buffer solution with cyclic voltammetry. The reduction peak height of Fe(CN)6(3-) at the multilayer film could reach ∼221μA at pH 3.0 while 0μA at pH 9.0. The linear range for the detection of H2O2 at pH 3.0 was from 12.5μM to 10.4mM, which was much wider than that at pH 9.0. Our results demonstrated that the detection of H2O2 with the proposed modified electrode is dependent on pH values of phosphate buffer solution. Moreover, the component of multilayer films has impacts on the performance of biosensors with pH-switchable behaviors. Copyright © 2015 Elsevier B.V. All rights reserved.

Temperature-Switchable Agglomeration of Magnetic Particles Designed for Continuous Separation Processes in Biotechnology.

PubMed

Paulus, Anja S; Heinzler, Raphael; Ooi, Huey Wen; Franzreb, Matthias

2015-07-08

The purpose of this work was the synthesis and characterization of thermally switchable magnetic particles for use in biotechnological applications such as protein purification and enzymatic conversions. Reversible addition-fragmentation chain-transfer polymerization was employed to synthesize poly(N-isopropylacrylamide) brushes via a "graft-from" approach on the surface of magnetic microparticles. The resulting particles were characterized by infrared spectroscopy and thermogravimetric analysis and their temperature-dependent agglomeration behavior was assessed. The influence of several factors on particle agglomeration (pH, temperature, salt type, and particle concentration) was evaluated. The results showed that a low pH value (pH 3-4), a kosmotropic salt (ammonium sulfate), and a high particle concentration (4 g/L) resulted in improved agglomeration at elevated temperature (40 °C). Recycling of particles and reversibility of the temperature-switchable agglomeration were successfully demonstrated for ten heating-cooling cycles. Additionally, enhanced magnetic separation was observed for the modified particles. Ionic monomers were integrated into the polymer chain to create end-group functionalized particles as well as two- and three-block copolymer particles for protein binding. The adsorption of lactoferrin, bovine serum albumin, and lysozyme to these ion exchange particles was evaluated and showed a binding capacity of up to 135 mg/g. The dual-responsive particles combined magnetic and thermoresponsive properties for switchable agglomeration, easy separability, and efficient protein adsorption.

Detection of DNA hybridization using graphene-coated black phosphorus surface plasmon resonance sensor

NASA Astrophysics Data System (ADS)

Pal, Sarika; Verma, Alka; Raikwar, S.; Prajapati, Y. K.; Saini, J. P.

2018-05-01

In this paper, graphene-coated black phosphorus at the metal surface for the detection of DNA hybridization event is numerically demonstrated. The strategy consists of placing the sensing medium on top of black phosphorus-graphene-coated SPR which interfaces with phosphate-buffered saline solution carrying single-stranded DNA. Upon hybridization with its complementary DNA, desorption of the nanostructures takes place and thus enables the sensitive detection of the DNA hybridization event. The proposed sensor exhibits a sensitivity (125 ο/RIU), detection accuracy (0.95) and quality factor (13.62 RIU-1) for complementary DNA. In comparison with other reported papers, our suggested sensor provides much better performance. Thus, this label-free DNA detection platform should spur off new interest towards the use of black phosphorus-graphene-coated SPR interfaces.

A discriminatory function for prediction of protein-DNA interactions based on alpha shape modeling.

PubMed

Zhou, Weiqiang; Yan, Hong

2010-10-15

Protein-DNA interaction has significant importance in many biological processes. However, the underlying principle of the molecular recognition process is still largely unknown. As more high-resolution 3D structures of protein-DNA complex are becoming available, the surface characteristics of the complex become an important research topic. In our work, we apply an alpha shape model to represent the surface structure of the protein-DNA complex and developed an interface-atom curvature-dependent conditional probability discriminatory function for the prediction of protein-DNA interaction. The interface-atom curvature-dependent formalism captures atomic interaction details better than the atomic distance-based method. The proposed method provides good performance in discriminating the native structures from the docking decoy sets, and outperforms the distance-dependent formalism in terms of the z-score. Computer experiment results show that the curvature-dependent formalism with the optimal parameters can achieve a native z-score of -8.17 in discriminating the native structure from the highest surface-complementarity scored decoy set and a native z-score of -7.38 in discriminating the native structure from the lowest RMSD decoy set. The interface-atom curvature-dependent formalism can also be used to predict apo version of DNA-binding proteins. These results suggest that the interface-atom curvature-dependent formalism has a good prediction capability for protein-DNA interactions. The code and data sets are available for download on http://www.hy8.com/bioinformatics.htm kenandzhou@hotmail.com.

mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences

PubMed Central

Lee, Hwan Young; Song, Injee; Ha, Eunho; Cho, Sung-Bae; Yang, Woo Ick; Shin, Kyoung-Jin

2008-01-01

Background For the past few years, scientific controversy has surrounded the large number of errors in forensic and literature mitochondrial DNA (mtDNA) data. However, recent research has shown that using mtDNA phylogeny and referring to known mtDNA haplotypes can be useful for checking the quality of sequence data. Results We developed a Web-based bioinformatics resource "mtDNAmanager" that offers a convenient interface supporting the management and quality analysis of mtDNA sequence data. The mtDNAmanager performs computations on mtDNA control-region sequences to estimate the most-probable mtDNA haplogroups and retrieves similar sequences from a selected database. By the phased designation of the most-probable haplogroups (both expected and estimated haplogroups), mtDNAmanager enables users to systematically detect errors whilst allowing for confirmation of the presence of clear key diagnostic mutations and accompanying mutations. The query tools of mtDNAmanager also facilitate database screening with two options of "match" and "include the queried nucleotide polymorphism". In addition, mtDNAmanager provides Web interfaces for users to manage and analyse their own data in batch mode. Conclusion The mtDNAmanager will provide systematic routines for mtDNA sequence data management and analysis via easily accessible Web interfaces, and thus should be very useful for population, medical and forensic studies that employ mtDNA analysis. mtDNAmanager can be accessed at . PMID:19014619

Helicity multiplexed broadband metasurface holograms.

PubMed

Wen, Dandan; Yue, Fuyong; Li, Guixin; Zheng, Guoxing; Chan, Kinlong; Chen, Shumei; Chen, Ming; Li, King Fai; Wong, Polis Wing Han; Cheah, Kok Wai; Pun, Edwin Yue Bun; Zhang, Shuang; Chen, Xianzhong

2015-09-10

Metasurfaces are engineered interfaces that contain a thin layer of plasmonic or dielectric nanostructures capable of manipulating light in a desirable manner. Advances in metasurfaces have led to various practical applications ranging from lensing to holography. Metasurface holograms that can be switched by the polarization state of incident light have been demonstrated for achieving polarization multiplexed functionalities. However, practical application of these devices has been limited by their capability for achieving high efficiency and high image quality. Here we experimentally demonstrate a helicity multiplexed metasurface hologram with high efficiency and good image fidelity over a broad range of frequencies. The metasurface hologram features the combination of two sets of hologram patterns operating with opposite incident helicities. Two symmetrically distributed off-axis images are interchangeable by controlling the helicity of the input light. The demonstrated helicity multiplexed metasurface hologram with its high performance opens avenues for future applications with functionality switchable optical devices.

Giant switchable Rashba effect in oxide heterostructures

DOE PAGES

Zhong, Zhicheng; Si, Liang; Zhang, Qinfang; ...

2015-03-01

One of the most fundamental phenomena and a reminder of the electron’s relativistic nature is the Rashba spin splitting for broken inversion symmetry. Usually this splitting is a tiny relativistic correction. Interfacing ferroelectric BaTiO₃ and a 5d (or 4d) transition metal oxide with a large spin-orbit coupling, Ba(Os,Ir,Ru)O₃, we show that giant Rashba spin splittings are indeed possible and even controllable by an external electric field. Based on density functional theory and a microscopic tight binding understanding, we conclude that the electric field is amplified and stored as a ferroelectric Ti-O distortion which, through the network of oxygen octahedra, inducesmore » a large (Os,Ir,Ru)-O distortion. The BaTiO₃/Ba(Os,Ru,Ir)O₃ heterostructure is hence the ideal test station for switching and studying the Rashba effect and allows applications at room temperature.« less

Helicity multiplexed broadband metasurface holograms

PubMed Central

Wen, Dandan; Yue, Fuyong; Li, Guixin; Zheng, Guoxing; Chan, Kinlong; Chen, Shumei; Chen, Ming; Li, King Fai; Wong, Polis Wing Han; Cheah, Kok Wai; Yue Bun Pun, Edwin; Zhang, Shuang; Chen, Xianzhong

2015-01-01

Metasurfaces are engineered interfaces that contain a thin layer of plasmonic or dielectric nanostructures capable of manipulating light in a desirable manner. Advances in metasurfaces have led to various practical applications ranging from lensing to holography. Metasurface holograms that can be switched by the polarization state of incident light have been demonstrated for achieving polarization multiplexed functionalities. However, practical application of these devices has been limited by their capability for achieving high efficiency and high image quality. Here we experimentally demonstrate a helicity multiplexed metasurface hologram with high efficiency and good image fidelity over a broad range of frequencies. The metasurface hologram features the combination of two sets of hologram patterns operating with opposite incident helicities. Two symmetrically distributed off-axis images are interchangeable by controlling the helicity of the input light. The demonstrated helicity multiplexed metasurface hologram with its high performance opens avenues for future applications with functionality switchable optical devices. PMID:26354497

Mechano-regulated surface for manipulating liquid droplets

NASA Astrophysics Data System (ADS)

Tang, Xin; Zhu, Pingan; Tian, Ye; Zhou, Xuechang; Kong, Tiantian; Wang, Liqiu

2017-04-01

The effective transfer of tiny liquid droplets is vital for a number of processes such as chemical and biological microassays. Inspired by the tarsi of meniscus-climbing insects, which can climb menisci by deforming the water/air interface, we developed a mechano-regulated surface consisting of a background mesh and a movable microfibre array with contrastive wettability. The adhesion of this mechano-regulated surface to liquid droplets can be reversibly switched through mechanical reconfiguration of the microfibre array. The adhesive force can be tuned by varying the number and surface chemistry of the microfibres. The in situ adhesion of the mechano-regulated surface can be used to manoeuvre micro-/nanolitre liquid droplets in a nearly loss-free manner. The mechano-regulated surface can be scaled up to handle multiple droplets in parallel. Our approach offers a miniaturized mechano-device with switchable adhesion for handling micro-/nanolitre droplets, either in air or in a fluid that is immiscible with the droplets.

Dynamic patterns in a supported lipid bilayer driven by standing surface acoustic waves.

PubMed

Hennig, Martin; Neumann, Jürgen; Wixforth, Achim; Rädler, Joachim O; Schneider, Matthias F

2009-11-07

In the past decades supported lipid bilayers (SLBs) have been an important tool in order to study the physical properties of biological membranes and cells. So far, controlled manipulation of SLBs is very limited. Here we present a new technology to create lateral patterns in lipid membranes controllable in both space and time. Surface acoustic waves (SAWs) are used to generate lateral standing waves on a piezoelectric substrate which create local "traps" in the lipid bilayer and lead to a lateral modulation in lipid concentration. We demonstrate that pattern formation is reversible and does not affect the integrity of the lipid bilayer as shown by extracting the diffusion constant of fluid membranes. The described method could possibly be used to design switchable interfaces for the lateral transport and organization of membrane bound macromolecules to create dynamic bioarrays and control biofilm formation.

Heat-transfer resistance at solid-liquid interfaces: a tool for the detection of single-nucleotide polymorphisms in DNA.

PubMed

van Grinsven, Bart; Vanden Bon, Natalie; Strauven, Hannelore; Grieten, Lars; Murib, Mohammed; Monroy, Kathia L Jiménez; Janssens, Stoffel D; Haenen, Ken; Schöning, Michael J; Vermeeren, Veronique; Ameloot, Marcel; Michiels, Luc; Thoelen, Ronald; De Ceuninck, Ward; Wagner, Patrick

2012-03-27

In this article, we report on the heat-transfer resistance at interfaces as a novel, denaturation-based method to detect single-nucleotide polymorphisms in DNA. We observed that a molecular brush of double-stranded DNA grafted onto synthetic diamond surfaces does not notably affect the heat-transfer resistance at the solid-to-liquid interface. In contrast to this, molecular brushes of single-stranded DNA cause, surprisingly, a substantially higher heat-transfer resistance and behave like a thermally insulating layer. This effect can be utilized to identify ds-DNA melting temperatures via the switching from low- to high heat-transfer resistance. The melting temperatures identified with this method for different DNA duplexes (29 base pairs without and with built-in mutations) correlate nicely with data calculated by modeling. The method is fast, label-free (without the need for fluorescent or radioactive markers), allows for repetitive measurements, and can also be extended toward array formats. Reference measurements by confocal fluorescence microscopy and impedance spectroscopy confirm that the switching of heat-transfer resistance upon denaturation is indeed related to the thermal on-chip denaturation of DNA. © 2012 American Chemical Society

NPIDB: Nucleic acid-Protein Interaction DataBase.

PubMed

Kirsanov, Dmitry D; Zanegina, Olga N; Aksianov, Evgeniy A; Spirin, Sergei A; Karyagina, Anna S; Alexeevski, Andrei V

2013-01-01

The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid-Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved water molecules on the DNA-protein interface.

From face to interface recognition: a differential geometric approach to distinguish DNA from RNA binding surfaces

PubMed Central

Shazman, Shula; Elber, Gershon; Mandel-Gutfreund, Yael

2011-01-01

Protein nucleic acid interactions play a critical role in all steps of the gene expression pathway. Nucleic acid (NA) binding proteins interact with their partners, DNA or RNA, via distinct regions on their surface that are characterized by an ensemble of chemical, physical and geometrical properties. In this study, we introduce a novel methodology based on differential geometry, commonly used in face recognition, to characterize and predict NA binding surfaces on proteins. Applying the method on experimentally solved three-dimensional structures of proteins we successfully classify double-stranded DNA (dsDNA) from single-stranded RNA (ssRNA) binding proteins, with 83% accuracy. We show that the method is insensitive to conformational changes that occur upon binding and can be applicable for de novo protein-function prediction. Remarkably, when concentrating on the zinc finger motif, we distinguish successfully between RNA and DNA binding interfaces possessing the same binding motif even within the same protein, as demonstrated for the RNA polymerase transcription-factor, TFIIIA. In conclusion, we present a novel methodology to characterize protein surfaces, which can accurately tell apart dsDNA from an ssRNA binding interfaces. The strength of our method in recognizing fine-tuned differences on NA binding interfaces make it applicable for many other molecular recognition problems, with potential implications for drug design. PMID:21693557

Switchable and Tunable Bulk Acoustic Wave Devices Based on Ferroelectric Material

NASA Astrophysics Data System (ADS)

Mansour, Almonir

The explosive development of personal communications systems, navigation, satellite communications as well as personal computer and data processing systems together with the constant demand for higher speeds and larger bandwidths has driven fabrication technology to its limits. This, in turn, necessitates the development of novel functional materials for the fabrication of devices with superior performance and higher capacity at reduced manufacturing costs. Ferroelectric materials such as barium strontium titanate (BST) and strontium titanium oxide (STO) have received more attention by researchers and industry because of their field-induced piezoelectric property. This property gives these types of ferroelectric materials the ability to be switchable and tunable in the presence of an electric field. These features have allowed the ferroelectric materials to be used in many applications such as non-volatile memory and DRAMs, sensors, pyroelectric detectors, and tunable microwave devices. Therefore, with the ever increasing complexity in RF front-end receivers, and the demand for services (which in turn requires more functionalities), ferroelectric bulk acoustic wave (BAW) resonators and filters that are intrinsically switchable and tunable promise to reduce the size and complexity of component parts. In this work, we present the design, fabrication and experimental evaluation of switchable and tunable thin film bulk acoustic wave (BAW) resonators, filters and duplexers for radio frequency (RF) applications. The switchability and tunability of these devices come from utilizing the electrostrictive effect of ferroelectric materials such as barium strontium titanate (BST) with the application of an external DC-bias voltage. The BAW resonators, filters and duplexers in this work were fabricated on different substrates as solidly mounted resonator (SMR) structure with number of periodic layers of silicon dioxide and tantalum oxide as a Bragg reflector in order to acoustically isolate the resonator from the damping effect of the substrate, enhancing the quality factor and temperature compensation.

Ferroelectric nanostructure having switchable multi-stable vortex states

DOEpatents

Naumov, Ivan I [Fayetteville, AR; Bellaiche, Laurent M [Fayetteville, AR; Prosandeev, Sergey A [Fayetteville, AR; Ponomareva, Inna V [Fayetteville, AR; Kornev, Igor A [Fayetteville, AR

2009-09-22

A ferroelectric nanostructure formed as a low dimensional nano-scale ferroelectric material having at least one vortex ring of polarization generating an ordered toroid moment switchable between multi-stable states. A stress-free ferroelectric nanodot under open-circuit-like electrical boundary conditions maintains such a vortex structure for their local dipoles when subject to a transverse inhomogeneous static electric field controlling the direction of the macroscopic toroidal moment. Stress is also capable of controlling the vortex's chirality, because of the electromechanical coupling that exists in ferroelectric nanodots.

Quenching of giant hysteresis effects in La(1-z)Y(z)Hx switchable mirrors

PubMed

van Gogh AT; Nagengast; Kooij; Koeman; Griessen

2000-09-04

The giant intrinsic hysteresis as a function of hydrogen concentration x in the optical and electrical properties of the archetypal switchable mirror YHx is eliminated by alloying Y with the chemically similar La. The La(1-z)Y(z)Hx films with z/=0.86 is the large uniaxial lattice expansion that accompanies their fcc to hexagonal phase transition in combination with lateral clamping.

New Materials for Smart Structures: a US: Japan Global Initiative

DTIC Science & Technology

2004-03-01

realization of the MPB in the Gallate:Scandate system and in the modified bismuth lanthanum ferrate lead titanate systems. A major puzzle in BiFeO3 which has...magnetization. A new major clue as to the origin of the high switchable polarization is provided by our most recent work on the modified bismuth lanthanum ...ferrate: gallate solid solutions with MPBs. In suitable composition switchability is only possible with limited electrode in a larger disk, and the fully

Simulation and Micro-Fabrication of Optically Switchable Split Ring Resonators

DTIC Science & Technology

2007-01-01

Simulation and micro-fabrication of optically switchable split ring resonators T.F. Gundogdu a,*, Mutlu Gökkavas b, Kaan Güven b, M. Kafesaki a...mail address: tamara@iesl.forth.gr (T.F. Gundogdu ). 1569-4410/$ – see front matter # 2007 Published by Elsevier B.V. doi:10.1016/j.photonics...ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 T.F. Gundogdu et al. / Photonics and

A symmetry breaking phase transition-triggered high-temperature solid-state quadratic nonlinear optical switch coupled with a switchable dielectric constant in an organic-inorganic hybrid compound.

PubMed

Mei, Guang-Quan; Zhang, Han-Yue; Liao, Wei-Qiang

2016-09-25

An organic-inorganic hybrid compound, [NH3(CH2)5NH3]SbCl5, exhibits a switchable second harmonic generation (SHG) effect between SHG-OFF and SHG-ON states and tunable dielectric behaviors between high and low dielectric states, connected with the changes in the dynamics of 1,5-pentanediammonium cations during its centrosymmetric-to-noncentrosymmetric symmetry breaking phase transition at 365.4 K.

Cooperative Assembly of Co-Smad4 MH1 with R-Smad1/3 MH1 on DNA: A Molecular Dynamics Simulation Study

PubMed Central

Wang, Guihong; Li, Chaoqun; Wang, Yan; Chen, Guangju

2013-01-01

Background Smads, the homologs of Sma and MAD proteins, play a key role in gene expression regulation in the transforming growth factor-β (TGF-β) signaling pathway. Recent experimental studies have revealed that Smad4/R-Smad heterodimers bound on DNA are energetically more favorable than homodimeric R-Smad/R-Smad complexes bound on DNA, which indicates that Smad4 might act as binding vehicle to cooperatively assemble with activated R-Smads on DNA in the nucleus. However, the details of interaction mechanism for cooperative recruitment of Smad4 protein to R-Smad proteins on DNA, and allosteric communication between the Smad4-DNA and R-Smad-DNA interfaces via DNA mediating are not yet clear so far. Methodology In the present work, we have constructed a series of Smadn+DNA+Smadn (n = 1, 3, 4) models and carried out molecular dynamics simulations, free energy calculations and DNA dynamics analysis for them to study the interaction properties of Smadn (n = 1, 3, 4) with DNA molecule. Results The results revealed that the binding of Smad4 protein to DNA molecule facilitates energetically the formation of the heteromeric Smad4+DNA+Smad1/3 complex by increasing the affinity of Smad1/3 with DNA molecule. Further investigations through the residue/base motion correlation and DNA dynamics analyses predicted that the binding of Smad4 protein to DNA molecule in the heteromeric Smad4+DNA+Smad1/3 model induces an allosteric communication from the Smad4-DNA interface to Smad1/Smad3-DNA interface via DNA base-pair helical motions, surface conformation changes and new hydrogen bond formations. The present work theoretically explains the mechanism of cooperative recruitment of Smad4 protein to Smad1/3 protein via DNA-mediated indirect readout mode in the nucleus. PMID:23326519

Recognition of platinum-DNA adducts by HMGB1a.

PubMed

Ramachandran, Srinivas; Temple, Brenda; Alexandrova, Anastassia N; Chaney, Stephen G; Dokholyan, Nikolay V

2012-09-25

Cisplatin (CP) and oxaliplatin (OX), platinum-based drugs used widely in chemotherapy, form adducts on intrastrand guanines (5'GG) in genomic DNA. DNA damage recognition proteins, transcription factors, mismatch repair proteins, and DNA polymerases discriminate between CP- and OX-GG DNA adducts, which could partly account for differences in the efficacy, toxicity, and mutagenicity of CP and OX. In addition, differential recognition of CP- and OX-GG adducts is highly dependent on the sequence context of the Pt-GG adduct. In particular, DNA binding protein domain HMGB1a binds to CP-GG DNA adducts with up to 53-fold greater affinity than to OX-GG adducts in the TGGA sequence context but shows much smaller differences in binding in the AGGC or TGGT sequence contexts. Here, simulations of the HMGB1a-Pt-DNA complex in the three sequence contexts revealed a higher number of interface contacts for the CP-DNA complex in the TGGA sequence context than in the OX-DNA complex. However, the number of interface contacts was similar in the TGGT and AGGC sequence contexts. The higher number of interface contacts in the CP-TGGA sequence context corresponded to a larger roll of the Pt-GG base pair step. Furthermore, geometric analysis of stacking of phenylalanine 37 in HMGB1a (Phe37) with the platinated guanines revealed more favorable stacking modes correlated with a larger roll of the Pt-GG base pair step in the TGGA sequence context. These data are consistent with our previous molecular dynamics simulations showing that the CP-TGGA complex was able to sample larger roll angles than the OX-TGGA complex or either CP- or OX-DNA complexes in the AGGC or TGGT sequences. We infer that the high binding affinity of HMGB1a for CP-TGGA is due to the greater flexibility of CP-TGGA compared to OX-TGGA and other Pt-DNA adducts. This increased flexibility is reflected in the ability of CP-TGGA to sample larger roll angles, which allows for a higher number of interface contacts between the Pt-DNA adduct and HMGB1a.

Passband switchable microwave photonic multiband filter

PubMed Central

Ge, Jia; Fok, Mable P.

2015-01-01

A reconfigurable microwave photonic (MWP) multiband filter with selectable and switchable passbands is proposed and experimentally demonstrated, with a maximum of 12 simultaneous passbands evenly distributed from 0 to 10 GHz. The scheme is based on the generation of tunable optical comb lines using a two-stage Lyot loop filter, such that various filter tap spacings and spectral combinations are obtained for the configuration of the MWP filter. Through polarization state adjustment inside the Lyot loop filter, an optical frequency comb with 12 different comb spacings is achieved, which corresponds to a MWP filter with 12 selectable passbands. Center frequencies of the filter passbands are switchable, while the number of simultaneous passbands is tunable from 1 to 12. Furthermore, the MWP multiband filter can either work as an all-block, single-band or multiband filter with various passband combinations, which provide exceptional operation flexibility. All the passbands have over 30 dB sidelobe suppression and 3-dB bandwidth of 200 MHz, providing good filter selectivity. PMID:26521693

Switchable photovoltaic windows enabled by reversible photothermal complex dissociation from methylammonium lead iodide

DOE PAGES

Wheeler, Lance M.; Moore, David T.; Ihly, Rachelle; ...

2017-11-23

Materials with switchable absorption properties have been widely used for smart window applications to reduce energy consumption and enhance occupant comfort in buildings. In this work, we combine the benefits of smart windows with energy conversion by producing a photovoltaic device with a switchable absorber layer that dynamically responds to sunlight. Upon illumination, photothermal heating switches the absorber layer - composed of a metal halide perovskite-methylamine complex - from a transparent state (68% visible transmittance) to an absorbing, photovoltaic colored state (less than 3% visible transmittance) due to dissociation of methylamine. After cooling, the methylamine complex is re-formed, returning themore » absorber layer to the transparent state in which the device acts as a window to visible light. The thermodynamics of switching and performance of the device are described. In conclusion, this work validates a photovoltaic window technology that circumvents the fundamental tradeoff between efficient solar conversion and high visible light transmittance that limits conventional semitransparent PV window designs.« less

Passband switchable microwave photonic multiband filter.

PubMed

Ge, Jia; Fok, Mable P

2015-11-02

A reconfigurable microwave photonic (MWP) multiband filter with selectable and switchable passbands is proposed and experimentally demonstrated, with a maximum of 12 simultaneous passbands evenly distributed from 0 to 10 GHz. The scheme is based on the generation of tunable optical comb lines using a two-stage Lyot loop filter, such that various filter tap spacings and spectral combinations are obtained for the configuration of the MWP filter. Through polarization state adjustment inside the Lyot loop filter, an optical frequency comb with 12 different comb spacings is achieved, which corresponds to a MWP filter with 12 selectable passbands. Center frequencies of the filter passbands are switchable, while the number of simultaneous passbands is tunable from 1 to 12. Furthermore, the MWP multiband filter can either work as an all-block, single-band or multiband filter with various passband combinations, which provide exceptional operation flexibility. All the passbands have over 30 dB sidelobe suppression and 3-dB bandwidth of 200 MHz, providing good filter selectivity.

Switchable dual-wavelength SLM narrow linewidth fiber laser based on nonlinear amplifying loop mirror

NASA Astrophysics Data System (ADS)

Fu, Pan; Feng, Xiao-qiang; Lu, Baole; Qi, Xin-yuan; Chen, Haowei; Sun, Bo; Jiang, Man; Wang, Kaile; Bai, Jintao

2018-01-01

We demonstrate a stable switchable dual-wavelength single longitudinal mode (SLM) narrow linewidth ytterbium-doped fiber (YDF) laser using a nonlinear amplifying fiber loop mirror (NALM) at 1064 nm. The NALM of intensity-dependent transmission acts as a saturable absorber filter and an amplitude equalizer to suppress mode competition and the fiber Bragg grating (FBG) pair is used as one wavelength selection component. By properly adjusting the polarization controllers (PCs), the switchable dual-wavelength SLM fiber laser can be operated steadily at room temperature. The optical signal-to-noise ratio (OSNR) is better than 50 dB for both lasing wavelengths. Meanwhile, the linewidth of the fiber laser for each wavelength is approximate 17.07 kHz and 18.64 kHz with a 20 dB linewidth, which means the laser linewidth is approximate 853 Hz and 932 Hz FWHM. Correspondingly, the measured relative intensity noise (RIN) is less than -120 dB/Hz at frequencies over 5.0 MHz.

Switchable photovoltaic windows enabled by reversible photothermal complex dissociation from methylammonium lead iodide.

PubMed

Wheeler, Lance M; Moore, David T; Ihly, Rachelle; Stanton, Noah J; Miller, Elisa M; Tenent, Robert C; Blackburn, Jeffrey L; Neale, Nathan R

2017-11-23

Materials with switchable absorption properties have been widely used for smart window applications to reduce energy consumption and enhance occupant comfort in buildings. In this work, we combine the benefits of smart windows with energy conversion by producing a photovoltaic device with a switchable absorber layer that dynamically responds to sunlight. Upon illumination, photothermal heating switches the absorber layer-composed of a metal halide perovskite-methylamine complex-from a transparent state (68% visible transmittance) to an absorbing, photovoltaic colored state (less than 3% visible transmittance) due to dissociation of methylamine. After cooling, the methylamine complex is re-formed, returning the absorber layer to the transparent state in which the device acts as a window to visible light. The thermodynamics of switching and performance of the device are described. This work validates a photovoltaic window technology that circumvents the fundamental tradeoff between efficient solar conversion and high visible light transmittance that limits conventional semitransparent PV window designs.

Switchable photovoltaic windows enabled by reversible photothermal complex dissociation from methylammonium lead iodide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wheeler, Lance M.; Moore, David T.; Ihly, Rachelle

Materials with switchable absorption properties have been widely used for smart window applications to reduce energy consumption and enhance occupant comfort in buildings. In this work, we combine the benefits of smart windows with energy conversion by producing a photovoltaic device with a switchable absorber layer that dynamically responds to sunlight. Upon illumination, photothermal heating switches the absorber layer - composed of a metal halide perovskite-methylamine complex - from a transparent state (68% visible transmittance) to an absorbing, photovoltaic colored state (less than 3% visible transmittance) due to dissociation of methylamine. After cooling, the methylamine complex is re-formed, returning themore » absorber layer to the transparent state in which the device acts as a window to visible light. The thermodynamics of switching and performance of the device are described. In conclusion, this work validates a photovoltaic window technology that circumvents the fundamental tradeoff between efficient solar conversion and high visible light transmittance that limits conventional semitransparent PV window designs.« less

In situ alcoholysis of triacylglycerols by application of switchable-polarity solvents. A new derivatization procedure for the gas-chromatographic analysis of vegetable oils.

PubMed

Saliu, Francesco; Orlandi, Marco

2013-10-01

We describe a new use of switchable-polarity solvents for the simultaneous derivatization and extraction of triacylglycerols from vegetable oils before gas-chromatographic analysis. Different equimolecular mixtures of the commercially available amidine 1,8-diazabicyclo[5.4.0]undec-7-ene and n-alkyl alcohols were tested. Triolein was used as a model compound. Very good results were achieved by using butanol (recovery of butyl oleate was 89 ± 4%). The procedure was applied for the characterization of the fatty acid profile of different vegetable oils. No statistically significant differences from the results obtained with the application of two traditional methods were evidenced. Moreover, the use of switchable-polarity solvents showed many advantages: owing to the basicity of the amidines, no catalyst was required; the transterification reaction was conducted under mild conditions, one step and in situ; no particular matrix interferences were evidenced; the solvent was recovered.

pH-switchable electrochemical sensing platform based on chitosan-reduced graphene oxide/concanavalin a layer for assay of glucose and urea.

PubMed

Song, Yonghai; Liu, Hongyu; Tan, Hongliang; Xu, Fugang; Jia, Jianbo; Zhang, Lixue; Li, Zhuang; Wang, Li

2014-02-18

A facile and effective electrochemical sensing platform for the detection of glucose and urea in one sample without separation was developed using chitosan-reduced graphene oxide (CS-rGO)/concanavalin A (Con A) as a sensing layer. The CS-rGO/Con A with pH-dependent surface net charges exhibited pH-switchable response to negatively charged Fe(CN)6(3-). The principle for glucose and urea detection was essentially based on in situ pH-switchable enzyme-catalyzed reaction in which the oxidation of glucose catalyzed by glucose oxidase or the hydrolyzation of urea catalyzed by urease resulted in a pH change of electrolyte solution to give different electrochemical responses toward Fe(CN)6(3-). It was verified by cyclic voltammograms, differential pulse voltammograms, and electrochemical impedance spectroscopy. The resistance to charge transfer or amperometric current changed proportionally toward glucose concentration from 1.0 to 10.0 mM and urea concentration from 1.0 to 7.0 mM. On the basis of human serum experiments, the sensing platform was proved to be suitable for simultaneous assay of glucose and urea in a practical biosystem. This work not only gives a way to detect glucose and urea in one sample without separation but also provides a potential strategy for the detection of nonelectroactive species based on the enzyme-catalyzed reaction and pH-switchable biosensor.

MCM ring hexamerization is a prerequisite for DNA-binding

DOE PAGES

Froelich, Clifford A.; Nourse, Amanda; Enemark, Eric J.

2015-09-13

The hexameric Minichromosome Maintenance (MCM) protein complex forms a ring that unwinds DNA at the replication fork in eukaryotes and archaea. Our recent crystal structure of an archaeal MCM N-terminal domain bound to single-stranded DNA (ssDNA) revealed ssDNA associating across tight subunit interfaces but not at the loose interfaces, indicating that DNA-binding is governed not only by the DNA-binding residues of the subunits (MCM ssDNA-binding motif, MSSB) but also by the relative orientation of the subunits. We now extend these findings to show that DNA-binding by the MCM N-terminal domain of the archaeal organism Pyrococcus furiosus occurs specifically in themore » hexameric oligomeric form. We show that mutants defective for hexamerization are defective in binding ssDNA despite retaining all the residues observed to interact with ssDNA in the crystal structure. One mutation that exhibits severely defective hexamerization and ssDNA-binding is at a conserved phenylalanine that aligns with the mouse Mcm4(Chaos3) mutation associated with chromosomal instability, cancer, and decreased intersubunit association.« less

Cohesin Function in Cohesion, Condensation, and DNA Repair Is Regulated by Wpl1p via a Common Mechanism in Saccharomyces cerevisiae.

PubMed

Bloom, Michelle S; Koshland, Douglas; Guacci, Vincent

2018-01-01

Cohesin tethers DNA to mediate sister chromatid cohesion, chromosome condensation, and DNA repair. How the cell regulates cohesin to perform these distinct functions remains to be elucidated. One cohesin regulator, Wpl1p, was characterized in Saccharomyces cerevisiae as a promoter of efficient cohesion and an inhibitor of condensation. Wpl1p is also required for resistance to DNA-damaging agents. Here, we provide evidence that Wpl1p promotes the timely repair of DNA damage induced during S-phase. Previous studies have indicated that Wpl1p destabilizes cohesin's binding to DNA by modulating the interface between the cohesin subunits Mcd1p and Smc3p Our results suggest that Wpl1p likely modulates this interface to regulate all of cohesin's biological functions. Furthermore, we show that Wpl1p regulates cohesion and condensation through the formation of a functional complex with another cohesin-associated factor, Pds5p In contrast, Wpl1p regulates DNA repair independently of its interaction with Pds5p Together, these results suggest that Wpl1p regulates distinct biological functions of cohesin by Pds5p-dependent and -independent modulation of the Smc3p/Mcd1p interface. Copyright © 2018 by the Genetics Society of America.

Cohesin Function in Cohesion, Condensation, and DNA Repair Is Regulated by Wpl1p via a Common Mechanism in Saccharomyces cerevisiae

PubMed Central

Bloom, Michelle S.; Koshland, Douglas; Guacci, Vincent

2018-01-01

Cohesin tethers DNA to mediate sister chromatid cohesion, chromosome condensation, and DNA repair. How the cell regulates cohesin to perform these distinct functions remains to be elucidated. One cohesin regulator, Wpl1p, was characterized in Saccharomyces cerevisiae as a promoter of efficient cohesion and an inhibitor of condensation. Wpl1p is also required for resistance to DNA-damaging agents. Here, we provide evidence that Wpl1p promotes the timely repair of DNA damage induced during S-phase. Previous studies have indicated that Wpl1p destabilizes cohesin’s binding to DNA by modulating the interface between the cohesin subunits Mcd1p and Smc3p. Our results suggest that Wpl1p likely modulates this interface to regulate all of cohesin’s biological functions. Furthermore, we show that Wpl1p regulates cohesion and condensation through the formation of a functional complex with another cohesin-associated factor, Pds5p. In contrast, Wpl1p regulates DNA repair independently of its interaction with Pds5p. Together, these results suggest that Wpl1p regulates distinct biological functions of cohesin by Pds5p-dependent and -independent modulation of the Smc3p/Mcd1p interface. PMID:29158426

Molecular threading: mechanical extraction, stretching and placement of DNA molecules from a liquid-air interface.

PubMed

Payne, Andrew C; Andregg, Michael; Kemmish, Kent; Hamalainen, Mark; Bowell, Charlotte; Bleloch, Andrew; Klejwa, Nathan; Lehrach, Wolfgang; Schatz, Ken; Stark, Heather; Marblestone, Adam; Church, George; Own, Christopher S; Andregg, William

2013-01-01

We present "molecular threading", a surface independent tip-based method for stretching and depositing single and double-stranded DNA molecules. DNA is stretched into air at a liquid-air interface, and can be subsequently deposited onto a dry substrate isolated from solution. The design of an apparatus used for molecular threading is presented, and fluorescence and electron microscopies are used to characterize the angular distribution, straightness, and reproducibility of stretched DNA deposited in arrays onto elastomeric surfaces and thin membranes. Molecular threading demonstrates high straightness and uniformity over length scales from nanometers to micrometers, and represents an alternative to existing DNA deposition and linearization methods. These results point towards scalable and high-throughput precision manipulation of single-molecule polymers.

Database of amino acid-nucleotide contacts in contacts in DNA-homeodomain protein

NASA Astrophysics Data System (ADS)

Grokhlina, T. I.; Zrelov, P. V.; Ivanov, V. V.; Polozov, R. V.; Chirgadze, Yu. N.; Sivozhelezov, V. S.

2013-09-01

The analysis of amino acid-nucleotide contacts in interfaces of the protein-DNA complexes, intended to find consistencies in the protein-DNA recognition, is a complex problem that requires an analysis of the physicochemical characteristics of these contacts and the positions of the participating amino acids and nucleotides in the chains of the protein and the DNA, respectively, as well as conservatism of these contacts. Thus, those heterogeneous data should be systematized. For this purpose we have developed a database of amino acid-nucleotide contacts ANTPC (Amino acid Nucleotide Type Position Conservation) following the archetypal example of the proteins in the homeodomain family. We show that it can be used to compare and classify the interfaces of the protein-DNA complexes.

Supramolecular 1-D polymerization of DNA origami through a dynamic process at the 2-dimensionally confined air-water interface.

PubMed

Yonamine, Yusuke; Cervantes-Salguero, Keitel; Minami, Kosuke; Kawamata, Ibuki; Nakanishi, Waka; Hill, Jonathan P; Murata, Satoshi; Ariga, Katsuhiko

2016-05-14

In this study, a Langmuir-Blodgett (LB) system has been utilized for the regulation of polymerization of a DNA origami structure at the air-water interface as a two-dimensionally confined medium, which enables dynamic condensation of DNA origami units through variation of the film area at the macroscopic level (ca. 10-100 cm(2)). DNA origami sheets were conjugated with a cationic lipid (dioctadecyldimethylammonium bromide, 2C18N(+)) by electrostatic interaction and the corresponding LB-film was prepared. By applying dynamic pressure variation through compression-expansion processes, the lipid-modified DNA origami sheets underwent anisotropic polymerization forming a one-dimensionally assembled belt-shaped structure of a high aspect ratio although the thickness of the polymerized DNA origami was maintained at the unimolecular level. This approach opens up a new field of mechanical induction of the self-assembly of DNA origami structures.

Irradiation effects on electrical properties of DNA solution/Al Schottky diodes

NASA Astrophysics Data System (ADS)

Al-Ta'ii, Hassan Maktuff Jaber; Periasamy, Vengadesh; Iwamoto, Mitsumasa

2018-04-01

Deoxyribonucleic acid (DNA) has emerged as one of the most exciting organic material and as such extensively studied as a smart electronic material since the last few decades. DNA molecules have been reported to be utilized in the fabrication of small-scaled sensors and devices. In this current work, the effect of alpha radiation on the electrical properties of an Al/DNA/Al device using DNA solution was studied. It was observed that the carrier transport was governed by electrical interface properties at the Al-DNA interface. Current ( I)-voltage ( V) curves were analyzed by employing the interface limited Schottky current equations, i.e., conventional and Cheung and Cheung's models. Schottky parameters such as ideality factor, barrier height and series resistance were also determined. The extracted barrier height of the Schottky contact before and after radiation was calculated as 0.7845, 0.7877, 0.7948 and 0.7874 eV for the non-radiated, 12, 24 and 36 mGy, respectively. Series resistance of the structure was found to decline with the increase in the irradiation, which was due to the increase in the free radical root effects in charge carriers in the DNA solution. Results pertaining to the electronic profiles obtained in this work may provide a better understanding for the development of precise and rapid radiation sensors using DNA solution.

Electrical potential induced switchable wettability of super-aligned carbon nanotube films

NASA Astrophysics Data System (ADS)

Zhang, Guang; Duan, Zheng; Wang, Qinggong; Li, Long; Yao, Wei; Liu, Changhong

2018-01-01

Controlling of the wettability of micro-nano scale surfaces not only plays important roles in basic science but also presents some significant applications in interference shielding materials, microfluidics and phase-change heat transfer enhancement, etc. Here, the superhydrophobic super-aligned carbon nanotube (SACNT) films are firstly obtained by the chemical vapor deposition method and the annealing process. Then their wettabilities are in-situ switched by the electrowetting strategy. Specifically, the fascinating transformation of superhydrophobicity to the superhydrophilicity is achieved by exerting external DC voltages across the CNT-liquid interfaces, and the transitions of Cassie-to-Wenzel states are observed on the multilayer SACNT films. In addition, the electrowetting induced salt absorption of the porous SACNT is also reported here. Finally, the threshold voltages of the electrowetting behaviors for different liquids on the SACNT films and unit capacitances across the CNT-liquid interfaces are obtained, which reveal that the SACNT films have much more outstanding electrowetting properties than the previously reported works. Our approach reported here demonstrates that the wettability of SACNT films could be simply, effectively and in-situ controlled by the electrowetting method, which will have many profound implications in numerous applications such as phase-change heat transfer enhancement, optical lens with variable focal length and microfluidics, etc.

Allosteric regulation in NMDA receptors revealed by the genetically encoded photo-cross-linkers

PubMed Central

Tian, Meilin; Ye, Shixin

2016-01-01

Allostery is essential to neuronal receptor function, but its transient nature poses a challenge for characterization. The N-terminal domains (NTDs) distinct from ligand binding domains are a major locus for allosteric regulation of NMDA receptors (NMDARs), where different modulatory binding sites have been observed. The inhibitor ifenprodil, and related phenylethanoamine compounds specifically targeting GluN1/GluN2B NMDARs have neuroprotective activity. However, whether they use differential structural pathways than the endogenous inhibitor Zn2+ for regulation is unknown. We applied genetically encoded unnatural amino acids (Uaas) and monitored the functional changes in living cells with photo-cross-linkers specifically incorporated at the ifenprodil binding interface between GluN1 and GluN2B subunits. We report constraining the NTD domain movement, by a light induced crosslinking bond that introduces minimal perturbation to the ligand binding, specifically impedes the transduction of ifenprodil but not Zn2+ inhibition. Subtle distance changes reveal interfacial flexibility and NTD rearrangements in the presence of modulators. Our results present a much richer dynamic picture of allostery than conventional approaches targeting the same interface, and highlight key residues that determine functional and subtype specificity of NMDARs. The light-sensitive mutant neuronal receptors provide complementary tools to the photo-switchable ligands for opto-neuropharmacology. PMID:27713495

Emerging ferroelectric transistors with nanoscale channel materials: the possibilities, the limitations

NASA Astrophysics Data System (ADS)

Hong, Xia

2016-03-01

Combining the nonvolatile, locally switchable polarization field of a ferroelectric thin film with a nanoscale electronic material in a field effect transistor structure offers the opportunity to examine and control a rich variety of mesoscopic phenomena and interface coupling. It is also possible to introduce new phases and functionalities into these hybrid systems through rational design. This paper reviews two rapidly progressing branches in the field of ferroelectric transistors, which employ two distinct classes of nanoscale electronic materials as the conducting channel, the two-dimensional (2D) electron gas graphene and the strongly correlated transition metal oxide thin films. The topics covered include the basic device physics, novel phenomena emerging in the hybrid systems, critical mechanisms that control the magnitude and stability of the field effect modulation and the mobility of the channel material, potential device applications, and the performance limitations of these devices due to the complex interface interactions and challenges in achieving controlled materials properties. Possible future directions for this field are also outlined, including local ferroelectric gate control via nanoscale domain patterning and incorporating other emergent materials in this device concept, such as the simple binary ferroelectrics, layered 2D transition metal dichalcogenides, and the 4d and 5d heavy metal compounds with strong spin-orbit coupling.

DNA Nanotechnology-Enabled Interfacial Engineering for Biosensor Development.

PubMed

Ye, Dekai; Zuo, Xiaolei; Fan, Chunhai

2018-06-12

Biosensors represent biomimetic analytical tools for addressing increasing needs in medical diagnosis, environmental monitoring, security, and biodefense. Nevertheless, widespread real-world applications of biosensors remain challenging due to limitations of performance, including sensitivity, specificity, speed, and reproducibility. In this review, we present a DNA nanotechnology-enabled interfacial engineering approach for improving the performance of biosensors. We first introduce the main challenges of the biosensing interfaces, especially under the context of controlling the DNA interfacial assembly. We then summarize recent progress in DNA nanotechnology and efforts to harness DNA nanostructures to engineer various biological interfaces, with a particular focus on the use of framework nucleic acids. We also discuss the implementation of biosensors to detect physiologically relevant nucleic acids, proteins, small molecules, ions, and other biomarkers. This review highlights promising applications of DNA nanotechnology in interfacial engineering for biosensors and related areas.

Reconfigurable liquid metal circuits by Laplace pressure shaping

NASA Astrophysics Data System (ADS)

Cumby, Brad L.; Hayes, Gerard J.; Dickey, Michael D.; Justice, Ryan S.; Tabor, Christopher E.; Heikenfeld, Jason C.

2012-10-01

We report reconfigurable circuits formed by liquid metal shaping with <10 pounds per square inch (psi) Laplace and vacuum pressures. Laplace pressure drives liquid metals into microreplicated trenches, and upon release of vacuum, the liquid metal dewets into droplets that are compacted to 10-100× less area than when in the channel. Experimental validation includes measurements of actuation speeds exceeding 30 cm/s, simple erasable resistive networks, and switchable 4.5 GHz antennas. Such capability may be of value for next generation of simple electronic switches, tunable antennas, adaptive reflectors, and switchable metamaterials.

Thermally switchable dielectrics

DOEpatents

Dirk, Shawn M.; Johnson, Ross S.

2013-04-30

Precursor polymers to conjugated polymers, such as poly(phenylene vinylene), poly(poly(thiophene vinylene), poly(aniline vinylene), and poly(pyrrole vinylene), can be used as thermally switchable capacitor dielectrics that fail at a specific temperature due to the non-conjugated precursor polymer irreversibly switching from an insulator to the conjugated polymer, which serves as a bleed resistor. The precursor polymer is a good dielectric until it reaches a specific temperature determined by the stability of the leaving groups. Conjugation of the polymer backbone at high temperature effectively disables the capacitor, providing a `built-in` safety mechanism for electronic devices.

Switchable molecular magnets

PubMed Central

SATO, Osamu

2012-01-01

Various molecular magnetic compounds whose magnetic properties can be controlled by external stimuli have been developed, including electrochemically, photochemically, and chemically tunable bulk magnets as well as a phototunable antiferromagnetic phase of single chain magnet. In addition, we present tunable paramagnetic mononuclear complexes ranging from spin crossover complexes and valence tautomeric complexes to Co complexes in which orbital angular momentum can be switched. Furthermore, we recently developed several switchable clusters and one-dimensional coordination polymers. The switching of magnetic properties can be achieved by modulating metals, ligands, and molecules/ions in the second sphere of the complexes. PMID:22728438

Preparation of a Magnetically Switchable Bioelectrocatalytic System Employing Cross-Linked Enzyme Aggregates in Magnetic Mesocellular Carbon Foam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Jinwoo; Lee, Dohun; Oh, Eunkeu

2005-11-18

Nanostructured magnetic materials (NMMs)[1] have attracted much attention recently because of their broad biotechnological applications including support matrices for enzyme immobilization,[2] immunoassays,[3] drug delivery,[4] and biosensors.[ 5] Specifically, the easy separation and controlled placement of NMMs by means of an external magnetic field enables their application in the development of immobilized enzyme processes[2] and the construction of magnetically controllable bio-electrocatalytic systems.[5, 6] Herein, we demonstrate the use of immobilized enzymes in NMMs for magnetically switchable bio-electrocatalysis.

Self-assembly of DNA functionalized gold nanoparticles at the liquid-vapor interface

DOE PAGES

Zhang, Honghu; Wang, Wenjie; Hagen, Noah; ...

2016-05-30

Here, surface sensitive synchrotron X-ray scattering and spectroscopy are used to monitor and characterize the spontaneous formation of 2D Gibbs monolayers of thiolated single-stranded DNA-functionalized gold nanoparticles (ssDNAAuNPs) at the vapor–solution interface by manipulating salt concentrations. Grazing incidence small-angle X-ray scattering and X-ray refl ectivity show that the noncomplementary ssDNA-AuNPs dispersed in aqueous solution spontaneously accumulate at the vapor–liquid interface in the form of a single layer by increasing MgCl 2 or CaCl 2 concentrations. Furthermore, the monoparticle layer undergoes a transformation from short- to long-range (hexagonal) order above a threshold salt-concentration. Using various salts at similar ionic strength tomore » those of MgCl 2 or CaCl 2 such as, NaCl or LaCl 3, it is found that surface adsorbed NPs lack any order. X-ray fluorescence near total reflection of the same samples provides direct evidence of interfacial gold and more importantly a significant surface enrichment of the cations. Quantitative analysis reveals that divalent cations screen the charge of ssDNA, and that the hydrophobic hexyl-thiol group, commonly used to functionalize the ssDNA (for capping the AuNPs), is likely the driving force for the accumulation of the NPs at the interface.« less

Channel plate for DNA sequencing

DOEpatents

Douthart, R.J.; Crowell, S.L.

1998-01-13

This invention is a channel plate that facilitates data compaction in DNA sequencing. The channel plate has a length, a width and a thickness, and further has a plurality of channels that are parallel. Each channel has a depth partially through the thickness of the channel plate. Additionally an interface edge permits electrical communication across an interface through a buffer to a deposition membrane surface. 15 figs.

Conductive Boron-Doped Graphene as an Ideal Material for Electrocatalytically Switchable and High-Capacity Hydrogen Storage.

PubMed

Tan, Xin; Tahini, Hassan A; Smith, Sean C

2016-12-07

Electrocatalytic, switchable hydrogen storage promises both tunable kinetics and facile reversibility without the need for specific catalysts. The feasibility of this approach relies on having materials that are easy to synthesize, possessing good electrical conductivities. Graphitic carbon nitride (g-C 4 N 3 ) has been predicted to display charge-responsive binding with molecular hydrogen-the only such conductive sorbent material that has been discovered to date. As yet, however, this conductive variant of graphitic carbon nitride is not readily synthesized by scalable methods. Here, we examine the possibility of conductive and easily synthesized boron-doped graphene nanosheets (B-doped graphene) as sorbent materials for practical applications of electrocatalytically switchable hydrogen storage. Using first-principle calculations, we find that the adsorption energy of H 2 molecules on B-doped graphene can be dramatically enhanced by removing electrons from and thereby positively charging the adsorbent. Thus, by controlling charge injected or depleted from the adsorbent, one can effectively tune the storage/release processes which occur spontaneously without any energy barriers. At full hydrogen coverage, the positively charged BC 5 achieves high storage capacities up to 5.3 wt %. Importantly, B-doped graphene, such as BC 49 , BC 7 , and BC 5 , have good electrical conductivity and can be easily synthesized by scalable methods, which positions this class of material as a very good candidate for charge injection/release. These predictions pave the route for practical implementation of electrocatalytic systems with switchable storage/release capacities that offer high capacity for hydrogen storage.

Switchable silver mirrors with long memory effects† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c4sc01912a Click here for additional data file. Click here for additional data file.

PubMed Central

Park, Chihyun; Seo, Seogjae; Shin, Haijin; Sarwade, Bhimrao D.; Na, Jongbeom

2015-01-01

An electrochemically stable and bistable switchable mirror was achieved for the first time by introducing (1) a thiol-modified indium tin oxide (ITO) electrode for the stabilization of the metallic film and (2) ionic liquids as an anion-blocking layer, to achieve a long memory effect. The growth of the metallic film was denser and faster at the thiol-modified ITO electrode than at a bare ITO electrode. The electrochemical stability of the metallic film on the thiol-modified ITO was enhanced, maintaining the metallic state without rupture. In the voltage-off state, the metal film maintained bistability for a long period (>2 h) when ionic liquids were introduced as electrolytes for the switchable mirror. The electrical double layer in the highly viscous ionic liquid electrolyte seemed to effectively form a barrier to the bromide ions, to protect the metal thin film from them when in the voltage-off state. PMID:28936310

Tunable and switchable dual-wavelength single polarization narrow linewidth SLM erbium-doped fiber laser based on a PM-CMFBG filter.

PubMed

Yin, Bin; Feng, Suchun; Liu, Zhibo; Bai, Yunlong; Jian, Shuisheng

2014-09-22

A tunable and switchable dual-wavelength single polarization narrow linewidth single-longitudinal-mode (SLM) erbium-doped fiber (EDF) ring laser based on polarization-maintaining chirped moiré fiber Bragg grating (PM-CMFBG) filter is proposed and demonstrated. For the first time as we know, the CMFBG inscribed on the PM fiber is applied for the wavelength-tunable and-switchable dual-wavelength laser. The PM-CMFBG filter with ultra-narrow transmission band (0.1 pm) and a uniform polarization-maintaining fiber Bragg grating (PM-FBG) are used to select the laser longitudinal mode. The stable single polarization SLM operation is guaranteed by the PM-CMFBG filter and polarization controller. A tuning range of about 0.25 nm with about 0.075 nm step is achieved by stretching the uniform PM-FBG. Meanwhile, the linewidth of the fiber laser for each wavelength is approximate 6.5 and 7.1 kHz with a 20 dB linewidth, which indicates the laser linewidth is approximate 325 Hz and 355 Hz FWHM.

Tunable and switchable dual-waveband ultrafast fiber laser with 100 GHz repetition-rate.

PubMed

Tan, Xiao-Mei; Chen, Hong-Jie; Cui, Hu; Lv, Yao-Kun; Zhao, Guan-Kai; Luo, Zhi-Chao; Luo, Ai-Ping; Xu, Wen-Cheng

2017-07-10

We demonstrate a tunable and switchable dual-waveband 100 GHz high-repetition-rate (HRR) ultrafast fiber laser based on dissipative four-wave-mixing (DFWM) mode-locked technique. Each waveband maintains HRR operation. The DFWM effect was realized by combining a Fabry-Perot (F-P) filter and a piece of highly nonlinear fiber (HNLF). The tunable and switchable operations were achieved by nonlinear polarization rotation (NPR) technique. Through appropriately controlling the filtering effect induced by NPR, the laser could operate at two kinds of tunable regimes. One is that the spacing between these two wavebands could be tuned while keeping their center at 1559 nm. The other is that the central position of the entire dual-waveband is tunable while with the same separation between these two wavebands of 13.2 nm. Moreover, the laser could switch between these two wavebands. Correspondingly, the center of the single-waveband has a tuning range of 15.2 nm. This versatile ultrafast fiber laser may find applications in fields of optical frequency combs, high speed optical communications, where HRR pulses are necessary.

Conductive properties of switchable photoluminescence thermosetting systems based on liquid crystals.

PubMed

Tercjak, Agnieszka; Gutierrez, Junkal; Ocando, Connie; Mondragon, Iñaki

2010-03-16

Conductive properties of different thermosetting materials modified with nematic 4'-(hexyl)-4-biphenyl-carbonitrile (HBC) liquid crystal and rutile TiO(2) nanoparticles were successfully studied by means of tunneling atomic force miscroscopy (TUNA). Taking into account the liquid crystal state of the HBC at room temperature, depending on both the HBC content and the presence of TiO(2) nanoparticles, designed materials showed different TUNA currents passed through the sample. The addition of TiO(2) nanoparticles into the systems multiply the detected current if compared to the thermosetting systems without TiO(2) nanoparticles and simultaneously stabilized the current passed through the sample, making the process reversible since the absolute current values were almost the same applying both negative and positive voltage. Moreover, thermosetting systems modified with liquid crystals with and without TiO(2) nanoparticles are photoluminescence switchable materials as a function of temperature gradient during repeatable heating/cooling cycle. Conductive properties of switchable photoluminescence thermosetting systems based on liquid crystals can allow them to find potential application in the field of photoresponsive devices, with a high contrast ratio between transparent and opaque states.

Switchable multi-wavelength erbium-doped fiber ring laser based on a tapered in-line Mach–Zehnder interferometer

NASA Astrophysics Data System (ADS)

Zhou, Yuxin; Wang, Xin; Tang, Zijuan; Lou, Shuqin

2018-05-01

In this paper, a switchable multi-wavelength erbium-doped fiber ring laser based on a tapered in-line Mach–Zehnder interferometer is proposed. The in-line Mach–Zehnder interferometer is fabricated by splicing a large-core fiber between two segments of single mode fibers, in which the first splicing point is tapered and the second splicing point is connected directly. By carefully rotating the polarization controller, switchable single-, dual-, triple- and quad-wavelength lasing outputs can be obtained with a side mode suppression ratio higher than 50 dB. The maximal peak power difference of multi-wavelength lasing is 3.67 dB, demonstrating a good power equalization performance. Furthermore, the proposed laser is proven to be very stable at room temperature. The wavelength shifts and peak power fluctuations are less than 0.02 nm and 1.3 dB over half an hour. In addition, stable quintuple-wavelength lasing with a side mode suppression ratio higher than 50 dB can also be realized when the filter length is changed.

Frequency-Switchable Microfluidic CSRR-Loaded QMSIW Band-Pass Filter Using a Liquid Metal Alloy

PubMed Central

Eom, Seunghyun; Memon, Muhammad Usman; Lim, Sungjoon

2017-01-01

In this paper, we have proposed a frequency-switchable complementary split-ring resonator (CSRR)-loaded quarter-mode substrate-integrated-waveguide (QMSIW) band-pass filter. For frequency switching, a microfluidic channel and liquid metal are used. The liquid metal used is eutectic gallium-indium (EGaIn), consisting of 24.5% indium and 75.5% gallium. The microfluidic channels are built using the elastomer polydimethylsiloxane (PDMS) and three-dimensional-printed microfluidic channel frames. The CSRR-loaded QMSIW band-pass filter is designed to have two states. Before the injection of the liquid metal, the measured center frequency and fractional bandwidths are 2.205 GHz and 6.80%, respectively. After injection, the center frequency shifts from 2.205 GHz to 2.56 GHz. Although the coupling coefficient is practically unchanged, the fractional bandwidth changes from 6.8% to 9.38%, as the CSRR shape changes and the external quality factor decreases. After the removal of the liquid metal, the measured values are similar to the values recorded before the liquid metal was injected. The repeatability of the frequency-switchable mechanism is, therefore, verified. PMID:28350355

SWITCHABLE POLARITY SOLVENTS AS DRAW SOLUTES FOR FORWARD OSMOSIS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frederick F. Stewart; Mark L. Stone; Aaron D. Wilson

2013-03-01

Switchable polarity solvents (SPS), mixtures of carbon dioxide, water, and tertiary amines, are presented as viable forward osmosis (FO) draw solutes allowing a novel SPS FO process. In this study substantial osmotic strengths of SPS are measured with freezing point osmometry and were demonstrated to induce competitive ?uxes at high salt concentrations on a laboratory-scale FO unit utilizing a ?at sheet cellulose triacetate (CTA) membrane. Under the experimental conditions the SPS degrades the CTA membrane; however experiments with polyamide reverse osmosis (RO) membranes display stability towards SPS. Once the draw is diluted the major fraction of the switchable polarity solventmore » can be mechanically separated from the puri?ed water after polar to nonpolar phase shift induced by introduction of 1 atm carbon dioxide to 1 atm of air or nitrogen with mild heating. Trace amounts of SPS can be removed from the separated water with RO in a process that avoids solution concentration polarization. The separated nonpolar phase can be regenerated to a full strength draw and recycled with the re-addition of 1 atm of carbon dioxide.« less

A Multi-Addressable Dyad with Switchable CMY Colors for Full-Color Rewritable Papers.

PubMed

Qin, Tianyou; Han, Jiaqi; Geng, Yue; Ju, Le; Sheng, Lan; Zhang, Sean Xiao-An

2018-06-23

Reversible multicolor displays on solid media using single molecule pigments have been a long-awaited goal. Herein, a new and simple molecular dyad, which can undergo switchable CMY color changes both in solution and solid substrate upon exposure to light, water/acid, and nucleophiles, is designed and synthesized. The stimuli used in this work can be applied independent of each other, which is beneficial for color changes without mutual interference. As a comparison, the mixtures of the two molecular switching motifs forming the basis of the dyad were also studied. The dyad greatly outperforms the corresponding mixed system with respect to reversible color-switching on the paper substrate. Its potential for full-color rewritable paper with excellent reversibility has been demonstrated. Legible multicolor prints, that is, high color contrast and resolution, good dispersion, excellent reversibility, were achieved using common water-jet and light-based printers. This work provides a very promising approach for further development of full-color switchable molecules, materials and displays. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adhesion of Chlamydomonas microalgae to surfaces is switchable by light

NASA Astrophysics Data System (ADS)

Kreis, Christian Titus; Le Blay, Marine; Linne, Christine; Makowski, Marcin Michal; Bäumchen, Oliver

2018-01-01

Microalgae are photoactive microbes that live in liquid-infused environments, such as soil, temporary pools and rocks, where they encounter and colonize a plethora of surfaces. Their photoactivity manifests itself in a variety of processes, including light-directed motility (phototaxis), the growth of microalgal populations, and their photosynthetic machinery. Although microbial responses to light have been widely recognized, any influence of light on cell-surface interactions remains elusive. Here, we reveal that the unspecific adhesion of microalgae to surfaces can be reversibly switched on and off by light. Using a micropipette force spectroscopy technique, we measured in vivo single-cell adhesion forces and show that the microalga's flagella provide light-switchable adhesive contacts with the surface. This light-induced adhesion to surfaces is an active and completely reversible process that occurs on a timescale of seconds. Our results suggest that light-switchable adhesiveness is a natural functionality of microalgae to regulate the transition between the planktonic and the surface-associated state, which yields an adhesive adaptation to optimize the photosynthetic efficiency in conjunction with phototaxis.

Programmable ion-sensitive transistor interfaces. II. Biomolecular sensing and manipulation.

PubMed

Jayant, Krishna; Auluck, Kshitij; Funke, Mary; Anwar, Sharlin; Phelps, Joshua B; Gordon, Philip H; Rajwade, Shantanu R; Kan, Edwin C

2013-07-01

The chemoreceptive neuron metal-oxide-semiconductor transistor described in the preceding paper is further used to monitor the adsorption and interaction of DNA molecules and subsequently manipulate the adsorbed biomolecules with injected static charge. Adsorption of DNA molecules onto poly-L-lysine-coated sensing gates (SGs) modulates the floating gate (FG) potential ψ(O), which is reflected as a threshold voltage shift measured from the control gate (CG) V(th_CG). The asymmetric capacitive coupling between the CG and SG to the FG results in V(th_CG) amplification. The electric field in the SG oxide E(SG_ox) is fundamentally different when we drive the current readout with V(CG) and V(ref) (i.e., the potential applied to the CG and reference electrode, respectively). The V(CG)-driven readout induces a larger E(SG_ox), leading to a larger V(th_CG) shift when DNA is present. Simulation studies indicate that the counterion screening within the DNA membrane is responsible for this effect. The DNA manipulation mechanism is enabled by tunneling electrons (program) or holes (erase) onto FGs to produce repulsive or attractive forces. Programming leads to repulsion and eventual desorption of DNA, while erasing reestablishes adsorption. We further show that injected holes or electrons prior to DNA addition either aids or disrupts the immobilization process, which can be used for addressable sensor interfaces. To further substantiate DNA manipulation, we used impedance spectroscopy with a split ac-dc technique to reveal the net interface impedance before and after charge injection.

Redesigning the specificity of protein-DNA interactions with Rosetta.

PubMed

Thyme, Summer; Baker, David

2014-01-01

Building protein tools that can selectively bind or cleave specific DNA sequences requires efficient technologies for modifying protein-DNA interactions. Computational design is one method for accomplishing this goal. In this chapter, we present the current state of protein-DNA interface design with the Rosetta macromolecular modeling program. The LAGLIDADG endonuclease family of DNA-cleaving enzymes, under study as potential gene therapy reagents, has been the main testing ground for these in silico protocols. At this time, the computational methods are most useful for designing endonuclease variants that can accommodate small numbers of target site substitutions. Attempts to engineer for more extensive interface changes will likely benefit from an approach that uses the computational design results in conjunction with a high-throughput directed evolution or screening procedure. The family of enzymes presents an engineering challenge because their interfaces are highly integrated and there is significant coordination between the binding and catalysis events. Future developments in the computational algorithms depend on experimental feedback to improve understanding and modeling of these complex enzymatic features. This chapter presents both the basic method of design that has been successfully used to modulate specificity and more advanced procedures that incorporate DNA flexibility and other properties that are likely necessary for reliable modeling of more extensive target site changes.

Structure of the Response Regulator PhoP from Mycobacterium tuberculosis Reveals a Dimer Through the Receiver Domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

S Menon; S Wang

The PhoP protein from Mycobacterium tuberculosis is a response regulator of the OmpR/PhoB subfamily, whose structure consists of an N-terminal receiver domain and a C-terminal DNA-binding domain. How the DNA-binding activities are regulated by phosphorylation of the receiver domain remains unclear due to a lack of structural information on the full-length proteins. Here we report the crystal structure of the full-length PhoP of M. tuberculosis. Unlike other known structures of full-length proteins of the same subfamily, PhoP forms a dimer through its receiver domain with the dimer interface involving {alpha}4-{beta}5-{alpha}5, a common interface for activated receiver domain dimers. However, themore » switch residues, Thr99 and Tyr118, are in a conformation resembling those of nonactivated receiver domains. The Tyr118 side chain is involved in the dimer interface interactions. The receiver domain is tethered to the DNA-binding domain through a flexible linker and does not impose structural constraints on the DNA-binding domain. This structure suggests that phosphorylation likely facilitates/stabilizes receiver domain dimerization, bringing the DNA-binding domains to close proximity, thereby increasing their binding affinity for direct repeat DNA sequences.« less

PREFACE Surface Modifications of Diamond and Related Materials (Session D, E-MRS Spring Meeting)

NASA Astrophysics Data System (ADS)

Nebel, Christoph E.

2010-11-01

This special issue contains selected papers which were presented at the E-MRS Symposium BIOMATERIALS, SENSORS & SURFACES, D: 'Surface modifications of diamond and related materials' which was held on 7-9 June 2010 in Strasbourg (France). With about 54 oral and poster presentations given from teams all over the world it was a very interesting, dense and lively meeting. The symposium focused on chemical modifications applied to graft surfaces of diamond, nano-diamond particles, diamond-like carbon, graphene, graphite and carbon nano-tubes with linker molecular layers for realization of bio-sensors, bio-markers, separation techniques, and switchable chemical links. Presented techniques span spontaneous bonding to photo-chemical attachment, electrochemical modifications, to Suzuki-coupling of aryl molecules. Special attention was drawn to mechanisms driving bonding kinetics such as electron transfer reactions, hydrogen cleavage reactions by nucleophilic molecules and growths schemas which vary from correlated two-dimensional chain reactions to three-dimensional cross polymerization. Hydrogen terminations, surface defects, surface roughness and atomic arrangements of surface carbon atoms were of interest to elucidate bonding mechanisms. In addition, bonding stability, either of linker molecules or of complex functionalized surfaces with DNA, proteins and enzymes was discussed by several speakers as well as details of the electronic interfaces between solid transducers and bio-layers. Here the characterization of surface and interface defect densities, of Fermi level pinning and of electron transfer rates was a major topic. Miniaturization of sensor area and application of new detection schemas was discussed. Diamond nano-particles which are increasingly used as biomarkers in drug delivery experiments also attracted attention. The organizers express our gratitude to the international members of the scientific committee who actively contributed to ensure an attractive program in proposing invited speakers. Finally, our symposium would not have been successful without the strong involvement and implication of the EMRS headquarter especially P Siffert, T Lippert, S Schoeffter and C Kocher. They will all find here our sincere thanks. Christoph E Nebel (Chair) Fraunhofer-Institute for Applied Solid State Physics (IAF), Germany Takako Nakamura National Institute of Advanced Industrial Science and Technology (AIST), Japan Philippe Bergonzo CEA-LIST, France John Foord University of Oxford, United Kingdom Kian-Ping Loh National University of Singapore, Singapore

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo Hailu; Zhou Xinxing; Shu Weixing

We theorize an enhanced and switchable spin Hall effect (SHE) of light near the Brewster angle on reflection and demonstrate it experimentally. The obtained spin-dependent splitting reaches 3200 nm near the Brewster angle, which is 50 times larger than the previously reported values in refraction. We find that the amplifying factor in weak measurement is not a constant, which is significantly different from that in refraction. As an analogy of SHE in an electronic system, a switchable spin accumulation in SHE of light is detected. We were able to switch the direction of the spin accumulations by slightly adjusting themore » incident angle.« less

Smart window using a thermally and optically switchable liquid crystal cell

NASA Astrophysics Data System (ADS)

Oh, Seung-Won; Kim, Sang-Hyeok; Baek, Jong-Min; Yoon, Tae-Hoon

2018-02-01

Light shutter technologies that can control optical transparency have been studied extensively for developing curtain-free smart windows. We introduce thermally and optically switchable light shutters using LCs doped with push-pull azobenzene, which is known to speed up thermal relaxation. The liquid crystal light shutter can be switched between translucent and transparent states or transparent and opaque states by phase transition through changing temperature or photo-isomerization of doped azobenzene. The liquid crystal light shutter can be used for privacy windows with an initial translucent state or energy-saving windows with an initial transparent state.

Interaction investigations of HipA binding to HipB dimer and HipB dimer + DNA complex: a molecular dynamics simulation study.

PubMed

Li, Chaoqun; Wang, Yaru; Wang, Yan; Chen, Guangju

2013-11-01

We carried out molecular dynamics simulations and free energy calculations for a series of ternary and diplex models for the HipA protein, HipB dimer, and DNA molecule to address the mechanism of HipA sequestration and the binding order of events from apo HipB/HipA to 2HipA + HipB dimer + DNA complex. The results revealed that the combination of DNA with the HipB dimer is energetically favorable for the combination of HipB dimer with HipA protein. The binding of DNA to HipB dimer induces a long-range allosteric communication from the HipB2 -DNA interface to the HipA-HipB2 interface, which involves the closeness of α1 helices of HipB dimer to HipA protein and formations of extra hydrogen bonds in the HipA-HipB2 interface through the extension of α2/3 helices in the HipB dimer. These simulated results suggested that the DNA molecule, as a regulative media, modulates the HipB dimer conformation, consequently increasing the interactions of HipB dimer with the HipA proteins, which explains the mechanism of HipA sequestration reported by the previous experiment. Simultaneously, these simulations also explored that the thermodynamic binding order in a simulated physiological environment, that is, the HipB dimer first bind to DNA to form HipB dimer + DNA complex, then capturing strongly the HipA proteins to form a ternary complex, 2HipA + HipB dimer + DNA, for sequestrating HipA in the nucleoid. Copyright © 2013 John Wiley & Sons, Ltd.

Discrimination against RNA Backbones by a ssDNA Binding Protein.

PubMed

Lloyd, Neil R; Wuttke, Deborah S

2018-05-01

Pot1 is the shelterin component responsible for the protection of the single-stranded DNA (ssDNA) overhang at telomeres in nearly all eukaryotic organisms. The C-terminal domain of the DNA-binding domain, Pot1pC, exhibits non-specific ssDNA recognition, achieved through thermodynamically equivalent alternative binding conformations. Given this flexibility, it is unclear how specificity for ssDNA over RNA, an activity required for biological function, is achieved. Examination of the ribose-position specificity of Pot1pC shows that ssDNA specificity is additive but not uniformly distributed across the ligand. High-resolution structures of several Pot1pC complexes with RNA-DNA chimeric ligands reveal Pot1pC discriminates against RNA by utilizing non-compensatory binding modes that feature significant rearrangement of the binding interface. These alternative conformations, accessed through both ligand and protein flexibility, recover much, but not all, of the binding energy, leading to the observed reduction in affinities. These findings suggest that intermolecular interfaces are remarkably sophisticated in their tuning of specificity toward flexible ligands. Copyright © 2018 Elsevier Ltd. All rights reserved.

Fabrications and Applications of Stimulus-Responsive Polymer Films and Patterns on Surfaces: A Review

PubMed Central

Chen, Jem-Kun; Chang, Chi-Jung

2014-01-01

In the past two decades, we have witnessed significant progress in developing high performance stimuli-responsive polymeric materials. This review focuses on recent developments in the preparation and application of patterned stimuli-responsive polymers, including thermoresponsive layers, pH/ionic-responsive hydrogels, photo-responsive film, magnetically-responsive composites, electroactive composites, and solvent-responsive composites. Many important new applications for stimuli-responsive polymers lie in the field of nano- and micro-fabrication, where stimuli-responsive polymers are being established as important manipulation tools. Some techniques have been developed to selectively position organic molecules and then to obtain well-defined patterned substrates at the micrometer or submicrometer scale. Methods for patterning of stimuli-responsive hydrogels, including photolithography, electron beam lithography, scanning probe writing, and printing techniques (microcontact printing, ink-jet printing) were surveyed. We also surveyed the applications of nanostructured stimuli-responsive hydrogels, such as biotechnology (biological interfaces and purification of biomacromoles), switchable wettability, sensors (optical sensors, biosensors, chemical sensors), and actuators. PMID:28788489

Polarization fatigue of BiFeO3 films with ferromagnetic metallic electrodes

NASA Astrophysics Data System (ADS)

Chen, Chen; Wang, Ji; Li, Chen; Wen, Zheng; Xu, Qingyu; Du, Jun

2017-05-01

BiFeO3 (BFO) thin films were epitaxially grown on (001) SrTiO3 substrates using LaNiO3 as bottom electrode by pulsed laser deposition. The ferroelectric properties of BFO layer with ferromagnetic Ni21Fe79 (NiFe) or non-magnetic Pt electrode are investigated. Well saturated polarization-electric field (P-E) hysteresis loops are observed. Significant fatigue and associated drastic decrease in switchable polarization have been observed with cycling number exceeds 106, which can be explained by the domain wall pinning due to the oxygen vacancies trapping. With increasing cycle number to above 107, the polarization is rejuvenated. The polarization for BFO layer with NiFe electrode recovers to the initial value, while only about 75% of initial polarization is recovered for BFO layer with Pt electrode. Furthermore, the imprint is alleviated and the P-E hysteresis loops become more symmetric after the polarization recovery. The difference can be understood by the different interface state of NiFe/BFO and Pt/BFO.

Coupled Molecular Switching Processes in Ordered Mono- and Multilayers of Stimulus-Responsive Rotaxanes on Gold Surfaces

PubMed Central

2015-01-01

Interfaces provide the structural basis for function as, for example, encountered in nature in the membrane-embedded photosystem or in technology in solar cells. Synthetic functional multilayers of molecules cooperating in a coupled manner can be fabricated on surfaces through layer-by-layer self-assembly. Ordered arrays of stimulus-responsive rotaxanes undergoing well-controlled axle shuttling are excellent candidates for coupled mechanical motion. Such stimulus-responsive surfaces may help integrate synthetic molecular machines in larger systems exhibiting even macroscopic effects or generating mechanical work from chemical energy through cooperative action. The present work demonstrates the successful deposition of ordered mono- and multilayers of chemically switchable rotaxanes on gold surfaces. Rotaxane mono- and multilayers are shown to reversibly switch in a coupled manner between two ordered states as revealed by linear dichroism effects in angle-resolved NEXAFS spectra. Such a concerted switching process is observed only when the surfaces are well packed, while less densely packed surfaces lacking lateral order do not exhibit such effects. PMID:25782057

Wide and ultra-wide bandgap oxides: where paradigm-shift photovoltaics meets transparent power electronics

NASA Astrophysics Data System (ADS)

Pérez-Tomás, Amador; Chikoidze, Ekaterine; Jennings, Michael R.; Russell, Stephen A. O.; Teherani, Ferechteh H.; Bove, Philippe; Sandana, Eric V.; Rogers, David J.

2018-03-01

Oxides represent the largest family of wide bandgap (WBG) semiconductors and also offer a huge potential range of complementary magnetic and electronic properties, such as ferromagnetism, ferroelectricity, antiferroelectricity and high-temperature superconductivity. Here, we review our integration of WBG and ultra WBG semiconductor oxides into different solar cells architectures where they have the role of transparent conductive electrodes and/or barriers bringing unique functionalities into the structure such above bandgap voltages or switchable interfaces. We also give an overview of the state-of-the-art and perspectives for the emerging semiconductor β- Ga2O3, which is widely forecast to herald the next generation of power electronic converters because of the combination of an UWBG with the capacity to conduct electricity. This opens unprecedented possibilities for the monolithic integration in solar cells of both self-powered logic and power electronics functionalities. Therefore, WBG and UWBG oxides have enormous promise to become key enabling technologies for the zero emissions smart integration of the internet of things.

Title: Studies on drug switchability showed heterogeneity in methodological approaches: a scoping review.

PubMed

Belleudi, Valeria; Trotta, Francesco; Vecchi, Simona; Amato, Laura; Addis, Antonio; Davoli, Marina

2018-05-16

Several drugs share the same therapeutic indication, including those undergoing patent expiration. Concerns on the interchangeability are frequent in clinical practice, challenging the evaluation of switchability through observational research. To conduct a scoping review of observational studies on drug switchability to identify methodological strategies adopted to deal with bias and confounding. We searched PubMed, EMBASE, and Web of Science (updated 1/31/2017) to identify studies evaluating switchability in terms of effectiveness/safety outcomes or compliance. Three reviewers independently screened studies extracting all characteristics. Strategies to address confounding, particularly, previous drug use and switching reasons were considered. All findings were summarized in descriptive analyses. Thirty-two studies, published in the last 10 years, met the inclusion criteria. Epilepsy, cardiovascular and rheumatology were the most frequently represented clinical areas. 75% of the studies reported data on effectiveness/safety outcomes. The most frequent study design was cohort (65.6%) followed by case-control (21.9%) and self-controlled (12.5%). Case-control and case-crossover studies showed homogeneous methodological strategies to deal with bias and confounding. Among cohort studies, the confounding associated with previous drug use was addressed introducing variables in multivariate model (47.3%) or selecting only adherent patients (14.3%). Around 30% of cohort studies did not report reasons for switching. In the remaining 70%, clinical parameters or previous occurrence of outcomes were measured to identify switching connected with lack of effectiveness or adverse events. This study represents a starting point for researchers and administrators who are approaching the investigation and assessment of issues related to interchangeability of drugs. Copyright © 2018. Published by Elsevier Inc.

Switchable bio-inspired adhesives

NASA Astrophysics Data System (ADS)

Kroner, Elmar

2015-03-01

Geckos have astonishing climbing abilities. They can adhere to almost any surface and can run on walls and even stick to ceilings. The extraordinary adhesion performance is caused by a combination of a complex surface pattern on their toes and the biomechanics of its movement. These biological dry adhesives have been intensely investigated during recent years because of the unique combination of adhesive properties. They provide high adhesion, allow for easy detachment, can be removed residue-free, and have self-cleaning properties. Many aspects have been successfully mimicked, leading to artificial, bio-inspired, patterned dry adhesives, and were addressed and in some aspects they even outperform the adhesion capabilities of geckos. However, designing artificial patterned adhesion systems with switchable adhesion remains a big challenge; the gecko's adhesion system is based on a complex hierarchical surface structure and on advanced biomechanics, which are both difficult to mimic. In this paper, two approaches are presented to achieve switchable adhesion. The first approach is based on a patterned polydimethylsiloxane (PDMS) polymer, where adhesion can be switched on and off by applying a low and a high compressive preload. The switch in adhesion is caused by a reversible mechanical instability of the adhesive silicone structures. The second approach is based on a composite material consisting of a Nickel- Titanium (NiTi) shape memory alloy and a patterned adhesive PDMS layer. The NiTi alloy is trained to change its surface topography as a function of temperature, which results in a change of the contact area and of alignment of the adhesive pattern towards a substrate, leading to switchable adhesion. These examples show that the unique properties of bio-inspired adhesives can be greatly improved by new concepts such as mechanical instability or by the use of active materials which react to external stimuli.

A DNA origami nanorobot controlled by nucleic acid hybridization.

PubMed

Torelli, Emanuela; Marini, Monica; Palmano, Sabrina; Piantanida, Luca; Polano, Cesare; Scarpellini, Alice; Lazzarino, Marco; Firrao, Giuseppe

2014-07-23

A prototype for a DNA origami nanorobot is designed, produced, and tested. The cylindrical nanorobot (diameter of 14 nm and length of 48 nm) with a switchable flap, is able to respond to an external stimulus and reacts by a physical switch from a disarmed to an armed configuration able to deliver a cellular compatible message. In the tested design the robot weapon is a nucleic acid fully contained in the inner of the tube and linked to a single point of the internal face of the flap. Upon actuation the nanorobot moves the flap extracting the nucleic acid that assembles into a hemin/G-quadruplex horseradish peroxidase mimicking DNAzyme catalyzing a colorimetric reaction or chemiluminescence generation. The actuation switch is triggered by an external nucleic acid (target) that interacts with a complementary nucleic acid that is beard externally by the nanorobot (probe). Hybridization of probe and target produces a localized structural change that results in flap opening. The flap movement is studied on a two-dimensional prototype origami using Förster resonance energy transfer and is shown to be triggered by a variety of targets, including natural RNAs. The nanorobot has potential for in vivo biosensing and intelligent delivery of biological activators. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA.

PubMed

De Bruin, Lennart; Maddocks, John H

2018-06-14

The sequence-dependent statistical mechanical properties of fragments of double-stranded DNA is believed to be pertinent to its biological function at length scales from a few base pairs (or bp) to a few hundreds of bp, e.g. indirect read-out protein binding sites, nucleosome positioning sequences, phased A-tracts, etc. In turn, the equilibrium statistical mechanics behaviour of DNA depends upon its ground state configuration, or minimum free energy shape, as well as on its fluctuations as governed by its stiffness (in an appropriate sense). We here present cgDNAweb, which provides browser-based interactive visualization of the sequence-dependent ground states of double-stranded DNA molecules, as predicted by the underlying cgDNA coarse-grain rigid-base model of fragments with arbitrary sequence. The cgDNAweb interface is specifically designed to facilitate comparison between ground state shapes of different sequences. The server is freely available at cgDNAweb.epfl.ch with no login requirement.

Computational Design of DNA-Binding Proteins.

PubMed

Thyme, Summer; Song, Yifan

2016-01-01

Predicting the outcome of engineered and naturally occurring sequence perturbations to protein-DNA interfaces requires accurate computational modeling technologies. It has been well established that computational design to accommodate small numbers of DNA target site substitutions is possible. This chapter details the basic method of design used in the Rosetta macromolecular modeling program that has been successfully used to modulate the specificity of DNA-binding proteins. More recently, combining computational design and directed evolution has become a common approach for increasing the success rate of protein engineering projects. The power of such high-throughput screening depends on computational methods producing multiple potential solutions. Therefore, this chapter describes several protocols for increasing the diversity of designed output. Lastly, we describe an approach for building comparative models of protein-DNA complexes in order to utilize information from homologous sequences. These models can be used to explore how nature modulates specificity of protein-DNA interfaces and potentially can even be used as starting templates for further engineering.

Flexible particle flow-focusing in microchannel driven by droplet-directed induced-charge electroosmosis.

PubMed

Ren, Yukun; Liu, Xianyu; Liu, Weiyu; Tao, Ye; Jia, Yankai; Hou, Likai; Li, Wenying; Jiang, Hongyuan

2018-02-01

We report herein a novel microfluidic particle concentrator that utilizes constriction microchannels to enhance the flow-focusing performance of induced-charge electroosmosis (ICEO), where viscous hemi-spherical oil droplets are embedded within the mainchannel to form deformable converging-diverging constriction structures. The constriction region between symmetric oil droplets partially coated on the electrode strips can improve the focusing performance by inducing a granular wake flow area at the diverging channel, which makes almost all of the scattered sample particles trapped within a narrow stream on the floating electrode. Another asymmetric droplet pair arranged near the outlets can further direct the trajectory of focused particle stream to one specified outlet port depending on the symmetry breaking in the shape of opposing phase interfaces. By fully exploiting rectification properties of induced-charge electrokinetic phenomena at immiscible water/oil interfaces of tunable geometry, the expected function of continuous and switchable flow-focusing is demonstrated by preconcentrating both inorganic silica particles and biological yeast cells. Physical mechanisms responsible for particle focusing and locus deflection in the droplet-assisted concentrentor are analyzed in detail, and simulation results are in good accordance with experimental observations. Our work provides new routes to construct flexible electrokinetic framework for preprocessing on-chip biological samples before performing subsequent analysis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solid-state structures and properties of scandium hydride; hydrogen storage and switchable mirrors application

NASA Astrophysics Data System (ADS)

Khodja, Khadidja; Bouhadda, Youcef; Seddik, Larbi; Benyelloul, Kamel

2016-05-01

First-principles calculation has been performed on the rare earth hydride ScH2 for hydrogen storage and switchable mirror applications, using the pseudo-potentials and plane waves based on the density-functional theory (DFT). The electronic and structural properties are studied within both local-density and generalized gradient approximations for exchange energy. The formation energy and the optical properties have been investigated and discussed. Our calculated results are generally in good agreement with theoretical and experimental data. Contribution to the topical issue "Materials for Energy Harvesting, Conversion and Storage (ICOME 2015) - Elected submissions", edited by Jean-Michel Nunzi, Rachid Bennacer and Mohammed El Ganaoui

Switchable dual-wavelength single-longitudinal-mode erbium fiber laser utilizing a dual-ring scheme with a saturable absorber

NASA Astrophysics Data System (ADS)

Yang, Zi-Qing; Huang, Tzu-Jung; Chang, Yao-Jen; Yeh, Chien-Hung; Chow, Chi-Wai; Chen, Jing-Heng; Chen, Kun-Huang

2018-06-01

In this work, we propose and demonstrate a switchable dual-wavelength erbium-doped fiber (EDF) ring laser with stable single-longitudinal-mode (SLM) output. Here, a dual-ring (DR) structure with an unpumped EDF of 2 m is designed to achieve SLM oscillation. Five fiber Bragg gratings (FBGs) are applied in the laser cavity serving as the reflective element to generate different dual-wavelength outputs. In the measurement, six sets of generated dual-wavelengths with various mode-spacing (Δλ) can be achieved via the five FBGs. Additionally, the stability performance of the proposed EDF DR laser is also demonstrated.

A power-efficient switchable CML driver at 10 Gbps

NASA Astrophysics Data System (ADS)

Peipei, Chen; Lei, Li; Huihua, Liu

2016-02-01

High static power limits the application of conventional current-mode logic(CML). This paper presents a power-efficient switchable CML driver, which achieves a significant current saving by 75% compared with conventional ones. Implemented in the 130 nm CMOS technology process, the proposed CML driver just occupies an area about 0.003 mm2 and provides a robust differential signal of 1600 mV for 10 Gbps optical line terminal (OLT) with a total current of 10 mA. The peak-to-peak jitter is about 4 ps (0.04TUI) and the offset voltage is 347.2 mV @ 1600 mVPP.

A Polarization Reconfigurable Slot Antenna with a Novel Switchable Feeding Network

NASA Astrophysics Data System (ADS)

Xie, Peng; Wang, Guang Ming

2017-12-01

A polarization reconfigurable slot antenna is proposed in this paper. The antenna consists of a microstrip line-to-slotline transition structure, two radiation slots and a switchable feeding network. The feeding network is a gradually changed ring slot with six switching diodes on it. By controlling the diodes states, the antenna can generate y-direction polarization, z-direction polarization, left-hand circular polarization and right-hand circular polarization. Detailed design considerations of the proposed antenna, simulated and measured results are presented and discussed. Measured results agree well with simulated. The results proved that the antenna can realize polarization reconfiguration effectively at 5 GHz.

Direct generation of vector vortex beams with switchable radial and azimuthal polarizations in a monolithic Nd:YAG microchip laser

NASA Astrophysics Data System (ADS)

He, Hong-Sen; Chen, Zhen; Dong, Jun

2017-05-01

A hollow focus lens (HFL) has been designed to effectively produce a focused annular beam for high-intensity pumping. By applying the central-dark pump beam, a monolithic Nd:YAG microchip laser without any extra optical elements is demonstrated to generate vector vortex beams with switchable radially polarized (RP) and azimuthally polarized (AP) states by easily controlling the pump power. The order and handedness of the output vortex beam remain stable during the switching of the RP and AP states. The monolithic Nd:YAG microchip laser provides a new laser source for applications such as material processing and optical manipulation.

Controlled higher-order transverse mode conversion from a fiber laser by polarization manipulation

NASA Astrophysics Data System (ADS)

Huang, Bin; Yi, Qian; Yang, Lingling; Zhao, Chujun; Wen, Shuangchun

2018-02-01

We report a vectorial fiber laser with controlled transverse mode conversion by intra-cavity polarization manipulation. By combining a q-plate and two quarter-wave plates (QWPs), we can generate a switchable polarization state output represented by the higher-order Poincaré sphere (l = +1, l = -1), and distinguish the fourfold degenerate LP11 mode. The four transverse vector modes can be obtained and switched in a flexible way, and the slope efficiency of the fiber laser can reach up to 39.4%. This compactness, high efficiency, and switchable operation potential will benefit a range of applications, such as materials processing, particle manipulation, etc.

On-demand Hydrogen Production from Organosilanes at Ambient Temperature Using Heterogeneous Gold Catalysts

NASA Astrophysics Data System (ADS)

Mitsudome, Takato; Urayama, Teppei; Kiyohiro, Taizo; Maeno, Zen; Mizugaki, Tomoo; Jitsukawa, Koichiro; Kaneda, Kiyotomi

2016-11-01

An environmentally friendly (“green”), H2-generation system was developed that involved hydrolytic oxidation of inexpensive organosilanes as hydrogen storage materials with newly developed heterogeneous gold nanoparticle catalysts. The gold catalyst functioned well at ambient temperature under aerobic conditions, providing efficient production of pure H2. The newly developed size-selective gold nanoparticle catalysts could be separated easily from the reaction mixture containing organosilanes, allowing an on/off-switchable H2-production by the introduction and removal of the catalyst. This is the first report of an on/off-switchable H2-production system employing hydrolytic oxidation of inexpensive organosilanes without requiring additional energy.

Mechanically switchable polymer fibers for sensing in biological conditions

NASA Astrophysics Data System (ADS)

McMillan, Sean; Rader, Chris; Jorfi, Mehdi; Pickrell, Gary; Foster, E. Johan

2017-02-01

The area of in vivo sensing using optical fibers commonly uses materials such as silica and polymethyl methacrylate, both of which possess much higher modulus than human tissue. The mechanical mismatch between materials and living tissue has been seen to cause higher levels of glial encapsulation, scarring, and inflammation, leading to failure of the implanted medical device. We present the use of a fiber made from polyvinyl alcohol (PVA) for use as an implantable sensor as it is an easy to work with functionalized polymer that undergoes a transition from rigid to soft when introduced to water. This ability to switch from stiff to soft reduces the severity of the immune response. The fabricated PVA fibers labeled with fluorescein for sensing applications showed excellent response to various stimuli while exhibiting mechanical switchability. For the dry fibers, a tensile storage modulus of 4700 MPa was measured, which fell sharply to 145 MPa upon wetting. The fibers showed excellent response to changing pH levels, producing values that were detectable in a range consistent with those seen in the literature and in proposed applications. The results show that these mechanically switchable fibers are a viable option for future sensing applications.

S- Cis Diene Conformation: A New Bathochromic Shift Strategy for Near-Infrared Fluorescence Switchable Dye and the Imaging Applications.

PubMed

Chen, Hsiang-Jung; Chew, Chee Ying; Chang, En-Hao; Tu, Yu-Wei; Wei, Li-Yu; Wu, Bo-Han; Chen, Chien-Hung; Yang, Ya-Ting; Huang, Su-Chin; Chen, Jen-Kun; Chen, I-Chia; Tan, Kui-Thong

2018-04-18

In this paper, we present a novel charge-free fluorescence-switchable near-infrared (IR) dye based on merocyanine for target specific imaging. In contrast to the typical bathochromic shift approach by extending π-conjugation, the bathochromic shift of our merocyanine dye to the near-IR region is due to an unusual S- cis diene conformer. This is the first example where a fluorescent dye adopts the stable S- cis conformation. In addition to the novel bathochromic shift mechanism, the dye exhibits fluorescence-switchable properties in response to polarity and viscosity. By incorporating a protein-specific ligand to the dye, the probes (for SNAP-tag and hCAII proteins) exhibited dramatic fluorescence increase (up to 300-fold) upon binding with its target protein. The large fluorescence enhancement, near-IR absorption/emission, and charge-free scaffold enabled no-wash and site-specific imaging of target proteins in living cells and in vivo with minimum background fluorescence. We believe that our unconventional approach for a near-IR dye with the S- cis diene conformation can lead to new strategies for the design of near-IR dyes.

On/off-switchable anti-neoplastic nanoarchitecture

NASA Astrophysics Data System (ADS)

Patra, Hirak K.; Imani, Roghayeh; Jangamreddy, Jaganmohan R.; Pazoki, Meysam; Iglič, Aleš; Turner, Anthony P. F.; Tiwari, Ashutosh

2015-09-01

Throughout the world, there are increasing demands for alternate approaches to advanced cancer therapeutics. Numerous potentially chemotherapeutic compounds are developed every year for clinical trial and some of them are considered as potential drug candidates. Nanotechnology-based approaches have accelerated the discovery process, but the key challenge still remains to develop therapeutically viable and physiologically safe materials suitable for cancer therapy. Here, we report a high turnover, on/off-switchable functionally popping reactive oxygen species (ROS) generator using a smart mesoporous titanium dioxide popcorn (TiO2 Pops) nanoarchitecture. The resulting TiO2 Pops, unlike TiO2 nanoparticles (TiO2 NPs), are exceptionally biocompatible with normal cells. Under identical conditions, TiO2 Pops show very high photocatalytic activity compared to TiO2 NPs. Upon on/off-switchable photo activation, the TiO2 Pops can trigger the generation of high-turnover flash ROS and can deliver their potential anticancer effect by enhancing the intracellular ROS level until it crosses the threshold to open the ‘death gate’, thus reducing the survival of cancer cells by at least six times in comparison with TiO2 NPs without affecting the normal cells.

An Ultrafast Switchable Terahertz Polarization Modulator Based on III-V Semiconductor Nanowires.

PubMed

Baig, Sarwat A; Boland, Jessica L; Damry, Djamshid A; Tan, H Hoe; Jagadish, Chennupati; Joyce, Hannah J; Johnston, Michael B

2017-04-12

Progress in the terahertz (THz) region of the electromagnetic spectrum is undergoing major advances, with advanced THz sources and detectors being developed at a rapid pace. Yet, ultrafast THz communication is still to be realized, owing to the lack of practical and effective THz modulators. Here, we present a novel ultrafast active THz polarization modulator based on GaAs semiconductor nanowires arranged in a wire-grid configuration. We utilize an optical pump-terahertz probe spectroscopy system and vary the polarization of the optical pump beam to demonstrate ultrafast THz modulation with a switching time of less than 5 ps and a modulation depth of -8 dB. We achieve an extinction of over 13% and a dynamic range of -9 dB, comparable to microsecond-switchable graphene- and metamaterial-based THz modulators, and surpassing the performance of optically switchable carbon nanotube THz polarizers. We show a broad bandwidth for THz modulation between 0.1 and 4 THz. Thus, this work presents the first THz modulator which combines not only a large modulation depth but also a broad bandwidth and picosecond time resolution for THz intensity and phase modulation, making it an ideal candidate for ultrafast THz communication.

Micropatterned photoalignment for wavefront controlled switchable optical devices

NASA Astrophysics Data System (ADS)

Glazar, Nikolaus

Photoalignment is a well-established technique for surface alignment of the liquid crystal director. Previously, chrome masks were necessary for patterned photoalignment but were difficult to use, costly, and inflexible. To extend the capabilities of photoalignment we built an automated maskless multi-domain photoalignment device based on a DMD (digital multimirror device) projection system. The device is capable of creating arbitrary photoalignment patterns with micron-sized features. Pancharatnam-Berry phase (PB-phase) is a geometric phase that arises from cyclic change of polarization state. By varying the azimuthal anchoring angle in a hybrid-aligned liquid crystal cell we can control the spatial variation of the PB-phase shift. Using our automated photoalignment device to align the liquid crystal arbitrary wave front manipulations are possible. The PB-phase shift effect is maximized when the cell is tuned to have a half-wave retardation and disappears at full-wave retardation, so the cell can be switched on and off by applying a voltage. Two wavefront controlled devices developed using this technique will be discussed: A switchable liquid crystal phase shift mask for creating sub-diffraction sized photolithographic features, and a transparent diffractive display that utilizes a switchable liquid crystal diffraction grating.

A switchable and stable single-longitudinal-mode, dual-wavelength erbium-doped fiber laser assisted by Rayleigh backscattering in tapered fiber

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gu, Jian; Yang, Yanfu, E-mail: yangyanfu@hotmail.com; Zhang, Jianyu

We have proposed and demonstrated a novel switchable single-longitudinal-mode (SLM), dual-wavelength erbium-doped fiber laser (DWEDFL) assisted by Rayleigh backscattering (RBS) in a tapered fiber in a ring laser configuration. The RBS feedback in a tapered fiber is a key mechanism as linewidth narrowing for laser output. A compound laser cavity ensured that the EDFL operated in the SLM state and a saturable absorber (SA) is employed to form a gain grating for both filtering and improving wavelength stability. The fiber laser can output dual wavelengths simultaneously or operate at single wavelength in a switchable manner. Experiment results show that withmore » the proper SA, the peak power drift was improved from 1–2 dB to 0.31 dB and the optical signal to noise ratio was higher than 60 dB. Under the assistance of RBS feedback, the laser linewidths are compressed by around three times and the Lorentzian 3 dB linewidths of 445 Hz and 425 Hz are obtained at 1550 nm and 1554 nm, respectively.« less

On/off-switchable anti-neoplastic nanoarchitecture

PubMed Central

Patra, Hirak K.; Imani, Roghayeh; Jangamreddy, Jaganmohan R.; Pazoki, Meysam; Iglič, Aleš; Turner, Anthony P. F.; Tiwari, Ashutosh

2015-01-01

Throughout the world, there are increasing demands for alternate approaches to advanced cancer therapeutics. Numerous potentially chemotherapeutic compounds are developed every year for clinical trial and some of them are considered as potential drug candidates. Nanotechnology-based approaches have accelerated the discovery process, but the key challenge still remains to develop therapeutically viable and physiologically safe materials suitable for cancer therapy. Here, we report a high turnover, on/off-switchable functionally popping reactive oxygen species (ROS) generator using a smart mesoporous titanium dioxide popcorn (TiO2 Pops) nanoarchitecture. The resulting TiO2 Pops, unlike TiO2 nanoparticles (TiO2 NPs), are exceptionally biocompatible with normal cells. Under identical conditions, TiO2 Pops show very high photocatalytic activity compared to TiO2 NPs. Upon on/off-switchable photo activation, the TiO2 Pops can trigger the generation of high-turnover flash ROS and can deliver their potential anticancer effect by enhancing the intracellular ROS level until it crosses the threshold to open the ‘death gate’, thus reducing the survival of cancer cells by at least six times in comparison with TiO2 NPs without affecting the normal cells. PMID:26415561

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces.

PubMed

Sebastian, Alvaro; Contreras-Moreira, Bruno

2014-01-15

Traditional and high-throughput techniques for determining transcription factor (TF) binding specificities are generating large volumes of data of uneven quality, which are scattered across individual databases. FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites and systematically annotates the binding interfaces of the corresponding TFs. The first release contains 2422 unique TF sequences, 10 112 DNA binding sites and 3662 DNA motifs. A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while also containing bacterial regulatory data. A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries. Such predictions can also be extended to a single proteome chosen by the user, and results are ranked in terms of interface similarity. Benchmark experiments with bacterial, plant and human data were performed to measure the predictive power of footprintDB searches, which were able to correctly recover 10, 55 and 90% of the tested sequences, respectively. Correctly predicted TFs had a higher interface similarity than the average, confirming its diagnostic value. Web site implemented in PHP,Perl, MySQL and Apache. Freely available from http://floresta.eead.csic.es/footprintdb.

Structure and interactions of the Bacillus subtilis sporulation inhibitor of DNA replication, SirA, with domain I of DnaA

PubMed Central

Jameson, Katie H; Rostami, Nadia; Fogg, Mark J; Turkenburg, Johan P; Grahl, Anne; Murray, Heath; Wilkinson, Anthony J

2014-01-01

Chromosome copy number in cells is controlled so that the frequency of initiation of DNA replication matches that of cell division. In bacteria, this is achieved through regulation of the interaction between the initiator protein DnaA and specific DNA elements arrayed at the origin of replication. DnaA assembles at the origin and promotes DNA unwinding and the assembly of a replication initiation complex. SirA is a DnaA-interacting protein that inhibits initiation of replication in diploid Bacillus subtilis cells committed to the developmental pathway leading to formation of a dormant spore. Here we present the crystal structure of SirA in complex with the N-terminal domain of DnaA revealing a heterodimeric complex. The interacting surfaces of both proteins are α-helical with predominantly apolar side-chains packing in a hydrophobic interface. Site-directed mutagenesis experiments confirm the importance of this interface for the interaction of the two proteins in vitro and in vivo. Localization of GFP–SirA indicates that the protein accumulates at the replisome in sporulating cells, likely through a direct interaction with DnaA. The SirA interacting surface of DnaA corresponds closely to the HobA-interacting surface of DnaA from Helicobacter pylori even though HobA is an activator of DnaA and SirA is an inhibitor. PMID:25041308

Command Interface ASIC - Analog Interface ASIC Chip Set

NASA Technical Reports Server (NTRS)

Ruiz, Baldes; Jaffe, Burton; Burke, Gary; Lung, Gerald; Pixler, Gregory; Plummer, Joe; Katanyoutanant,, Sunant; Whitaker, William

2003-01-01

A command interface application-specific integrated circuit (ASIC) and an analog interface ASIC have been developed as a chip set for remote actuation and monitoring of a collection of switches, which can be used to control generic loads, pyrotechnic devices, and valves in a high-radiation environment. The command interface ASIC (CIA) can be used alone or in combination with the analog interface ASIC (AIA). Designed primarily for incorporation into spacecraft control systems, they are also suitable for use in high-radiation terrestrial environments (e.g., in nuclear power plants and facilities that process radioactive materials). The primary role of the CIA within a spacecraft or other power system is to provide a reconfigurable means of regulating the power bus, actuating all valves, firing all pyrotechnic devices, and controlling the switching of power to all switchable loads. The CIA is a mixed-signal (analog and digital) ASIC that includes an embedded microcontroller with supporting fault-tolerant switch control and monitoring circuitry that is capable of connecting to a redundant set of interintegrated circuit (I(sup 2)C) buses. Commands and telemetry requests are communicated to the CIA. Adherence to the I(sup 2)C bus standard helps to reduce development costs by facilitating the use of previously developed, commercially available components. The AIA is a mixed-signal ASIC that includes the analog circuitry needed to connect the CIA to a custom higher powered version of the I(sup 2)C bus. The higher-powered version is designed to enable operation with bus cables longer than those contemplated in the I(sup 2)C standard. If there are multiple higher-power I(sup 2)C-like buses, then there must an AIA between the CIA and each such bus. The AIA includes two identical interface blocks: one for the side-A I(sup 2)C clock and data buses and the other for the side B buses. All the AIAs on each side are powered from a common power converter module (PCM). Sides A and B of the I(sup 2)C buses are electrically isolated from each other (see figure). They are also isolated from the CIA by use of transformer coupling of signals between the AIA blocks and the CIA.

PNA-PEG modified silicon platforms as functional bio-interfaces for applications in DNA microarrays and biosensors.

PubMed

Cattani-Scholz, Anna; Pedone, Daniel; Blobner, Florian; Abstreiter, Gerhard; Schwartz, Jeffrey; Tornow, Marc; Andruzzi, Luisa

2009-03-09

The synthesis and characterization of two types of silicon-based biofunctional interfaces are reported; each interface bonds a dense layer of poly(ethylene glycol) (PEG(n)) and peptide nucleic acid (PNA) probes. Phosphonate self-assembled monolayers were derivatized with PNA using a maleimido-terminated PEG(45). Similarly, siloxane monolayers were functionalized with PNA using a maleimido-terminated PEG(45) spacer and were subsequently modified with a shorter methoxy-terminated PEG(12) ("back-filling"). The long PEG(45) spacer was used to distance the PNA probe from the surface and to minimize undesirable nonspecific adsorption of DNA analyte. The short PEG(12) "back-filler" was used to provide additional passivation of the surface against nonspecific DNA adsorption. X-ray photoelectron spectroscopic (XPS) analysis near the C 1s and N 1s ionization edges was done to characterize chemical groups formed in the near-surface region, which confirmed binding of PEG and PNA to the phosphonate and silane films. XPS also indicated that additional PEG chains were tethered to the surface during the back-filling process. Fluorescence hybridization experiments were carried out with complementary and noncDNA strands; both phosphonate and siloxane biofunctional surfaces were effective for hybridization of cDNA strands and significantly reduced nonspecific adsorption of the analyte. Spatial patterns were prepared by polydimethylsiloxane (PDMS) micromolding on the PNA-functionalized surfaces; selective hybridization of fluorescently labeled DNA was shown at the PNA functionalized regions, and physisorption at the probe-less PEG-functionalized regions was dramatically reduced. These results show that PNA-PEG derivatized phosphonate monolayers hold promise for the smooth integration of device surface chemistry with semiconductor technology for the fabrication of DNA biosensors. In addition, our results confirm that PNA-PEG derivatized self-assembled carboxyalkylsiloxane films are promising substrates for DNA microarray applications.

Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

PubMed Central

Goda, Tatsuro; Singi, Ankit Balram; Maeda, Yasuhiro; Matsumoto, Akira; Torimura, Masaki; Aoki, Hiroshi; Miyahara, Yuji

2013-01-01

Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry. PMID:23435052

MPEG-1 low-cost encoder solution

NASA Astrophysics Data System (ADS)

Grueger, Klaus; Schirrmeister, Frank; Filor, Lutz; von Reventlow, Christian; Schneider, Ulrich; Mueller, Gerriet; Sefzik, Nicolai; Fiedrich, Sven

1995-02-01

A solution for real-time compression of digital YCRCB video data to an MPEG-1 video data stream has been developed. As an additional option, motion JPEG and video telephone streams (H.261) can be generated. For MPEG-1, up to two bidirectional predicted images are supported. The required computational power for motion estimation and DCT/IDCT, memory size and memory bandwidth have been the main challenges. The design uses fast-page-mode memory accesses and requires only one single 80 ns EDO-DRAM with 256 X 16 organization for video encoding. This can be achieved only by using adequate access and coding strategies. The architecture consists of an input processing and filter unit, a memory interface, a motion estimation unit, a motion compensation unit, a DCT unit, a quantization control, a VLC unit and a bus interface. For using the available memory bandwidth by the processing tasks, a fixed schedule for memory accesses has been applied, that can be interrupted for asynchronous events. The motion estimation unit implements a highly sophisticated hierarchical search strategy based on block matching. The DCT unit uses a separated fast-DCT flowgraph realized by a switchable hardware unit for both DCT and IDCT operation. By appropriate multiplexing, only one multiplier is required for: DCT, quantization, inverse quantization, and IDCT. The VLC unit generates the video-stream up to the video sequence layer and is directly coupled with an intelligent bus-interface. Thus, the assembly of video, audio and system data can easily be performed by the host computer. Having a relatively low complexity and only small requirements for DRAM circuits, the developed solution can be applied to low-cost encoding products for consumer electronics.

DNA sequence determinants controlling affinity, stability and shape of DNA complexes bound by the nucleoid protein Fis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hancock, Stephen P.; Stella, Stefano; Cascio, Duilio

The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequencesmore » in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. Lastly, the affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.« less

DNA sequence determinants controlling affinity, stability and shape of DNA complexes bound by the nucleoid protein Fis

DOE PAGES

Hancock, Stephen P.; Stella, Stefano; Cascio, Duilio; ...

2016-03-09

The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequencesmore » in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. Lastly, the affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.« less

The self-assembled behavior of DNA bases on the interface.

PubMed

Liu, Lei; Xia, Dan; Klausen, Lasse H; Dong, Mingdong

2014-01-27

A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface.

The Self-Assembled Behavior of DNA Bases on the Interface

PubMed Central

Liu, Lei; Xia, Dan; Klausen, Lasse H.; Dong, Mingdong

2014-01-01

A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface. PMID:24473140

Detergent-mediated incorporation of transmembrane proteins in giant unilamellar vesicles with controlled physiological contents

PubMed Central

Dezi, Manuela; Di Cicco, Aurelie; Bassereau, Patricia; Lévy, Daniel

2013-01-01

Giant unilamellar vesicles (GUVs) are convenient biomimetic systems of the same size as cells that are increasingly used to quantitatively address biophysical and biochemical processes related to cell functions. However, current approaches to incorporate transmembrane proteins in the membrane of GUVs are limited by the amphiphilic nature or proteins. Here, we report a method to incorporate transmembrane proteins in GUVs, based on concepts developed for detergent-mediated reconstitution in large unilamellar vesicles. Reconstitution is performed either by direct incorporation from proteins purified in detergent micelles or by fusion of purified native vesicles or proteoliposomes in preformed GUVs. Lipid compositions of the membrane and the ionic, protein, or DNA compositions in the internal and external volumes of GUVs can be controlled. Using confocal microscopy and functional assays, we show that proteins are unidirectionally incorporated in the GUVs and keep their functionality. We have successfully tested our method with three types of transmembrane proteins. GUVs containing bacteriorhodopsin, a photoactivable proton pump, can generate large transmembrane pH and potential gradients that are light-switchable and stable for hours. GUVs with FhuA, a bacterial porin, were used to follow the DNA injection by T5 phage upon binding to its transmembrane receptor. GUVs incorporating BmrC/BmrD, a bacterial heterodimeric ATP-binding cassette efflux transporter, were used to demonstrate the protein-dependent translocation of drugs and their interactions with encapsulated DNA. Our method should thus apply to a wide variety of membrane or peripheral proteins for producing more complex biomimetic GUVs. PMID:23589883

Hmb(off/on) as a switchable thiol protecting group for native chemical ligation.

PubMed

Qi, Yun-Kun; Tang, Shan; Huang, Yi-Chao; Pan, Man; Zheng, Ji-Shen; Liu, Lei

2016-05-04

A new thiol protecting group Hmb(off/on) is described, which has a switchable activity that may be useful in the chemical synthesis of proteins. When placed on the side chain of Cys, Cys(Hmb(off)) is stable to trifluoroacetic acid (TFA) in the process of solid-phase peptide synthesis. When Cys(Hmb(off)) is treated with neutral aqueous buffers, it is cleanly converted to acid-labile Cys(Hmb(on)), which can later be fully deprotected by TFA to generate free Cys. The utility of Cys(Hmb(off/on)) is demonstrated by the chemical synthesis of an erythropoietin segment, EPO[Cys(98)-Arg(166)]-OH through native chemical ligation.

Self-alignment of plasmonic gold nanorods in reconfigurable anisotropic fluids for tunable bulk metamaterial applications.

PubMed

Liu, Qingkun; Cui, Yanxia; Gardner, Dennis; Li, Xin; He, Sailing; Smalyukh, Ivan I

2010-04-14

We demonstrate the bulk self-alignment of dispersed gold nanorods imposed by the intrinsic cylindrical micelle self-assembly in nematic and hexagonal liquid crystalline phases of anisotropic fluids. External magnetic field and shearing allow for alignment and realignment of the liquid crystal matrix with the ensuing long-range orientational order of well-dispersed plasmonic nanorods. This results in a switchable polarization-sensitive plasmon resonance exhibiting stark differences from that of the same nanorods in isotropic fluids. The device-scale bulk nanoparticle alignment may enable optical metamaterial mass production and control of properties arising from combining the switchable nanoscale structure of anisotropic fluids with the surface plasmon resonance properties of the plasmonic nanorods.

Switchable multi-wavelength fiber ring laser based on a compact in-fiber Mach-Zehnder interferometer with photonic crystal fiber

NASA Astrophysics Data System (ADS)

Chen, W. G.; Lou, S. Q.; Feng, S. C.; Wang, L. W.; Li, H. L.; Guo, T. Y.; Jian, S. S.

2009-11-01

Switchable multi-wavelength fiber ring laser with an in-fiber Mach-Zehnder interferometer incorporated into the ring cavity serving as wavelength-selective filter at room temperature is demonstrated. The filter is formed by splicing a section of few-mode photonic crystal fiber (PCF) and two segments of single mode fiber (SMF) with the air-holes on the both sides of PCF intentionally collapsed in the vicinity of the splices. By adjusting the states of the polarization controller (PC) appropriately, the laser can be switched among the stable single-, dual- and triple-wavelength lasing operations by exploiting polarization hole burning (PHB) effect.

Switchable dual-wavelength erbium-doped fiber laser based on the photonic crystal fiber loop mirror and chirped fiber Bragg grating

NASA Astrophysics Data System (ADS)

Chen, Wei-Guo; Lou, Shu-Qin; Wang, Li-Wen; Li, Hong-Lei; Guo, Tieying; Jian, Shui-Sheng

2010-03-01

The switchable dual-wavelength erbium-doped fiber laser (EDFL) with a two-mode photonic crystal fiber (PCF) loop mirror and a chirped fiber Bragg grating (CFBG) at room temperature is proposed and experimentally demonstrated. The two-mode PCF loop mirror is formed by inserting a piece of two-mode PCF into a Sagnac loop mirror, with the air-holes of the PCF intentionally collapsing at the splices. By adjusting the state of the polarization controller (PC) appropriately, the laser can be switched between the stable single- and dual-wavelength operations by means of the polarization hole burning (PHB) and spectral hole burning (SHB) effects.

Breaking the diffraction limit of light-sheet fluorescence microscopy by RESOLFT

PubMed Central

Hoyer, Patrick; de Medeiros, Gustavo; Balázs, Bálint; Norlin, Nils; Besir, Christina; Hanne, Janina; Kräusslich, Hans-Georg; Engelhardt, Johann; Sahl, Steffen J.; Hell, Stefan W.; Hufnagel, Lars

2016-01-01

We present a plane-scanning RESOLFT [reversible saturable/switchable optical (fluorescence) transitions] light-sheet (LS) nanoscope, which fundamentally overcomes the diffraction barrier in the axial direction via confinement of the fluorescent molecular state to a sheet of subdiffraction thickness around the focal plane. To this end, reversibly switchable fluorophores located right above and below the focal plane are transferred to a nonfluorescent state at each scanning step. LS-RESOLFT nanoscopy offers wide-field 3D imaging of living biological specimens with low light dose and axial resolution far beyond the diffraction barrier. We demonstrate optical sections that are thinner by 5–12-fold compared with their conventional diffraction-limited LS analogs. PMID:26984498

Direct observation of fatigue in epitaxially grown Pb(Zr,Ti)O3 thin films using second harmonic piezoresponse force microscopy

NASA Astrophysics Data System (ADS)

Murari, Nishit M.; Hong, Seungbum; Lee, Ho Nyung; Katiyar, Ram. S.

2011-08-01

Here, we present a direct observation of fatigue phenomena in epitaxially grown Pb(Zr0.2Ti0.8)O3 (PZT) thin films using second harmonic piezoresponse force microscopy (SH-PFM). We observed strong correlation between the SH-PFM amplitude and phase signals with the remnant piezoresponse at different switching cycles. The SH-PFM results indicate that the average fraction of switchable domains decreases globally and the phase delays of polarization switching differ locally. In addition, we found that the fatigue developed uniformly over the whole area without developing region-by-region suppression of switchable polarization as in polycrystalline PZT thin films.

Frequency-Switchable Metamaterial Absorber Injecting Eutectic Gallium-Indium (EGaIn) Liquid Metal Alloy

PubMed Central

Ling, Kenyu; Kim, Hyung Ki; Yoo, Minyeong; Lim, Sungjoon

2015-01-01

In this study, we demonstrated a new class of frequency-switchable metamaterial absorber in the X-band. Eutectic gallium-indium (EGaIn), a liquid metal alloy, was injected in a microfluidic channel engraved on polymethyl methacrylate (PMMA) to achieve frequency switching. Numerical simulation and experimental results are presented for two cases: when the microfluidic channels are empty, and when they are filled with liquid metal. To evaluate the performance of the fabricated absorber prototype, it is tested with a rectangular waveguide. The resonant frequency was successfully switched from 10.96 GHz to 10.61 GHz after injecting liquid metal while maintaining absorptivity higher than 98%. PMID:26561815

Switchable narrow linewidth fiber laser with LP11 transverse mode output

NASA Astrophysics Data System (ADS)

Shen, Ya; Ren, Guobin; Yang, Yuguang; Yao, Shuzhi; Wu, Yue; Jiang, Youchao; Xu, Yao; Jin, Wenxing; Zhu, Bofeng; Jian, Shuisheng

2018-01-01

We experimentally demonstrate a switchable narrow linewidth single-longitudinal-mode (SLM) erbium-doped fiber (EDF) ring laser with LP11 transverse mode output. The laser is based on a mode selective all-fiber fused coupler which is composed of a single-mode fiber (SMF) and a two-mode fiber (TMF). By controlling the polarization state of the output light, the laser can provide narrow linewidth SLM output with LP11 transverse mode at two specific wavelengths, which correspond to two transmission peaks of the chirped moiré fiber grating (CMFBG). The 20 dB linewidth of the fiber laser for each wavelength is approximately 7.2 and 6.4 kHz.

Switchable Ni–Mn–Ga Heusler nanocrystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zayak, Alexey T.; Beckman, Scott P.; Tiago, Murilo L.

2008-10-02

Here, we examined bulk-like Heusler nanocrystals using real-space pseudopotentials constructed within density functional theory. The nanocrystals were made of various compositions of Ni-Mn-Ga in the size range from 15 up to 169 atoms. Among these compositions, the closest to the stoichiometric Ni 2MnGa were found to be the most stable. The Ni-based nanocrystals retained a tendency for tetragonal distortion, which is inherited from the bulk properties. Surface effects suppress the tetragonal structure in the smaller Ni-based nanocrystals, while bigger nanocrystals develop a bulk-like tetragonal distortion. We suggest the possibility of switchable Ni-Mn-Ga nanocrystals, which could be utilized for magnetic nano-shape-memorymore » applications.« less

Dynamically Babinet-invertible metasurface: a capacitive-inductive reconfigurable filter for terahertz waves using vanadium-dioxide metal-insulator transition

NASA Astrophysics Data System (ADS)

Urade, Yoshiro; Nakata, Yosuke; Okimura, Kunio; Nakanishi, Toshihiro; Miyamaru, Fumiaki; Takeda, Mitsuo W.; Kitano, Masao

2016-03-01

This paper proposes a reconfigurable planar metamaterial that can be switched between capacitive and inductive responses using local changes in the electrical conductivity of its constituent material. The proposed device is based on Babinet's principle and exploits the singular electromagnetic responses of metallic checkerboard structures, which are dependent on the local electrical conductivity. Utilizing the heating-induced metal-insulator transition of vanadium dioxide ($\\mathrm{VO}_2$), the proposed metamaterial is designed to compensate for the effect of the substrate and is experimentally characterized in the terahertz regime. This reconfigurable metamaterial can be utilized as a switchable filter and as a switchable phase shifter for terahertz waves.

Dynamically Babinet-invertible metasurface: a capacitive-inductive reconfigurable filter for terahertz waves using vanadium-dioxide metal-insulator transition.

PubMed

Urade, Yoshiro; Nakata, Yosuke; Okimura, Kunio; Nakanishi, Toshihiro; Miyamaru, Fumiaki; Takeda, Mitsuo W; Kitano, Masao

2016-03-07

This paper proposes a reconfigurable planar metamaterial that can be switched between capacitive and inductive responses using local changes in the electrical conductivity of its constituent material. The proposed device is based on Babinet's principle and exploits the singular electromagnetic responses of metallic checkerboard structures, which are dependent on the local electrical conductivity. Utilizing the heating-induced metal-insulator transition of vanadium dioxide (VO 2 ), the proposed meta-material is designed to compensate for the effect of the substrate and is experimentally characterized in the terahertz regime. This reconfigurable metamaterial can be utilized as a switchable filter and as a switchable phase shifter for terahertz waves.

DNA Bipedal Motor Achieves a Large Number of Steps Due to Operation Using Microfluidics-Based Interface.

PubMed

Tomov, Toma E; Tsukanov, Roman; Glick, Yair; Berger, Yaron; Liber, Miran; Avrahami, Dorit; Gerber, Doron; Nir, Eyal

2017-04-25

Realization of bioinspired molecular machines that can perform many and diverse operations in response to external chemical commands is a major goal in nanotechnology, but current molecular machines respond to only a few sequential commands. Lack of effective methods for introduction and removal of command compounds and low efficiencies of the reactions involved are major reasons for the limited performance. We introduce here a user interface based on a microfluidics device and single-molecule fluorescence spectroscopy that allows efficient introduction and removal of chemical commands and enables detailed study of the reaction mechanisms involved in the operation of synthetic molecular machines. The microfluidics provided 64 consecutive DNA strand commands to a DNA-based motor system immobilized inside the microfluidics, driving a bipedal walker to perform 32 steps on a DNA origami track. The microfluidics enabled removal of redundant strands, resulting in a 6-fold increase in processivity relative to an identical motor operated without strand removal and significantly more operations than previously reported for user-controlled DNA nanomachines. In the motor operated without strand removal, redundant strands interfere with motor operation and reduce its performance. The microfluidics also enabled computer control of motor direction and speed. Furthermore, analysis of the reaction kinetics and motor performance in the absence of redundant strands, made possible by the microfluidics, enabled accurate modeling of the walker processivity. This enabled identification of dynamic boundaries and provided an explanation, based on the "trap state" mechanism, for why the motor did not perform an even larger number of steps. This understanding is very important for the development of future motors with significantly improved performance. Our universal interface enables two-way communication between user and molecular machine and, relying on concepts similar to that of solid-phase synthesis, removes limitations on the number of external stimuli. This interface, therefore, is an important step toward realization of reliable, processive, reproducible, and useful externally controlled DNA nanomachines.

Disposable DNA biosensor with the carbon nanotubes-polyethyleneimine interface at a screen-printed carbon electrode for tests of DNA layer damage by quinazolines.

PubMed

Galandová, Júlia; Ovádeková, Renáta; Ferancová, Adriana; Labuda, Ján

2009-06-01

A screen-printed carbon working electrode within a commercially available screen-printed three-electrode assembly was modified by using a composite of multiwalled carbon nanotubes (MWCNT) dispersed in polyethylenimine (PEI) followed by covering with the calf thymus dsDNA layer. Several electrochemical methods were used to characterize the biosensor and to evaluate damage to the surface-attached DNA: square wave voltammetry of the [Ru(bpy)(3)](2+) redox indicator and mediator of the guanine moiety oxidation, cyclic voltammetry and electrochemical impedance spectroscopy in the presence of the [Fe(CN)(6)](3-/4-) indicator in solution. Due to high electroconductivity and large surface area of MWCNT and positive charge of PEI, the MWCNT-PEI composite is an advantageous platform for the DNA immobilization by the polyelectrolyte complexation and its voltammetric and impedimetric detection. In this respect, the MWCNT-PEI interface exhibited better properties than the MWCNT-chitosan one reported from our laboratory previously. A deep DNA layer damage at incubation of the biosensor in quinazoline solution was found, which depends on the quinazoline concentration and incubation time.

Structure of p73 DNA-binding domain tetramer modulates p73 transactivation

PubMed Central

Ethayathulla, Abdul S.; Tse, Pui-Wah; Monti, Paola; Nguyen, Sonha; Inga, Alberto; Fronza, Gilberto; Viadiu, Hector

2012-01-01

The transcription factor p73 triggers developmental pathways and overlaps stress-induced p53 transcriptional pathways. How p53-family response elements determine and regulate transcriptional specificity remains an unsolved problem. In this work, we have determined the first crystal structures of p73 DNA-binding domain tetramer bound to response elements with spacers of different length. The structure and function of the adaptable tetramer are determined by the distance between two half-sites. The structures with zero and one base-pair spacers show compact p73 DNA-binding domain tetramers with large tetramerization interfaces; a two base-pair spacer results in DNA unwinding and a smaller tetramerization interface, whereas a four base-pair spacer hinders tetramerization. Functionally, p73 is more sensitive to spacer length than p53, with one base-pair spacer reducing 90% of transactivation activity and longer spacers reducing transactivation to basal levels. Our results establish the quaternary structure of the p73 DNA-binding domain required as a scaffold to promote transactivation. PMID:22474346

Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics

NASA Astrophysics Data System (ADS)

Ordu, Orkide; Kremser, Leopold; Lusser, Alexandra; Dekker, Nynke H.

2018-03-01

Nucleosomes consisting of a short piece of deoxyribonucleic acid (DNA) wrapped around an octamer of histone proteins form the fundamental unit of chromatin in eukaryotes. Their role in DNA compaction comes with regulatory functions that impact essential genomic processes such as replication, transcription, and repair. The assembly of nucleosomes obeys a precise pathway in which tetramers of histones H3 and H4 bind to the DNA first to form tetrasomes, and two dimers of histones H2A and H2B are subsequently incorporated to complete the complex. As viable intermediates, we previously showed that tetrasomes can spontaneously flip between a left-handed and right-handed conformation of DNA-wrapping. To pinpoint the underlying mechanism, here we investigated the role of the H3-H3 interface for tetramer flexibility in the flipping process at the single-molecule level. Using freely orbiting magnetic tweezers, we studied the assembly and structural dynamics of individual tetrasomes modified at the cysteines close to this interaction interface by iodoacetamide (IA) in real time. While such modification did not affect the structural properties of the tetrasomes, it caused a 3-fold change in their flipping kinetics. The results indicate that the IA-modification enhances the conformational plasticity of tetrasomes. Our findings suggest that subnucleosomal dynamics may be employed by chromatin as an intrinsic and adjustable mechanism to regulate DNA supercoiling.

Lance Wheeler | NREL

Science.gov Websites

solution-phase phenomena of nanomaterials Switchable photovoltaics Solar thermochemical fuel production methylammonium lead halide perovskites during thermal processing from solution," Energy & Environmental

A Low Voltage Liquid Crystal Phase Grating with Switchable Diffraction Angles

PubMed Central

Chen, Haiwei; Tan, Guanjun; Huang, Yuge; Weng, Yishi; Choi, Tae-Hoon; Yoon, Tae-Hoon; Wu, Shin-Tson

2017-01-01

We demonstrate a simple yet high performance phase grating with switchable diffraction angles using a fringe field switching (FFS) liquid crystal (LC) cell. The LC rubbing angle is parallel to the FFS electrodes (i.e. α = 0°), leading to symmetric LC director distribution in a voltage-on state. Such a grating exhibits three unique features: 1) Two grating periods can be formed by controlling the applied voltage, resulting in switchable diffraction angles. In our design, the 1st diffraction order occurs at 4.3°, while the 2nd order appears at 8.6°. 2) The required voltage to achieve peak diffraction efficiency (η~32%) for the 1st order is only 4.4 V at λ = 633 nm as compared to 70 V for a conventional FFS-based phase grating in which α ≈ 7°, while the 2nd order (η~27%) is 15 V. 3). The measured rise and decay time for the 1st order is 7.62 ms and 6.75 ms, and for the 2nd order is 0.75 ms and 3.87 ms, respectively. To understand the physical mechanisms, we also perform device simulations. Good agreement between experiment and simulation is obtained. PMID:28054592

Maximal switchability of centralized networks

NASA Astrophysics Data System (ADS)

Vakulenko, Sergei; Morozov, Ivan; Radulescu, Ovidiu

2016-08-01

We consider continuous time Hopfield-like recurrent networks as dynamical models for gene regulation and neural networks. We are interested in networks that contain n high-degree nodes preferably connected to a large number of N s weakly connected satellites, a property that we call n/N s -centrality. If the hub dynamics is slow, we obtain that the large time network dynamics is completely defined by the hub dynamics. Moreover, such networks are maximally flexible and switchable, in the sense that they can switch from a globally attractive rest state to any structurally stable dynamics when the response time of a special controller hub is changed. In particular, we show that a decrease of the controller hub response time can lead to a sharp variation in the network attractor structure: we can obtain a set of new local attractors, whose number can increase exponentially with N, the total number of nodes of the nework. These new attractors can be periodic or even chaotic. We provide an algorithm, which allows us to design networks with the desired switching properties, or to learn them from time series, by adjusting the interactions between hubs and satellites. Such switchable networks could be used as models for context dependent adaptation in functional genetics or as models for cognitive functions in neuroscience.

Wideband-Switchable Metamaterial Absorber Using Injected Liquid Metal.

PubMed

Kim, Hyung Ki; Lee, Dongju; Lim, Sungjoon

2016-08-22

Metamaterial absorbers can provide good solutions for radar-cross-section (RCS) reduction. In spite of their attractive features of thinness, lightness, and low cost, resonant metamaterial absorbers have a drawback of narrow bandwidth. For practical radar applications, wideband absorbers are necessary. In this paper, we propose a wideband-switchable metamaterial absorber using liquid metal. In order to reduce RCS both for X-band and C-band, the switchable Jerusalem cross (JC) resonator is introduced. The JC resonator consists of slotted circular rings, chip resistors, and microfluidic channels. The JC resonator is etched on a flexible printed circuit board (FPCB), and the microfluidic channels are laser-etched on a polydimethylsiloxane (PDMS) material. The proposed absorber can switch the absorption frequency band by injecting a liquid metal alloy into the channels. The performance of the absorber was demonstrated through full-wave simulation and through measurements employing prototypes. The experimental results showed absorption ratios of over 90% from 7.43 GHz to 14.34 GHz, and from 5.62 GHz to 7.3 GHz, with empty channels and liquid metal-filled channels, respectively. Therefore, the absorption band was successfully switched between the C-band (4-8 GHz) and the X-band (8-12 GHz) by injecting liquid metal eutectic gallium indium alloy (EGaIn) into the channels.

Switchable skin window induced by optical clearing method for dermal blood flow imaging

NASA Astrophysics Data System (ADS)

Wang, Jing; Shi, Rui; Zhu, Dan

2013-06-01

Optical imaging techniques have shown tremendous potential for assessing cutaneous microcirculation, but the imaging depth and contrast is limited by the strong scattering of skin. Current skin windows have to be fulfilled by surgical operation and suffer from some side effects. In this study, a switchable skin window was developed by topical application of an optical clearing agent (OCA) and saline on rat skin in vivo. The validity of the skin window was evaluated by the laser speckle contrast imaging technique, and the safety of OCA to the body was tested through histologic examinations. The results indicated that administration of OCA or saline on rat skin in vivo can open or close the window of skin repeatedly for three days. With the repair effect of hyaluronic acid and Vaseline, it is able to repeatedly visualize the dermal blood vessels and flow distribution. Long-term observation shows that there is no abnormal reflection in micro-structure, body weight, organ coefficients, histopathologic lesions, or toxic reactions compared with a control group. This switchable window will provide an effective tool not only for cutaneous microcirculation with laser speckle contrast imaging, but also for diagnosis and treatment of peripheral vascular diseases, including tumor research with various optical imaging techniques.

Nanoscale Ultrasound-Switchable FRET-Based Liposomes for Near-Infrared Fluorescence Imaging in Optically Turbid Media.

PubMed

Zhang, Qimei; Morgan, Stephen P; Mather, Melissa L

2017-09-01

A new approach for fluorescence imaging in optically turbid media centered on the use of nanoscale ultrasound-switchable FRET-based liposome contrast agents is reported. Liposomes containing lipophilic carbocyanine dyes as FRET pairs with emission wavelengths located in the near-infrared window are prepared. The efficacy of FRET and self-quenching for liposomes with a range of fluorophore concentrations is first calculated from measurement of the liposome emission spectra. Exposure of the liposomes to ultrasound results in changes in the detected fluorescent signal, the nature of which depends on the fluorophores used, detection wavelength, and the fluorophore concentration. Line scanning of a tube containing the contrast agents with 1 mm inner diameter buried at a depth of 1 cm in a heavily scattering tissue phantom demonstrates an improvement in image spatial resolution by a factor of 6.3 as compared with images obtained in the absence of ultrasound. Improvements are also seen in image contrast with the highest obtained being 9% for a liposome system containing FRET pairs. Overall the results obtained provide evidence of the potential the nanoscale ultrasound-switchable FRET-based liposomes studied here have for in vivo fluorescence imaging. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Wideband-Switchable Metamaterial Absorber Using Injected Liquid Metal

NASA Astrophysics Data System (ADS)

Kim, Hyung Ki; Lee, Dongju; Lim, Sungjoon

2016-08-01

Metamaterial absorbers can provide good solutions for radar-cross-section (RCS) reduction. In spite of their attractive features of thinness, lightness, and low cost, resonant metamaterial absorbers have a drawback of narrow bandwidth. For practical radar applications, wideband absorbers are necessary. In this paper, we propose a wideband-switchable metamaterial absorber using liquid metal. In order to reduce RCS both for X-band and C-band, the switchable Jerusalem cross (JC) resonator is introduced. The JC resonator consists of slotted circular rings, chip resistors, and microfluidic channels. The JC resonator is etched on a flexible printed circuit board (FPCB), and the microfluidic channels are laser-etched on a polydimethylsiloxane (PDMS) material. The proposed absorber can switch the absorption frequency band by injecting a liquid metal alloy into the channels. The performance of the absorber was demonstrated through full-wave simulation and through measurements employing prototypes. The experimental results showed absorption ratios of over 90% from 7.43 GHz to 14.34 GHz, and from 5.62 GHz to 7.3 GHz, with empty channels and liquid metal-filled channels, respectively. Therefore, the absorption band was successfully switched between the C-band (4-8 GHz) and the X-band (8-12 GHz) by injecting liquid metal eutectic gallium indium alloy (EGaIn) into the channels.

Magic-angle spinning NMR of intact bacteriophages: Insights into the capsid, DNA and their interface

NASA Astrophysics Data System (ADS)

Abramov, Gili; Morag, Omry; Goldbourt, Amir

2015-04-01

Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses.

Optical properties of metal-hydride switchable films

NASA Astrophysics Data System (ADS)

Griessen, Ronald

2001-03-01

In 1996 we discovered that yttrium-, lanthanum-, and rare-earth-hydride (REHx) films [1] protected by a thin palladium layer, exhibit spectacular changes in their optical properties when the hydrogen concentration x is increased from 2 to 3. For example, a 500 nm thick YH2 film is metallic and shiny while YH3 is yellowish and transparent. The transition is reversible, fast [2, 3], and can simply be induced by adding or removing hydrogen from the gas phase, an electrolyte or from an H containing liquid. The optical switching that occurs near the metal-insulator transition of these hydrides is remarkably robust as it is not affected by structural or compositional disorder. It occurs in polycrystalline and epitaxial films, in alloys with cubic or hexagonal crystal structures,and deuterides [4] switch as well as hydrides. At small length scales epitaxial YHx films exhibit surprising structural properties which open the way to pixel-by-pixel optical switching [5]. Colour-neutral switchable mirrors based on RE-Mg alloys [6] can be used in all-solid-state switchable devices. Newest results for Rare-Earth free switchable mirrors will be presented. [1] J. N. Huiberts, R. Griessen, J. H. Rector, R. J. Wijngaarden, J. P. Dekker, D. G. de Groot and N. J. Koeman, Nature 380 (1996) 231; [2] S. J. van der Molen, J. W. J. Kerssemakers, J. H. Rector, N. J. Koeman, B. Dam, R. Griessen, J. Appl. Phys. 86 (1999) 6107; [3] F. J. A. den Broeder, S. J. van der Molen, et al., Nature 394 (1998)656; [4] A. T. M. van Gogh, E. S. Kooij, R. Griessen, Phys. Rev. Lett. 83 (1999) 4614; [5] J. W. J. Kerssemakers, S. J. van der Molen and R. Griessen, Nature 406 (2000) 489; [6] P. van der Sluis, M. Ouwerkerk and P. A. Duine, Appl. Phys. Lett. 70 (1997) 3356.

Changes in conformational dynamics of basic side chains upon protein–DNA association

PubMed Central

Esadze, Alexandre; Chen, Chuanying; Zandarashvili, Levani; Roy, Sourav; Pettitt, B. Montgometry; Iwahara, Junji

2016-01-01

Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein–DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1–DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains. PMID:27288446

Histone Core Phosphorylation Regulates DNA Accessibility*

PubMed Central

Brehove, Matthew; Wang, Tao; North, Justin; Luo, Yi; Dreher, Sarah J.; Shimko, John C.; Ottesen, Jennifer J.; Luger, Karolin; Poirier, Michael G.

2015-01-01

Nucleosome unwrapping dynamics provide transient access to the complexes involved in DNA transcription, repair, and replication, whereas regulation of nucleosome unwrapping modulates occupancy of these complexes. Histone H3 is phosphorylated at tyrosine 41 (H3Y41ph) and threonine 45 (H3T45ph). H3Y41ph is implicated in regulating transcription, whereas H3T45ph is involved in DNA replication and apoptosis. These modifications are located in the DNA-histone interface near where the DNA exits the nucleosome, and are thus poised to disrupt DNA-histone interactions. However, the impact of histone phosphorylation on nucleosome unwrapping and accessibility is unknown. We find that the phosphorylation mimics H3Y41E and H3T45E, and the chemically correct modification, H3Y41ph, significantly increase nucleosome unwrapping. This enhances DNA accessibility to protein binding by 3-fold. H3K56 acetylation (H3K56ac) is also located in the same DNA-histone interface and increases DNA unwrapping. H3K56ac is implicated in transcription regulation, suggesting that H3Y41ph and H3K56ac could function together. We find that the combination of H3Y41ph with H3K56ac increases DNA accessibility by over an order of magnitude. These results suggest that phosphorylation within the nucleosome DNA entry-exit region increases access to DNA binding complexes and that the combination of phosphorylation with acetylation has the potential to significantly influence DNA accessibility to transcription regulatory complexes. PMID:26175159

Pattern Switchable Antenna System Using Inkjet-Printed Directional Bow-Tie for Bi-Direction Sensing Applications

PubMed Central

Eom, Seung-Hyun; Seo, Yunsik; Lim, Sungjoon

2015-01-01

In this paper, we propose a paper-based pattern switchable antenna system using inkjet-printing technology for bi-direction sensor applications. The proposed antenna system is composed of two directional bow-tie antennas and a switching network. The switching network consists of a single-pole-double-throw (SPDT) switch and a balun element. A double-sided parallel-strip line (DSPSL) is employed to convert the unbalanced microstrip mode to the balanced strip mode. Two directional bow-tie antennas have different radiation patterns because of the different orientation of the reflectors and antennas. It is demonstrated from electromagnetic (EM) simulation and measurement that the radiation patterns of the proposed antenna are successfully switched by the SPDT switch. PMID:26690443

Wavelength switchable high-power diode-side-pumped rod Tm:YAG Laser around 2µm.

PubMed

Wang, Caili; Du, Shifeng; Niu, Yanxiong; Wang, Zhichao; Zhang, Chao; Bian, Qi; Guo, Chuan; Xu, Jialin; Bo, Yong; Peng, Qinjun; Cui, Dafu; Zhang, Jingyuan; Lei, Wenqiang; Xu, Zuyan

2013-03-25

We report a high-power diode-side-pumped rod Tm:YAG laser operated at either 2.07 or 2.02 µm depending on the transmission of pumped output coupler. The laser yields 115W of continuous-wave output power at 2.07 µm with 5% output coupling, which is the highest output power for all solid-state 2.07 μm cw rod Tm:YAG laser reported so far. With an output coupler of 10% transmission, the center wavelength of the laser is switched to 2.02 μm with an output power of 77.1 W. This is the first observation of high-power wavelength switchable diode-side-pumped rod Tm:YAG laser around 2 µm.

Compact Mach-Zehnder interferometer based on photonic crystal fiber and its application in switchable multi-wavelength fiber laser

NASA Astrophysics Data System (ADS)

Chen, Weiguo; Lou, Shuqin; Wang, Liwen; Li, Honglei; Guo, Tieying; Jian, Shuisheng

2009-08-01

The compact Mach-Zehnder interferometer is proposed by splicing a section of photonic crystal fiber (PCF) and two pieces of single mode fiber (SMF) with the air-holes of PCF intentionally collapsed in the vicinity of the splices. The depedence of the fringe spacing on the length of PCF is investigated. Based on the Mach-Zehnder interferometer as wavelength-selective filter, a switchable dual-wavelength fiber ring laser is demonstrated with a homemade erbiumdoped fiber amplifier (EDFA) as the gain medium at room temperature. By adjusting the states of the polarization controller (PC) appropriately, the laser can be switched among the stable single-and dual -wavelength lasing operations by exploiting polarization hole burning (PHB) effect.

Switchable and spacing-tunable dual-wavelength thulium-doped silica fiber laser based on a nonlinear amplifier loop mirror.

PubMed

Liu, Shuo; Yan, Fengping; Feng, Ting; Wu, Beilei; Dong, Ze; Chang, Gee-Kung

2014-08-20

A kind of switchable and spacing-tunable dual-wavelength thulium-doped silica fiber laser based on a nonlinear amplifier loop mirror is presented and experimentally demonstrated. By adjusting the polarization controllers (PCs), stable dual-wavelength operation is obtained at the 2 μm band. The optical signal-to-noise ratio (OSNR) is better than 56 dB. The wavelength tuning is performed by applying static strain into the fiber Bragg grating. A tuning range from 0 to 5.14 nm is achieved for the dual-wavelength spacing. By adjusting the PCs properly, the fiber laser can also operate in single-wavelength state with the OSNR for each wavelength more than 50 dB.

Pattern Switchable Antenna System Using Inkjet-Printed Directional Bow-Tie for Bi-Direction Sensing Applications.

PubMed

Eom, Seung-Hyun; Seo, Yunsik; Lim, Sungjoon

2015-12-10

In this paper, we propose a paper-based pattern switchable antenna system using inkjet-printing technology for bi-direction sensor applications. The proposed antenna system is composed of two directional bow-tie antennas and a switching network. The switching network consists of a single-pole-double-throw (SPDT) switch and a balun element. A double-sided parallel-strip line (DSPSL) is employed to convert the unbalanced microstrip mode to the balanced strip mode. Two directional bow-tie antennas have different radiation patterns because of the different orientation of the reflectors and antennas. It is demonstrated from electromagnetic (EM) simulation and measurement that the radiation patterns of the proposed antenna are successfully switched by the SPDT switch.

An L-section DC electric field switchable bulk acoustic wave solidly mounted resonator filter based on Ba0.5Sr0.5TiO3.

PubMed

Saddik, George N; York, Robert A

2012-09-01

This paper reports on the modeling, fabrication, and experimental results of a voltage switchable barium strontium titanate solidly mounted resonator filter at 6 GHz. The filter insertion loss was measured to be -4.26 dB and the return loss to be -13.5 dB. The 3-dB bandwidth was measured to be 72 MHz and the quality factor was calculated to be 83. The data were collected at a dc bias voltage of 10 V. Temperature data were also collected, and the filter demonstrated a 0.71-dB increase in insertion loss and a 7-MHz decrease in center frequency with increase in temperature.

Thermally Switchable Thin Films of an ABC Triblock Copolymer of Poly(n-butyl methacrylate)-poly(methyl methacrylate)-poly(2-fluoroethyl methacrylate)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Shanju; Liu, Zhan; Bucknall, David G.

2011-01-01

The thermo-responsive behavior of polymer films consisting of novel linear triblock copolymers of poly(n-butyl methacrylate)-poly(methyl methacrylate)-poly(2-fluoroethyl methacrylate) (PnBuMA-PMMA-P2FEMA) are reported using differential scanning calorimetry (DSC), atomic forcing microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and contacting angle (CA) measurements. The surface morphology, wettability and chemical structure of thin films of these triblock copolymers on silicon wafers as a function of temperature have been investigated. It has been shown that the wettability of the films is thermally switchable. Detailed structural analysis shows that thermo-responsive surface composition changes are produced. The underlying mechanism of the thermoresponsive behavior is discussed.

Switchable multi-wavelength fiber laser based on modal interference

NASA Astrophysics Data System (ADS)

Ma, Lin; Jiang, Sun; Qi, Yan-Hui; Kang, Ze-Xin; Jian, Shui-Sheng

2015-08-01

A comb fiber filter based on modal interference is proposed and demonstrated in this paper. Here two cascaded up-tapers are used to excite the cladding mode, and a core-offset jointing point is used to act as an interference component. Experimental results show that this kind of structure possesses a comb filter property in a range of the C-band. The measured extinction ratio is better than 12 dB with an insertion loss of about 11 dB. A switchable multi-wavelength erbium-doped fiber laser based on this novel comb filter is demonstrated. By adjusting the polarization controller, the output laser can be switched among single-, dual-, and three-wavelengths with a side mode suppression ratio of better than 45 dB.

Development of an automated electrical power subsystem testbed for large spacecraft

NASA Technical Reports Server (NTRS)

Hall, David K.; Lollar, Louis F.

1990-01-01

The NASA Marshall Space Flight Center (MSFC) has developed two autonomous electrical power system breadboards. The first breadboard, the autonomously managed power system (AMPS), is a two power channel system featuring energy generation and storage and 24-kW of switchable loads, all under computer control. The second breadboard, the space station module/power management and distribution (SSM/PMAD) testbed, is a two-bus 120-Vdc model of the Space Station power subsystem featuring smart switchgear and multiple knowledge-based control systems. NASA/MSFC is combining these two breadboards to form a complete autonomous source-to-load power system called the large autonomous spacecraft electrical power system (LASEPS). LASEPS is a high-power, intelligent, physical electrical power system testbed which can be used to derive and test new power system control techniques, new power switching components, and new energy storage elements in a more accurate and realistic fashion. LASEPS has the potential to be interfaced with other spacecraft subsystem breadboards in order to simulate an entire space vehicle. The two individual systems, the combined systems (hardware and software), and the current and future uses of LASEPS are described.

Adhesion behaviors on superhydrophobic surfaces.

PubMed

Zhu, Huan; Guo, Zhiguang; Liu, Weimin

2014-04-18

The adhesion behaviors of superhydrophobic surfaces have become an emerging topic to researchers in various fields as a vital step in the interactions between materials and organisms/materials. Controlling the chemical compositions and topological structures via various methods or technologies is essential to fabricate and modulate different adhesion properties, such as low-adhesion, high-adhesion and anisotropic adhesion on superhydrophobic surfaces. We summarize the recent developments in both natural superhydrophobic surfaces and artificial superhydrophobic surfaces with various adhesions and also pay attention to superhydrophobic surfaces switching between low- and high-adhesion. The methods to regulate or translate the adhesion of superhydrophobic surfaces can be considered from two perspectives. One is to control the chemical composition and change the surface geometric structure on the surfaces, respectively or simultaneously. The other is to provide external stimulations to induce transitions, which is the most common method for obtaining switchable adhesions. Additionally, adhesion behaviors on solid-solid interfaces, such as the behaviors of cells, bacteria, biomolecules and icing on superhydrophobic surfaces are also noticeable and controversial. This review is aimed at giving a brief and crucial overview of adhesion behaviors on superhydrophobic surfaces.

Silica nanoparticles with a substrate switchable luminescence

NASA Astrophysics Data System (ADS)

Bochkova, O. D.; Mustafina, A. R.; Fedorenko, S. V.; Konovalov, A. I.

2011-04-01

Silica nanoparticles with visible (Tb and Ru doped), near IR (Yb doped) and dual visible-near IR luminescence (Ru-Yb doped) were obtained by reverse w/o microemulsion procedure. Plenty of luminescent complexes (from 4900 to 10000) encapsulated into each nanoparticle ensures the intensive luminescence of nanoparticles and their applicability as biomarkers. The silica surface decoration by definite anchor groups is the required step for the gaining to these nanoparticles marking and sensing functions. Thus covalent and non-covalent surface modification of these nanoparticles was developed to provide the binding with biotargets and sensing of anions. The dicationic surfactant coating of negatively charged Tb(III)-TCAS doped silica nanoparticles was chosen as the basis for the anion responsible system. The reversible insertion of the quenching anions (namely phenol red) into the surfactant based layer at the surface of luminescent nanoparticles switches off the Tb-centered luminescence. In turn the reversible reestablishment of the luminescence results from the competitive insertion of the non-quenching anions into the surfactant layer at the silica/water interface. The hydrophobic anions exemplified by dodecylsulfates versus hydrophilic ones (hydrophosphates) are preferable in the competition with phenol red anions.

Biomolecular logic systems: applications to biosensors and bioactuators

NASA Astrophysics Data System (ADS)

Katz, Evgeny

2014-05-01

The paper presents an overview of recent advances in biosensors and bioactuators based on the biocomputing concept. Novel biosensors digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce output in the form of YES/NO response. Compared to traditional single-analyte sensing devices, biocomputing approach enables a high-fidelity multi-analyte biosensing, particularly beneficial for biomedical applications. Multi-signal digital biosensors thus promise advances in rapid diagnosis and treatment of diseases by processing complex patterns of physiological biomarkers. Specifically, they can provide timely detection and alert to medical emergencies, along with an immediate therapeutic intervention. Application of the biocomputing concept has been successfully demonstrated for systems performing logic analysis of biomarkers corresponding to different injuries, particularly exemplified for liver injury. Wide-ranging applications of multi-analyte digital biosensors in medicine, environmental monitoring and homeland security are anticipated. "Smart" bioactuators, for example for signal-triggered drug release, were designed by interfacing switchable electrodes and biocomputing systems. Integration of novel biosensing and bioactuating systems with the biomolecular information processing systems keeps promise for further scientific advances and numerous practical applications.

Role of biomolecular logic systems in biosensors and bioactuators

NASA Astrophysics Data System (ADS)

Mailloux, Shay; Katz, Evgeny

2014-09-01

An overview of recent advances in biosensors and bioactuators based on biocomputing systems is presented. Biosensors digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce an output in the form of a YES/NO response. Compared to traditional single-analyte sensing devices, the biocomputing approach enables high-fidelity multianalyte biosensing, which is particularly beneficial for biomedical applications. Multisignal digital biosensors thus promise advances in rapid diagnosis and treatment of diseases by processing complex patterns of physiological biomarkers. Specifically, they can provide timely detection and alert medical personnel of medical emergencies together with immediate therapeutic intervention. Application of the biocomputing concept has been successfully demonstrated for systems performing logic analysis of biomarkers corresponding to different injuries, particularly as exemplified for liver injury. Wide-ranging applications of multianalyte digital biosensors in medicine, environmental monitoring, and homeland security are anticipated. "Smart" bioactuators, for signal-triggered drug release, for example, were designed by interfacing switchable electrodes with biocomputing systems. Integration of biosensing and bioactuating systems with biomolecular information processing systems advances the potential for further scientific innovations and various practical applications.

Regulation of Response Regulator Autophosphorylation through Interdomain Contacts*♦

PubMed Central

Barbieri, Christopher M.; Mack, Timothy R.; Robinson, Victoria L.; Miller, Matthew T.; Stock, Ann M.

2010-01-01

DNA-binding response regulators (RRs) of the OmpR/PhoB subfamily alternate between inactive and active conformational states, with the latter having enhanced DNA-binding affinity. Phosphorylation of an aspartate residue in the receiver domain, usually via phosphotransfer from a cognate histidine kinase, stabilizes the active conformation. Many of the available structures of inactive OmpR/PhoB family proteins exhibit extensive interfaces between the N-terminal receiver and C-terminal DNA-binding domains. These interfaces invariably involve the α4-β5-α5 face of the receiver domain, the locus of the largest differences between inactive and active conformations and the surface that mediates dimerization of receiver domains in the active state. Structures of receiver domain dimers of DrrB, DrrD, and MtrA have been determined, and phosphorylation kinetics were analyzed. Analysis of phosphotransfer from small molecule phosphodonors has revealed large differences in autophosphorylation rates among OmpR/PhoB RRs. RRs with substantial domain interfaces exhibit slow rates of phosphorylation. Rates are greatly increased in isolated receiver domain constructs. Such differences are not observed between autophosphorylation rates of full-length and isolated receiver domains of a RR that lacks interdomain interfaces, and they are not observed in histidine kinase-mediated phosphotransfer. These findings suggest that domain interfaces restrict receiver domain conformational dynamics, stabilizing an inactive conformation that is catalytically incompetent for phosphotransfer from small molecule phosphodonors. Inhibition of phosphotransfer by domain interfaces provides an explanation for the observation that some RRs cannot be phosphorylated by small molecule phosphodonors in vitro and provides a potential mechanism for insulating some RRs from small molecule-mediated phosphorylation in vivo. PMID:20702407

Releasing the cohesin ring: A rigid scaffold model for opening the DNA exit gate by Pds5 and Wapl.

PubMed

Ouyang, Zhuqing; Yu, Hongtao

2017-04-01

The ring-shaped ATPase machine, cohesin, regulates sister chromatid cohesion, transcription, and DNA repair by topologically entrapping DNA. Here, we propose a rigid scaffold model to explain how the cohesin regulators Pds5 and Wapl release cohesin from chromosomes. Recent studies have established the Smc3-Scc1 interface as the DNA exit gate of cohesin, revealed a requirement for ATP hydrolysis in ring opening, suggested regulation of the cohesin ATPase activity by DNA and Smc3 acetylation, and provided insights into how Pds5 and Wapl open this exit gate. We hypothesize that Pds5, Wapl, and SA1/2 form a rigid scaffold that docks on Scc1 and anchors the N-terminal domain of Scc1 (Scc1N) to the Smc1 ATPase head. Relative movements between the Smc1-3 ATPase heads driven by ATP and Wapl disrupt the Smc3-Scc1 interface. Pds5 binds the dissociated Scc1N and prolongs this open state of cohesin, releasing DNA. We review the evidence supporting this model and suggest experiments that can further test its key principles. © 2017 WILEY Periodicals, Inc.

Dynamic assembly of Hda and the sliding clamp in the regulation of replication licensing.

PubMed

Kim, Jin S; Nanfara, Michael T; Chodavarapu, Sundari; Jin, Kyeong S; Babu, Vignesh M P; Ghazy, Mohamed A; Chung, Scisung; Kaguni, Jon M; Sutton, Mark D; Cho, Yunje

2017-04-20

Regulatory inactivation of DnaA (RIDA) is one of the major regulatory mechanisms of prokaryotic replication licensing. In RIDA, the Hda-sliding clamp complex loaded onto DNA directly interacts with adenosine triphosphate (ATP)-bound DnaA and stimulates the hydrolysis of ATP to inactivate DnaA. A prediction is that the activity of Hda is tightly controlled to ensure that replication initiation occurs only once per cell cycle. Here, we determined the crystal structure of the Hda-β clamp complex. This complex contains two pairs of Hda dimers sandwiched between two β clamp rings to form an octamer that is stabilized by three discrete interfaces. Two separate surfaces of Hda make contact with the β clamp, which is essential for Hda function in RIDA. The third interface between Hda monomers occludes the active site arginine finger, blocking its access to DnaA. Taken together, our structural and mutational analyses of the Hda-β clamp complex indicate that the interaction of the β clamp with Hda controls the ability of Hda to interact with DnaA. In the octameric Hda-β clamp complex, the inability of Hda to interact with DnaA is a novel mechanism that may regulate Hda function. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dynamic assembly of Hda and the sliding clamp in the regulation of replication licensing

PubMed Central

Kim, Jin S.; Nanfara, Michael T.; Chodavarapu, Sundari; Jin, Kyeong S.; Babu, Vignesh M. P.; Ghazy, Mohamed A.; Chung, Scisung

2017-01-01

Abstract Regulatory inactivation of DnaA (RIDA) is one of the major regulatory mechanisms of prokaryotic replication licensing. In RIDA, the Hda–sliding clamp complex loaded onto DNA directly interacts with adenosine triphosphate (ATP)-bound DnaA and stimulates the hydrolysis of ATP to inactivate DnaA. A prediction is that the activity of Hda is tightly controlled to ensure that replication initiation occurs only once per cell cycle. Here, we determined the crystal structure of the Hda–β clamp complex. This complex contains two pairs of Hda dimers sandwiched between two β clamp rings to form an octamer that is stabilized by three discrete interfaces. Two separate surfaces of Hda make contact with the β clamp, which is essential for Hda function in RIDA. The third interface between Hda monomers occludes the active site arginine finger, blocking its access to DnaA. Taken together, our structural and mutational analyses of the Hda–β clamp complex indicate that the interaction of the β clamp with Hda controls the ability of Hda to interact with DnaA. In the octameric Hda–β clamp complex, the inability of Hda to interact with DnaA is a novel mechanism that may regulate Hda function. PMID:28168278

Nucleosome accessibility governed by the dimer/tetramer interface

PubMed Central

Böhm, Vera; Hieb, Aaron R.; Andrews, Andrew J.; Gansen, Alexander; Rocker, Andrea; Tóth, Katalin; Luger, Karolin; Langowski, Jörg

2011-01-01

Nucleosomes are multi-component macromolecular assemblies which present a formidable obstacle to enzymatic activities that require access to the DNA, e.g. DNA and RNA polymerases. The mechanism and pathway(s) by which nucleosomes disassemble to allow DNA access are not well understood. Here we present evidence from single molecule FRET experiments for a previously uncharacterized intermediate structural state before H2A–H2B dimer release, which is characterized by an increased distance between H2B and the nucleosomal dyad. This suggests that the first step in nucleosome disassembly is the opening of the (H3–H4)2 tetramer/(H2A–H2B) dimer interface, followed by H2A–H2B dimer release from the DNA and, lastly, (H3–H4)2 tetramer removal. We estimate that the open intermediate state is populated at 0.2–3% under physiological conditions. This finding could have significant in vivo implications for factor-mediated histone removal and exchange, as well as for regulating DNA accessibility to the transcription and replication machinery. PMID:21177647

Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA.

PubMed

Odell, M; Shuman, S

1999-05-14

The 298-amino acid ATP-dependent DNA ligase of Chlorella virus PBCV-1 is the smallest eukaryotic DNA ligase known. The enzyme has intrinsic specificity for binding to nicked duplex DNA. To delineate the ligase-DNA interface, we have footprinted the enzyme binding site on DNA and the DNA binding site on ligase. The size of the exonuclease III footprint of ligase bound a single nick in duplex DNA is 19-21 nucleotides. The footprint is asymmetric, extending 8-9 nucleotides on the 3'-OH side of the nick and 11-12 nucleotides on the 5'-phosphate side. The 5'-phosphate moiety is essential for the binding of Chlorella virus ligase to nicked DNA. Here we show that the 3'-OH moiety is not required for nick recognition. The Chlorella virus ligase binds to a nicked ligand containing 2',3'-dideoxy and 5'-phosphate termini, but cannot catalyze adenylation of the 5'-end. Hence, the 3'-OH is important for step 2 chemistry even though it is not itself chemically transformed during DNA-adenylate formation. A 2'-OH cannot substitute for the essential 3'-OH in adenylation at a nick or even in strand closure at a preadenylated nick. The protein side of the ligase-DNA interface was probed by limited proteolysis of ligase with trypsin and chymotrypsin in the presence and absence of nicked DNA. Protease accessible sites are clustered within a short segment from amino acids 210-225 located distal to conserved motif V. The ligase is protected from proteolysis by nicked DNA. Protease cleavage of the native enzyme prior to DNA addition results in loss of DNA binding. These results suggest a bipartite domain structure in which the interdomain segment either comprises part of the DNA binding site or undergoes a conformational change upon DNA binding. The domain structure of Chlorella virus ligase inferred from the solution experiments is consistent with the structure of T7 DNA ligase determined by x-ray crystallography.

The Mechanisms and Biomedical Applications of an NIR BODIPY-Based Switchable Fluorescent Probe

PubMed Central

Cheng, Bingbing; Bandi, Venugopal; Yu, Shuai; D’Souza, Francis; Nguyen, Kytai T.; Hong, Yi; Tang, Liping; Yuan, Baohong

2017-01-01

Highly environment-sensitive fluorophores have been desired for many biomedical applications. Because of the noninvasive operation, high sensitivity, and high specificity to the microenvironment change, they can be used as excellent probes for fluorescence sensing/imaging, cell tracking/imaging, molecular imaging for cancer, and so on (i.e., polarity, viscosity, temperature, or pH measurement). In this work, investigations of the switching mechanism of a recently reported near-infrared environment-sensitive fluorophore, ADP(CA)2, were conducted. Besides, multiple potential biomedical applications of this switchable fluorescent probe have been demonstrated, including wash-free live-cell fluorescence imaging, in vivo tissue fluorescence imaging, temperature sensing, and ultrasound-switchable fluorescence (USF) imaging. The fluorescence of the ADP(CA)2 is extremely sensitive to the microenvironment, especially polarity and viscosity. Our investigations showed that the fluorescence of ADP(CA)2 can be switched on by low polarity, high viscosity, or the presence of protein and surfactants. In wash-free live-cell imaging, the fluorescence of ADP(CA)2 inside cells was found much brighter than the dye-containing medium and was retained for at least two days. In all of the fluorescence imaging applications conducted in this study, high target-to-noise (>5-fold) was achieved. In addition, a high temperature sensitivity (73-fold per Celsius degree) of ADP(CA)2-based temperature probes was found in temperature sensing. PMID:28208666

Borophene as a Promising Material for Charge-Modulated Switchable CO2 Capture.

PubMed

Tan, Xin; Tahini, Hassan A; Smith, Sean C

2017-06-14

Ideal carbon dioxide (CO 2 ) capture materials for practical applications should bind CO 2 molecules neither too weakly to limit good loading kinetics nor too strongly to limit facile release. Although charge-modulated switchable CO 2 capture has been proposed to be a controllable, highly selective, and reversible CO 2 capture strategy, the development of a practical gas-adsorbent material remains a great challenge. In this study, by means of density functional theory (DFT) calculations, we have examined the possibility of conductive borophene nanosheets as promising sorbent materials for charge-modulated switchable CO 2 capture. Our results reveal that the binding strength of CO 2 molecules on negatively charged borophene can be significantly enhanced by injecting extra electrons into the adsorbent. At saturation CO 2 capture coverage, the negatively charged borophene achieves CO 2 capture capacities up to 6.73 × 10 14 cm -2 . In contrast to the other CO 2 capture methods, the CO 2 capture/release processes on negatively charged borophene are reversible with fast kinetics and can be easily controlled via switching on/off the charges carried by borophene nanosheets. Moreover, these negatively charged borophene nanosheets are highly selective for separating CO 2 from mixtures with CH 4 , H 2 , and/or N 2 . This theoretical exploration will provide helpful guidance for identifying experimentally feasible, controllable, highly selective, and high-capacity CO 2 capture materials with ideal thermodynamics and reversibility.

Conductive Graphitic Carbon Nitride as an Ideal Material for Electrocatalytically Switchable CO2 Capture

PubMed Central

Tan, Xin; Kou, Liangzhi; Tahini, Hassan A.; Smith, Sean C.

2015-01-01

Good electrical conductivity and high electron mobility of the sorbent materials are prerequisite for electrocatalytically switchable CO2 capture. However, no conductive and easily synthetic sorbent materials are available until now. Here, we examined the possibility of conductive graphitic carbon nitride (g-C4N3) nanosheets as sorbent materials for electrocatalytically switchable CO2 capture. Using first-principle calculations, we found that the adsorption energy of CO2 molecules on g-C4N3 nanosheets can be dramatically enhanced by injecting extra electrons into the adsorbent. At saturation CO2 capture coverage, the negatively charged g-C4N3 nanosheets achieve CO2 capture capacities up to 73.9 × 1013 cm−2 or 42.3 wt%. In contrast to other CO2 capture approaches, the process of CO2 capture/release occurs spontaneously without any energy barriers once extra electrons are introduced or removed, and these processes can be simply controlled and reversed by switching on/off the charging voltage. In addition, these negatively charged g-C4N3 nanosheets are highly selective for separating CO2 from mixtures with CH4, H2 and/or N2. These predictions may prove to be instrumental in searching for a new class of experimentally feasible high-capacity CO2 capture materials with ideal thermodynamics and reversibility. PMID:26621618

Detection of nitro-based and peroxide-based explosives by fast polarity-switchable ion mobility spectrometer with ion focusing in vicinity of Faraday detector.

PubMed

Zhou, Qinghua; Peng, Liying; Jiang, Dandan; Wang, Xin; Wang, Haiyan; Li, Haiyang

2015-05-29

Ion mobility spectrometer (IMS) has been widely deployed for on-site detection of explosives. The common nitro-based explosives are usually detected by negative IMS while the emerging peroxide-based explosives are better detected by positive IMS. In this study, a fast polarity-switchable IMS was constructed to detect these two explosive species in a single measurement. As the large traditional Faraday detector would cause a trailing reactant ion peak (RIP), a Faraday detector with ion focusing in vicinity was developed by reducing the detector radius to 3.3 mm and increasing the voltage difference between aperture grid and its front guard ring to 591 V, which could remove trailing peaks from RIP without loss of signal intensity. This fast polarity-switchable IMS with ion focusing in vicinity of Faraday detector was employed to detect a mixture of 10 ng 2,4,6-trinitrotoluene (TNT) and 50 ng hexamethylene triperoxide diamine (HMTD) by polarity-switching, and the result suggested that [TNT-H](-) and [HMTD+H](+) could be detected in a single measurement. Furthermore, the removal of trailing peaks from RIP by the Faraday detector with ion focusing in vicinity also promised the accurate identification of KClO4, KNO3 and S in common inorganic explosives, whose product ion peaks were fairly adjacent to RIP.

Changes in conformational dynamics of basic side chains upon protein-DNA association.

PubMed

Esadze, Alexandre; Chen, Chuanying; Zandarashvili, Levani; Roy, Sourav; Pettitt, B Montgometry; Iwahara, Junji

2016-08-19

Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein-DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1-DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Switchable electrochemiluminescence aptasensor coupled with resonance energy transfer for selective attomolar detection of Hg2+ via CdTe@CdS/dendrimer probe and Au nanoparticle quencher.

PubMed

Babamiri, Bahareh; Salimi, Abdollah; Hallaj, Rahman

2018-04-15

In the present study, an ultrasensitive electrochemiluminescence (ECL) aptasensing assay for selective detection of Hg 2+ was designed. In this electrochemiluminescence resonance energy transfer (ECL-RET) approach, Fe 3 O 4 @SiO 2 /dendrimers/QDs exhibited amplified ECL emissions (switch "on" state) and with the hybridization between T-rich ssDNA(S 1 ) immobilized on the Fe 3 O 4 @SiO 2 /dendrimers/QDs and AuNPs modified with complementary aptamer (AuNPs-S 2 ), the ECL of QDs nanocomposites was efficiently quenched (switch "off" state). In the presence of Hg 2+ ions, formation of strong and stable T-Hg 2+ -T complex led to the release of the AuNPs-S 2 from double-stranded DNA(dsDNA) and the recovery of the ECL signal of QDs (second signal switch "on" state). Under optimal conditions, Hg 2+ can be detected in a wide linear range from 20aM to 2µM with a very low detection limit of 2aM. The proposed ECL aptasensor showed high selectivity for Hg 2+ determination compared to other environmentally relevant metal ions at concentration ratio more than 1000 times. The aptasensor was used for detection Hg 2+ ions from samples of tap waters, carp and saltwater fishes with satisfactory results. The aptasensor exhibited high sensitivity, wide linear response (11 orders of magnitude), excellent reproducibility and stability. The proposed aptasensor will be a promising candidate for facile and rapid determination of Hg 2＋ in environmental and fishery samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Switchable host-guest systems on surfaces.

PubMed

Yang, Ying-Wei; Sun, Yu-Long; Song, Nan

2014-07-15

CONSPECTUS: For device miniaturization, nanotechnology follows either the "top-down" approach scaling down existing larger-scale devices or the "bottom-up' approach assembling the smallest possible building blocks to functional nanoscale entities. For synthetic nanodevices, self-assembly on surfaces is a superb method to achieve useful functions and enable their interactions with the surrounding world. Consequently, adaptability and responsiveness to external stimuli are other prerequisites for their successful operation. Mechanically interlocked molecules such as rotaxanes and catenanes, and their precursors, that is, molecular switches and supramolecular switches including pseudorotaxanes, are molecular machines or prototypes of machines capable of mechanical motion induced by chemical signals, biological inputs, light or redox processes as the external stimuli. Switching of these functional host-guest systems on surfaces becomes a fundamental requirement for artificial molecular machines to work, mimicking the molecular machines in nature, such as proteins and their assemblies operating at dynamic interfaces such as the surfaces of cell membranes. Current research endeavors in material science and technology are focused on developing either a new class of materials or materials with novel/multiple functionalities by shifting host-guest chemistry from solution phase to surfaces. In this Account, we present our most recent attempts of building monolayers of rotaxanes/pseudorotaxanes on surfaces, providing stimuli-induced macroscopic effects and further understanding on the switchable host-guest systems at interfaces. Biocompatible versions of molecular machines based on synthetic macrocycles, such as cucurbiturils, pillararenes, calixarenes, and cyclodextrins, have been employed to form self-assembled monolayers of gates on the surfaces of mesoporous silica nanoparticles to regulate the controlled release of cargo/drug molecules under a range of external stimuli, such as light, pH variations, competitive binding, and enzyme. Rotaxanes have also been assembled onto the surfaces of gold nanodisks and microcantilevers to realize active molecular plasmonics and synthetic molecular actuators for device fabrication and function. Pillararenes have been successfully used to control and aid the synthesis of gold nanoparticles, semiconducting quantum dots, and magnetic nanoparticles. The resulting organic-inorganic hydrid nanomaterials have been successfully used for controlled self-assembly, herbicide sensing and detection, pesticide removal, and so forth, taking advantage of the selective binding of pillarenes toward target molecules. Cyclodextrins have also been successfully functionalized onto the surface of gold nanoparticles to serve as recycling extractors for C60. Many interesting prototypes of nanodevices based on synthetic macrocycles and their host-guest chemistry have been constructed and served for different potential applications. This Account will be a summary of the efforts made mainly by us, and others, on the host-guest chemistry of synthetic macrocyclic compounds on the surfaces of different solid supports.

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.

PubMed

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. This database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

hPDI: a database of experimental human protein-DNA interactions.

PubMed

Xie, Zhi; Hu, Shaohui; Blackshaw, Seth; Zhu, Heng; Qian, Jiang

2010-01-15

The human protein DNA Interactome (hPDI) database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The unique characteristics of hPDI are that it contains consensus DNA-binding sequences not only for nearly 500 human transcription factors but also for >500 unconventional DNA-binding proteins, which are completely uncharacterized previously. Users can browse, search and download a subset or the entire data via a web interface. This database is freely accessible for any academic purposes. http://bioinfo.wilmer.jhu.edu/PDI/.

Magic-angle spinning NMR of intact bacteriophages: insights into the capsid, DNA and their interface.

PubMed

Abramov, Gili; Morag, Omry; Goldbourt, Amir

2015-04-01

Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses. Copyright © 2015 Elsevier Inc. All rights reserved.

Electrically switchable polymer liquid crystal and polymer birefringent flake in fluid host systems and optical devices utilizing same

DOEpatents

Marshall, Kenneth L.; Kosc, Tanya Z.; Jacobs, Stephen D.; Faris, Sadeg M.; Li, Le

2003-12-16

Flakes or platelets of polymer liquid crystals (PLC) or other birefringent polymers (BP) suspended in a fluid host medium constitute a system that can function as the active element in an electrically switchable optical device when the suspension is either contained between a pair of rigid substrates bearing transparent conductive coatings or dispersed as microcapsules within the body of a flexible host polymer. Optical properties of these flake materials include large effective optical path length, different polarization states and high angular sensitivity in their selective reflection or birefringence. The flakes or platelets of these devices need only a 3-20.degree. rotation about the normal to the cell surface to achieve switching characteristics obtainable with prior devices using particle rotation or translation.

Switchable focus using a polymeric lenticular microlens array and a polarization rotator.

PubMed

Ren, Hongwen; Xu, Su; Liu, Yifan; Wu, Shin-Tson

2013-04-08

We demonstrate a flat polymeric lenticular microlens array using a mixture of rod-like diacrylate monomer and positive dielectric anisotropy nematic liquid crystal (LC). To create gradient refractive index profile in one microlens, we generate fringing fields from a planar top electrode and two striped bottom electrodes. After UV stabilization, the film is optically anisotropic and can stand alone. We then laminate this film on a 90° twisted-nematic LC cell, which works as a dynamic polarization rotator. The static polymeric lenticular lens exhibits focusing effect only to the extraordinary ray, but no optical effect to the ordinary ray. Such an integrated lens system offers several advantages, such as low voltage, fast response time, and temperature insensitivity, and can be used for switchable 2D/3D displays.

Switchable polarization-sensitive surface plasmon resonance of highly stable gold nanorods liquid crystals composites

NASA Astrophysics Data System (ADS)

Liu, Qingkun; Qian, Jun; Cai, Fuhong; Smalyukh, Ivan I.; He, Sailing

2011-12-01

In this work, we demonstrate the bulk self-alignment of gold nanorods (GNRs) dispersed in lyotropic nematic liquid crystals (LCs) with high optical absorption coefficient at the surface plasmon resonant wavelength. The polymer-coated GNRs which show spontaneous long-range orientational ordering along the director of LC host exhibit long-term stability as well as high concentration. External magnetic field and shearing allow for alignment and realignment of the orientation of gold nanorods by changing the director of the liquid crystal matrix. This results in a switchable polarization-sensitive surface plasmon resonance exhibiting stark differences from that of the same nanorods in isotropic fluids. The devise-scale bulk nanoparticle alignment may enable optical metamaterial mass production and control of surface plasmon resonance of nanoparticles.

Switchable diode effect in oxygen vacancy-modulated SrTiO3 single crystal

NASA Astrophysics Data System (ADS)

Pan, Xinqiang; Shuai, Yao; Wu, Chuangui; Luo, Wenbo; Sun, Xiangyu; Zeng, Huizhong; Bai, Xiaoyuan; Gong, Chaoguan; Jian, Ke; Zhang, Lu; Guo, Hongliang; Tian, Benlang; Zhang, Wanli

2017-09-01

SrTiO3 (STO) single crystal wafer was annealed in vacuum, and co-planar metal-insulator-metal structure of Pt/Ti/STO/Ti/Pt were formed by sputtering Pt/Ti electrodes onto the surface of STO after annealing. The forming-free resistive switching behavior with self-compliance property was observed in the sample. The sample showed switchable diode effect, which is explained by a simple model that redistribution of oxygen vacancies (OVs) under the external electric field results in the formation of n-n+ junction or n+-n junction (n donated n-type semiconductor; n+ donated heavily doped n-type semiconductor). The self-compliance property is also interpreted by the formation of n-n+/n+-n junction caused by the migration of the OVs under the electric field.

Switchable multiwavelength erbium-doped photonic crystal fiber ring laser based on a length of polarization-maintaining photonic crystal fiber

NASA Astrophysics Data System (ADS)

Cheng, Jianqun; Ruan, Shuangchen

2011-11-01

A switchable multi-wavelength Erbium-doped photonic crystal fiber (ED-PCF) ring laser based on a length of polarization-maintaining photonic crystal fiber(PM-PCF) is presented and demonstrated experimentally. A segment of ED-PCF is used as linear gain medium in the resonant cavity. Due to the polarization hole burning (PHB) caused by the PM-PCF and a polarization controller (PC), the laser can operate in stable dual- or triple- wavelength modes at room temperature. The optical signal-to-noise ratio (OSNR) of the laser without any wavelength-selective components is greater than 30 dB. The amplitude variations of lasing peaks in ten minutes are less than 0.26dB for two different operating modes.

Switchable single-longitudinal-mode dual-wavelength erbium-doped fiber ring laser based on one polarization-maintaining fiber Bragg grating incorporating saturable absorber and feedback fiber loop

NASA Astrophysics Data System (ADS)

Feng, Suchun; Xu, Ou; Lu, Shaohua; Ning, Tigang; Jian, Shuisheng

2009-06-01

Switchable single-longitudinal-mode (SLM) dual-wavelength erbium-doped fiber ring laser based on one polarization-maintaining fiber Bragg grating (PMFBG) is demonstrated. Due to the enhancement of the polarization hole burning (PHB) by the PMFBG, the laser can be designed to operate in stable dual-wavelength or wavelength-switching modes with a wavelength spacing of 0.336 nm at room temperature by adjusting a polarization controller (PC). The stable SLM operation is guaranteed by a compound-ring cavity and a saturable absorber (SA). The optical signal-to-noise ratio (OSNR) is over 45 dB. The amplitude variation in nearly one and half an hour is less than 0.2 dB.

A 100 mW-level single-mode switchable dual-wavelength erbium-doped fiber laser

NASA Astrophysics Data System (ADS)

Cheng, Jianqun; Zhang, Liaolin; Sharafudeen, Kaniyarakkal; Qiu, Jianrong

2013-10-01

A switchable dual-wavelength CW erbium-doped fiber laser with two cascaded fiber Bragg gratings has been proposed and demonstrated experimentally at room temperature. The laser uses a linear resonant cavity configuration incorporating a Sagnac loop with a polarization controller (PC) and can switch flexibly to output a single wavelength or dual wavelengths based on the polarization hole burning (PHB) effect. The slope efficiency and maximum output power can reach 23% and 96 mW, respectively. The two lasing peaks of the laser, with a narrow linewidth output and an optical signal-to-noise ratio of more than 50 dB, are located in the C and L bands of the optical communication window, respectively. The laser shows good stability with respect to the wavelength and output power.

Switchable multiwavelength erbium-doped photonic crystal fiber ring laser based on a length of polarization-maintaining photonic crystal fiber

NASA Astrophysics Data System (ADS)

Cheng, Jianqun; Ruan, Shuangchen

2012-03-01

A switchable multi-wavelength Erbium-doped photonic crystal fiber (ED-PCF) ring laser based on a length of polarization-maintaining photonic crystal fiber(PM-PCF) is presented and demonstrated experimentally. A segment of ED-PCF is used as linear gain medium in the resonant cavity. Due to the polarization hole burning (PHB) caused by the PM-PCF and a polarization controller (PC), the laser can operate in stable dual- or triple- wavelength modes at room temperature. The optical signal-to-noise ratio (OSNR) of the laser without any wavelength-selective components is greater than 30 dB. The amplitude variations of lasing peaks in ten minutes are less than 0.26dB for two different operating modes.

Tunable and switchable dual-wavelength dissipative soliton generation in an all-normal-dispersion Yb-doped fiber laser with birefringence fiber filter.

PubMed

Zhang, Z X; Xu, Z W; Zhang, L

2012-11-19

We report the generation of tunable single- and dual-wavelength dissipative solitons in an all-normal-dispersion mode-locked Yb-doped fiber laser, to the best of our knowledge, for the first time. Besides single-wavelength mode-locking, dual-wavelength mode-locking was achieved using an in-line birefringence fiber filter with periodic multiple passbands, which not only allows multiple wavelengths to oscillate simultaneously but also performs spectrum modulation on highly chirped dissipative pulse. Furthermore, taking advantage of the tunability of the birefringence fiber filter, wavelength tuning for both single- and dual-wavelength dissipative soliton mode-locking was realized. The dual-wavelength operation is also switchable. The all-fiber dissipative laser with flexible outputs can meet diverse application needs.

Application of a 1,1,3,3-tetramethylguanidine (TMG)/MeOH-CO2 in situ derivatization procedure for the gas chromatographic characterization of the fatty acid profile in olive oil.

PubMed

Saliu, F; Anzano, M; Franzetti, A

2015-03-01

1,1,3,3-Tetramethylguanidine (TMG), methanol and carbon dioxide were investigated as switchable polarity solvents (SPS) in the simultaneous derivatization and extraction of triacylglycerols for the gas chromatographic (GC) characterization of olive oil. Three commercial olive oils were used as test samples. Results of the developed method did not differ statistically from those provided by reference derivatization procedures. The transesterification reaction was carried out under a very mild condition, one step and in situ, and no particular matrix interferences were evidenced. The method represented the first example of the use of a switchable polarity mixture for the preparation of methyl ester derivatives of fatty acids (FAME).

Digitally switchable multi-focal lens using freeform optics.

PubMed

Wang, Xuan; Qin, Yi; Hua, Hong; Lee, Yun-Han; Wu, Shin-Tson

2018-04-16

Optical technologies offering electrically tunable optical power have found a broad range of applications, from head-mounted displays for virtual and augmented reality applications to microscopy. In this paper, we present a novel design and prototype of a digitally switchable multi-focal lens (MFL) that offers the capability of rapidly switching the optical power of the system among multiple foci. It consists of a freeform singlet and a customized programmable optical shutter array (POSA). Time-multiplexed multiple foci can be obtained by electrically controlling the POSA to switch the light path through different segments of the freeform singlet rapidly. While this method can be applied to a broad range of imaging and display systems, we experimentally demonstrate a proof-of-concept prototype for a multi-foci imaging system.

Switchable hydrophilicity solvents for lipid extraction from microalgae for biofuel production.

PubMed

Boyd, Alaina R; Champagne, Pascale; McGinn, Patrick J; MacDougall, Karen M; Melanson, Jeremy E; Jessop, Philip G

2012-08-01

A switchable hydrophilicity solvent (SHS) was studied for its effectiveness at extracting lipids from freeze-dried samples of Botryococcus braunii microalgae. The SHS N,N-dimethylcyclohexylamine extracted up to 22 wt.% crude lipid relative to the freeze-dried cell weight. The solvent was removed from the extract with water saturated with carbon dioxide at atmospheric pressure and recovered from the water upon de-carbonation of the mixture. Liquid chromatography-mass spectrometry (LC-MS) showed that the extracted lipids contained high concentrations of long chain tri-, di- and mono-acylglycerols, no phospholipids, and only 4-8% of residual solvent. Unlike extractions with conventional organic solvents, this new method requires neither distillation nor the use of volatile, flammable or chlorinated organic solvents. Copyright © 2012 Elsevier Ltd. All rights reserved.

Integrated all-optical infrared switchable plasmonic quantum cascade laser.

PubMed

Kohoutek, John; Bonakdar, Alireza; Gelfand, Ryan; Dey, Dibyendu; Nia, Iman Hassani; Fathipour, Vala; Memis, Omer Gokalp; Mohseni, Hooman

2012-05-09

We report a type of infrared switchable plasmonic quantum cascade laser, in which far field light in the midwave infrared (MWIR, 6.1 μm) is modulated by a near field interaction of light in the telecommunications wavelength (1.55 μm). To achieve this all-optical switch, we used cross-polarized bowtie antennas and a centrally located germanium nanoslab. The bowtie antenna squeezes the short wavelength light into the gap region, where the germanium is placed. The perturbation of refractive index of the germanium due to the free carrier absorption produced by short wavelength light changes the optical response of the antenna and the entire laser intensity at 6.1 μm significantly. This device shows a viable method to modulate the far field of a laser through a near field interaction.

Optical frequency switching scheme for a high-speed broadband THz measurement system based on the photomixing technique.

PubMed

Song, Hajun; Hwang, Sejin; Song, Jong-In

2017-05-15

This study presents an optical frequency switching scheme for a high-speed broadband terahertz (THz) measurement system based on the photomixing technique. The proposed system can achieve high-speed broadband THz measurements using narrow optical frequency scanning of a tunable laser source combined with a wavelength-switchable laser source. In addition, this scheme can provide a larger output power of an individual THz signal compared with that of a multi-mode THz signal generated by multiple CW laser sources. A swept-source THz tomography system implemented with a two-channel wavelength-switchable laser source achieves a reduced time for acquisition of a point spread function and a higher depth resolution in the same amount of measurement time compared with a system with a single optical source.

High-speed switchable lens enables the development of a volumetric stereoscopic display

PubMed Central

Love, Gordon D.; Hoffman, David M.; Hands, Philip J.W.; Gao, James; Kirby, Andrew K.; Banks, Martin S.

2011-01-01

Stereoscopic displays present different images to the two eyes and thereby create a compelling three-dimensional (3D) sensation. They are being developed for numerous applications including cinema, television, virtual prototyping, and medical imaging. However, stereoscopic displays cause perceptual distortions, performance decrements, and visual fatigue. These problems occur because some of the presented depth cues (i.e., perspective and binocular disparity) specify the intended 3D scene while focus cues (blur and accommodation) specify the fixed distance of the display itself. We have developed a stereoscopic display that circumvents these problems. It consists of a fast switchable lens synchronized to the display such that focus cues are nearly correct. The system has great potential for both basic vision research and display applications. PMID:19724571

Photo-switchable two-dimensional nanofluidic ionic diodes.

PubMed

Wang, Lili; Feng, Yaping; Zhou, Yi; Jia, Meijuan; Wang, Guojie; Guo, Wei; Jiang, Lei

2017-06-01

The bottom-up assembly of ion-channel-mimetic nanofluidic devices and materials with two-dimensional (2D) nano-building blocks paves a straightforward way towards the real-world applications of the novel transport phenomena on a nano- or sub-nanoscale. One immediate challenge is to provide the 2D nanofluidic systems with adaptive responsibilities and asymmetric ion transport characteristics. Herein, we introduce a facile and general strategy to provide a graphene-oxide-based 2D nanofluidic system with photo-switchable ionic current rectification (ICR). The degree of ICR can be prominently enhanced upon UV irradiation and it can be perfectly retrieved under irradiation with visible light. A maximum ICR ratio of about 48 was achieved. The smart and functional nanofluidic devices have applications in energy conversion, chemical sensing, water treatment, etc .

High quality factor, fully switchable terahertz superconducting metasurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scalari, G., E-mail: scalari@phys.ethz.ch; Maissen, C.; Faist, J.

2014-12-29

We present a complementary THz metasurface realised with Niobium thin film which displays a quality factor Q = 54 and a fully switchable behaviour as a function of the temperature. The switching behaviour and the high quality factor are due to a careful design of the metasurface aimed at maximising the ohmic losses when the Nb is above the critical temperature and minimising the radiative coupling. The superconductor allows the operation of the cavity with high Q and the use of inductive elements with a high aspect ratio. Comparison with three dimensional finite element simulations highlights the crucial role of the inductivemore » elements and of the kinetic inductance of the Cooper pairs in achieving the high quality factor and the high field enhancement.« less

Structural Insights into the Quadruplex-Duplex 3' Interface Formed from a Telomeric Repeat: A Potential Molecular Target.

PubMed

Russo Krauss, Irene; Ramaswamy, Sneha; Neidle, Stephen; Haider, Shozeb; Parkinson, Gary N

2016-02-03

We report here on an X-ray crystallographic and molecular modeling investigation into the complex 3' interface formed between putative parallel stranded G-quadruplexes and a duplex DNA sequence constructed from the human telomeric repeat sequence TTAGGG. Our crystallographic approach provides a detailed snapshot of a telomeric 3' quadruplex-duplex junction: a junction that appears to have the potential to form a unique molecular target for small molecule binding and interference with telomere-related functions. This unique target is particularly relevant as current high-affinity compounds that bind putative G-quadruplex forming sequences only rarely have a high degree of selectivity for a particular quadruplex. Here DNA junctions were assembled using different putative quadruplex-forming scaffolds linked at the 3' end to a telomeric duplex sequence and annealed to a complementary strand. We successfully generated a series of G-quadruplex-duplex containing crystals, both alone and in the presence of ligands. The structures demonstrate the formation of a parallel folded G-quadruplex and a B-form duplex DNA stacked coaxially. Most strikingly, structural data reveals the consistent formation of a TAT triad platform between the two motifs. This triad allows for a continuous stack of bases to link the quadruplex motif with the duplex region. For these crystal structures formed in the absence of ligands, the TAT triad interface occludes ligand binding at the 3' quadruplex-duplex interface, in agreement with in silico docking predictions. However, with the rearrangement of a single nucleotide, a stable pocket can be produced, thus providing an opportunity for the binding of selective molecules at the interface.

Structural and Functional Basis for an EBNA1 Hexameric Ring in Epstein-Barr Virus Episome Maintenance.

PubMed

Deakyne, Julianna S; Malecka, Kimberly A; Messick, Troy E; Lieberman, Paul M

2017-10-01

Epstein-Barr virus (EBV) establishes a stable latent infection that can persist for the life of the host. EBNA1 is required for the replication, maintenance, and segregation of the latent episome, but the structural features of EBNA1 that confer each of these functions are not completely understood. Here, we have solved the X-ray crystal structure of an EBNA1 DNA-binding domain (DBD) and discovered a novel hexameric ring oligomeric form. The oligomeric interface pivoted around residue T585 as a joint that links and stabilizes higher-order EBNA1 complexes. Substitution mutations around the interface destabilized higher-order complex formation and altered the cooperative DNA-binding properties of EBNA1. Mutations had both positive and negative effects on EBNA1-dependent DNA replication and episome maintenance with OriP. We found that one naturally occurring polymorphism in the oligomer interface (T585P) had greater cooperative DNA binding in vitro , minor defects in DNA replication, and pronounced defects in episome maintenance. The T585P mutant was compromised for binding to OriP in vivo as well as for assembling the origin recognition complex subunit 2 (ORC2) and trimethylated histone 3 lysine 4 (H3K4me3) at OriP. The T585P mutant was also compromised for forming stable subnuclear foci in living cells. These findings reveal a novel oligomeric structure of EBNA1 with an interface subject to naturally occurring polymorphisms that modulate EBNA1 functional properties. We propose that EBNA1 dimers can assemble into higher-order oligomeric structures important for diverse functions of EBNA1. IMPORTANCE Epstein-Barr virus is a human gammaherpesvirus that is causally associated with various cancers. Carcinogenic properties are linked to the ability of the virus to persist in the latent form for the lifetime of the host. EBNA1 is a sequence-specific DNA-binding protein that is consistently expressed in EBV tumors and is the only viral protein required to maintain the viral episome during latency. The structural and biochemical mechanisms by which EBNA1 allows the long-term persistence of the EBV genome are currently unclear. Here, we have solved the crystal structure of an EBNA1 hexameric ring and characterized key residues in the interface required for higher-order complex formation and long-term plasmid maintenance. Copyright © 2017 American Society for Microbiology.

Development and characterization of amorphous acrylate networks for use as switchable adhesives inspired from shapememory behavior

NASA Astrophysics Data System (ADS)

Lakhera, Nishant

Several types of insects and animals such as spiders and geckos are inherently able to climb along vertical walls and ceilings. This remarkable switchable adhesive behavior has been attributed to the fibrillar structures on their feet, with size ranging from few nanometers to a few micrometers depending on the species. Several studies have attempted to create synthetic micro-patterned surfaces trying to imitate this adhesive behavior seen in nature. The experimental procedures are scattered, with sole purpose of trying to increase adhesion, thereby making direct comparison between studies very difficult. There is a lack of fundamental understanding on adhesion of patterned surfaces. The influence of critical parameters like material modulus, glass transition temperature, viscoelastic effects, temperature and water absorption on adhesion is not fully explored and characterized. These parameters are expected to have a decisive influence on adhesion behavior of the polymer. Previous studies have utilized conventional "off-the-shelf" materials like epoxy, polyurethanes etc. It is however, impossible to change the material modulus, glass transition temperature etc. of these polymer systems without changing the base constituents itself, thereby explaining the gaps in the current research landscape. The purpose of this study was to use acrylate shape-memory polymers (SMPs) for their ability to be tailored to specific mechanical properties by control of polymer chemistry, without changing the base constituents. Polymer networks with tailorable glass transition, material modulus, water absorption etc. were developed and adhesion studies were performed to investigate the influence of temperature, viscoelastic effects, material modulus on the adhesion behavior of flat acrylate polymer surfaces. The knowledge base gained from these studies was utilized to better understand the fundamental mechanisms associated with adhesion behavior of patterned acrylate surfaces. Thermally induced switchable adhesion and water induced switchable adhesion of patterned acrylate surfaces was investigated. The viscoelastic energy dissipation occurring during the detachment phase was shown to dramatically increase adhesion under both thermally induced and water induced conditions. This effect was most pre-dominant at the glass transition temperature of the material. Increase in pre-load force and unloading velocity were also shown to increase the adhesive capability of the patterned acrylate SMPs.

Embedded CMOS basecalling for nanopore DNA sequencing.

PubMed

Chengjie Wang; Junli Zheng; Magierowski, Sebastian; Ghafar-Zadeh, Ebrahim

2016-08-01

DNA sequencing based on nanopore sensors is now entering the marketplace. The ability to interface this technology to established CMOS microelectronics promises significant improvements in functionality and miniaturization. Among the key functions to benefit from this interface will be basecalling, the conversion of raw electronic molecular signatures to nucleotide sequence predictions. This paper presents the design and performance potential of custom CMOS base-callers embedded alongside nanopore sensors. A basecalliing architecture implemented in 32-nm technology is discussed with the ability to process the equivalent of 20 human genomes per day in real-time at a power density of 5 W/cm2 assuming a 3-mer nanopore sensor.

ESTminer: a Web interface for mining EST contig and cluster databases.

PubMed

Huang, Yecheng; Pumphrey, Janie; Gingle, Alan R

2005-03-01

ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster datasets. The Web interface contains a query frame that allows the selection of contigs/clusters with specific cDNA library makeup or a threshold number of members. The results are displayed as color-coded tree nodes, where the color indicates the fractional size of each cDNA library component. The nodes are expandable, revealing library statistics as well as EST or contig members, with links to sequence data, GenBank records or user configurable links. Also, the interface allows 'queries within queries' where the result set of a query is further filtered by the subsequent query. ESTminer is implemented in Java/JSP and the package, including MySQL and Oracle schema creation scripts, is available from http://cggc.agtec.uga.edu/Data/download.asp agingle@uga.edu.

Universal computing by DNA origami robots in a living animal

PubMed Central

Levner, Daniel; Ittah, Shmulik; Abu-Horowitz, Almogit; Bachelet, Ido

2014-01-01

Biological systems are collections of discrete molecular objects that move around and collide with each other. Cells carry out elaborate processes by precisely controlling these collisions, but developing artificial machines that can interface with and control such interactions remains a significant challenge. DNA is a natural substrate for computing and has been used to implement a diverse set of mathematical problems1-3, logic circuits4-6 and robotics7-9. The molecule also naturally interfaces with living systems, and different forms of DNA-based biocomputing have previously been demonstrated10-13. Here we show that DNA origami14-16 can be used to fabricate nanoscale robots that are capable of dynamically interacting with each other17-18 in a living animal. The interactions generate logical outputs, which are relayed to switch molecular payloads on or off. As a proof-of-principle, we use the system to create architectures that emulate various logic gates (AND, OR, XOR, NAND, NOT, CNOT, and a half adder). Following an ex vivo prototyping phase, we successfully employed the DNA origami robots in living cockroaches (Blaberus discoidalis) to control a molecule that targets the cells of the animal. PMID:24705510

DyNAVacS: an integrative tool for optimized DNA vaccine design.

PubMed

Harish, Nagarajan; Gupta, Rekha; Agarwal, Parul; Scaria, Vinod; Pillai, Beena

2006-07-01

DNA vaccines have slowly emerged as keystones in preventive immunology due to their versatility in inducing both cell-mediated as well as humoral immune responses. The design of an efficient DNA vaccine, involves choice of a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses and providing additional sequence signals for efficient translation. DyNAVacS is a web-based tool created for rapid and easy design of DNA vaccines. It follows a step-wise design flow, which guides the user through the various sequential steps in the design of the vaccine. Further, it allows restriction enzyme mapping, design of primers spanning user specified sequences and provides information regarding the vectors currently used for generation of DNA vaccines. The web version uses Apache HTTP server. The interface was written in HTML and utilizes the Common Gateway Interface scripts written in PERL for functionality. DyNAVacS is an integrated tool consisting of user-friendly programs, which require minimal information from the user. The software is available free of cost, as a web based application at URL: http://miracle.igib.res.in/dynavac/.

Crystal Structure of the Vaccinia Virus DNA Polymerase Holoenzyme Subunit D4 in Complex with the A20 N-Terminal Domain

PubMed Central

Contesto-Richefeu, Céline; Tarbouriech, Nicolas; Brazzolotto, Xavier; Betzi, Stéphane; Morelli, Xavier; Burmeister, Wim P.; Iseni, Frédéric

2014-01-01

Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase E9, the uracil-DNA glycosylase D4 and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase co-factor whose function is essential for processive DNA synthesis. Genetic and biochemical data have established that residues located in the N-terminus of A20 are critical for binding to D4. However, no information regarding the residues of D4 involved in A20 binding is yet available. We expressed and purified the complex formed by D4 and the first 50 amino acids of A20 (D4/A201–50). We showed that whereas D4 forms homodimers in solution when expressed alone, D4/A201–50 clearly behaves as a heterodimer. The crystal structure of D4/A201–50 solved at 1.85 Å resolution reveals that the D4/A20 interface (including residues 167 to 180 and 191 to 206 of D4) partially overlaps the previously described D4/D4 dimer interface. A201–50 binding to D4 is mediated by an α-helical domain with important leucine residues located at the very N-terminal end of A20 and a second stretch of residues containing Trp43 involved in stacking interactions with Arg167 and Pro173 of D4. Point mutations of the latter residues disturb D4/A201–50 formation and reduce significantly thermal stability of the complex. Interestingly, small molecule docking with anti-poxvirus inhibitors selected to interfere with D4/A20 binding could reproduce several key features of the D4/A201–50 interaction. Finally, we propose a model of D4/A201–50 in complex with DNA and discuss a number of mutants described in the literature, which affect DNA synthesis. Overall, our data give new insights into the assembly of the poxvirus DNA polymerase cofactor and may be useful for the design and rational improvement of antivirals targeting the D4/A20 interface. PMID:24603707

Thermally switchable meta-material absorber involving vanadium dioxide semiconductor-metal transition for thermo photovoltaic conversion

NASA Astrophysics Data System (ADS)

Bendelala, Fathi; Cheknane, Ali; Hilal, Hikmat S.

2018-01-01

A new switchable absorber design using meta-materials for thermo photovoltaic applications is proposed here. Conventional absorbents are normally non-adjustable with narrow band-widths and polarization-dependence. The present study describes an alternative infrared absorber structure with tunable characteristics. The absorber is based on VO2 which exhibits transition from semiconductor to metallic conductor by thermal effect. With this design, the results show that wide-band absorption can be achieved. The absorption bandwidth can be improved from 15.94 to 36.75 THz. With 40.42% relative shift in the peak frequency, a maximum absorption efficiency of 99% can be achieved. This structure design is polarization-independent of normal incident radiations, and may accommodate radiations from wide oblique angles. These new features make the new thermally adjustable absorber potentially useful in thermo-photovoltaic conversion devices.

Reversible hydrogen storage using CO2 and a proton-switchable iridium catalyst in aqueous media under mild temperatures and pressures.

PubMed

Hull, Jonathan F; Himeda, Yuichiro; Wang, Wan-Hui; Hashiguchi, Brian; Periana, Roy; Szalda, David J; Muckerman, James T; Fujita, Etsuko

2012-03-18

Green plants convert CO(2) to sugar for energy storage via photosynthesis. We report a novel catalyst that uses CO(2) and hydrogen to store energy in formic acid. Using a homogeneous iridium catalyst with a proton-responsive ligand, we show the first reversible and recyclable hydrogen storage system that operates under mild conditions using CO(2), formate and formic acid. This system is energy-efficient and green because it operates near ambient conditions, uses water as a solvent, produces high-pressure CO-free hydrogen, and uses pH to control hydrogen production or consumption. The extraordinary and switchable catalytic activity is attributed to the multifunctional ligand, which acts as a proton-relay and strong π-donor, and is rationalized by theoretical and experimental studies.

Thermoresponsive electrospun fibers for water harvesting applications

NASA Astrophysics Data System (ADS)

Thakur, Neha; Baji, Avinash; Ranganath, Anupama Sargur

2018-03-01

Temperature triggered switchable cellulose acetate-poly(N-isopropylacrylamide) (CA-PNIPAM) core-shell and blend nanofibers are fabricated for controlled moisture harvesting applications. Core-shell fibers are fabricated using a co-axial electrospinning setup whereas the conventional electrospinning setup is employed for fabricating the blend fibers. Investigation of their wettability behaviour demonstrated that the blend fibers are superhydrophilic whereas the core-shell fibers are hydrophilic at ambient temperature. Furthermore, both the samples have an ability to switch between the two states viz. hydrophilic to hydrophobic state based on thermal stimulus. The core-shell fibers are shown to have higher moisture sorption ability compared to the blend fibers. This study investigates the mechanism behind the switchable wettability behaviour of the core-shell fibers and demonstrates the crucial role played by the functional groups present on the surface layer of fibers in governing their moisture collection efficiency.

Perching and takeoff of a robotic insect on overhangs using switchable electrostatic adhesion.

PubMed

Graule, M A; Chirarattananon, P; Fuller, S B; Jafferis, N T; Ma, K Y; Spenko, M; Kornbluh, R; Wood, R J

2016-05-20

For aerial robots, maintaining a high vantage point for an extended time is crucial in many applications. However, available on-board power and mechanical fatigue constrain their flight time, especially for smaller, battery-powered aircraft. Perching on elevated structures is a biologically inspired approach to overcome these limitations. Previous perching robots have required specific material properties for the landing sites, such as surface asperities for spines, or ferromagnetism. We describe a switchable electroadhesive that enables controlled perching and detachment on nearly any material while requiring approximately three orders of magnitude less power than required to sustain flight. These electroadhesives are designed, characterized, and used to demonstrate a flying robotic insect able to robustly perch on a wide range of materials, including glass, wood, and a natural leaf. Copyright © 2016, American Association for the Advancement of Science.

Electrical Switchability and Dry-Wash Durability of Conductive Textiles

PubMed Central

Wu, Bangting; Zhang, Bowu; Wu, Jingxia; Wang, Ziqiang; Ma, Hongjuan; Yu, Ming; Li, Linfan; Li, Jingye

2015-01-01

There is growing interest in the area of conductive textiles in the scientific and industrial community. Herein, we successfully prepared a conductive textile via covalently grafting polyaniline (PANI) onto cotton by a multi-step treatment process. The conductivity of the resultant fabric could be tuned by immersing in water having different pH values. The conductive and insulating properties of the textile could be conveniently switched by alternately immersing in acidic and alkaline bath solutions. Most importantly, the resultant conductive fabrics were able to withstand 40 simulated dry-wash cycles, with almost no decay in the electrical conductivity, indicating their excellent dry-wash durability. The present strategy for fabricating conductive fabrics with excellent switchability of electrical properties and dry-wash durability is expected to provide inspiration for the production of multifunctional conductive textiles for use in hash or sensitive conditions. PMID:26066704

Design of protein switches based on an ensemble model of allostery.

PubMed

Choi, Jay H; Laurent, Abigail H; Hilser, Vincent J; Ostermeier, Marc

2015-04-22

Switchable proteins that can be regulated through exogenous or endogenous inputs have a broad range of biotechnological and biomedical applications. Here we describe the design of switchable enzymes based on an ensemble allosteric model. First, we insert an enzyme domain into an effector-binding domain such that both domains remain functionally intact. Second, we induce the fusion to behave as a switch through the introduction of conditional conformational flexibility designed to increase the conformational entropy of the enzyme domain in a temperature- or pH-dependent fashion. We confirm the switching behaviour in vitro and in vivo. Structural and thermodynamic studies support the hypothesis that switching result from an increase in conformational entropy of the enzyme domain in the absence of effector. These results support the ensemble model of allostery and embody a strategy for the design of protein switches.

Crack-Free, Soft Wrinkles Enable Switchable Anisotropic Wetting.

PubMed

Rhee, Dongjoon; Lee, Won-Kyu; Odom, Teri W

2017-06-01

Soft skin layers on elastomeric substrates are demonstrated to support mechano-responsive wrinkle patterns that do not exhibit cracking under applied strain. Soft fluoropolymer skin layers on pre-strained poly(dimethylsiloxane) slabs achieved crack-free surface wrinkling at high strain regimes not possible by using conventional stiff skin layers. A side-by-side comparison between the soft and hard skin layers after multiple cycles of stretching and releasing revealed that the soft skin layer enabled dynamic control over wrinkle topography without cracks or delamination. We systematically characterized the evolution of wrinkle wavelength, amplitude, and orientation as a function of tensile strain to resolve the crack-free structural transformation. We demonstrated that wrinkled surfaces can guide water spreading along wrinkle orientation, and hence switchable, anisotropic wetting was realized. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterization of an active metasurface using terahertz ellipsometry

DOE PAGES

Karl, Nicholas; Heimbeck, Martin S.; Everitt, Henry O.; ...

2017-11-06

Switchable metasurfaces fabricated on a doped epi-layer have become an important platform for developing techniques to control terahertz (THz) radiation, as a DC bias can modulate the transmission characteristics of the metasurface. To model and understand this performance in new device configurations accurately, a quantitative understanding of the bias-dependent surface characteristics is required. In this work, we perform THz variable angle spectroscopic ellipsometry on a switchable metasurface as a function of DC bias. By comparing these data with numerical simulations, we extract a model for the response of the metasurface at any bias value. Using this model, we predict amore » giant bias-induced phase modulation in a guided wave configuration. Lastly, these predictions are in qualitative agreement with our measurements, offering a route to efficient modulation of THz signals.« less

Chromogenic switchable glazing: Towards the development of the smart window

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lampert, C.M.

1995-06-01

The science and technology of chromogenic materials for switchable glazings in building applications is discussed. These glazings can be used for dynamic control of solar and visible energy. Currently many researchers and engineers are involved with the development of products in this field. A summary of activities in Japan, Europe, Australia, USA and Canada is made. The activities of the International Energy Agency are included. Both non-electrically activated and electrically activated glazings are discussed. Technologies covered in the first category are photochromics, and thermochromics and thermotropics. A discussion of electrically activated chromogenic glazings includes dispersed liquid crystals, dispersed particles andmore » electrochromics. A selection of device structures and performance characteristics are compared. A discussion of transparent conductors is presented. Technical issues concerning large-area development of smart windows are discussed.« less

Utilizing stretch-tunable thermochromic elastomeric opal films as novel reversible switchable photonic materials.

PubMed

Schäfer, Christian G; Lederle, Christina; Zentel, Kristina; Stühn, Bernd; Gallei, Markus

2014-11-01

In this work, the preparation of highly thermoresponsive and fully reversible stretch-tunable elastomeric opal films featuring switchable structural colors is reported. Novel particle architectures based on poly(diethylene glycol methylether methacrylate-co-ethyl acrylate) (PDEGMEMA-co-PEA) as shell polymer are synthesized via seeded and stepwise emulsion polymerization protocols. The use of DEGMEMA as comonomer and herein established synthetic strategies leads to monodisperse soft shell particles, which can be directly processed to opal films by using the feasible melt-shear organization technique. Subsequent UV crosslinking strategies open access to mechanically stable and homogeneous elastomeric opal films. The structural colors of the opal films feature mechano- and thermoresponsiveness, which is found to be fully reversible. Optical characterization shows that the combination of both stimuli provokes a photonic bandgap shift of more than 50 nm from 560 nm in the stretched state to 611 nm in the fully swollen state. In addition, versatile colorful patterns onto the colloidal crystal structure are produced by spatial UV-induced crosslinking by using a photomask. This facile approach enables the generation of spatially cross-linked switchable opal films with fascinating optical properties. Herein described strategies for the preparation of PDEGMEMA-containing colloidal architectures, application of the melt-shear ordering technique, and patterned crosslinking of the final opal films open access to novel stimuli-responsive colloidal crystal films, which are expected to be promising materials in the field of security and sensing applications. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A DNA aptamer recognising a malaria protein biomarker can function as part of a DNA origami assembly

PubMed Central

Godonoga, Maia; Lin, Ting-Yu; Oshima, Azusa; Sumitomo, Koji; Tang, Marco S. L.; Cheung, Yee-Wai; Kinghorn, Andrew B.; Dirkzwager, Roderick M.; Zhou, Cunshan; Kuzuya, Akinori; Tanner, Julian A.; Heddle, Jonathan G.

2016-01-01

DNA aptamers have potential for disease diagnosis and as therapeutics, particularly when interfaced with programmable molecular technology. Here we have combined DNA aptamers specific for the malaria biomarker Plasmodium falciparum lactate dehydrogenase (PfLDH) with a DNA origami scaffold. Twelve aptamers that recognise PfLDH were integrated into a rectangular DNA origami and atomic force microscopy demonstrated that the incorporated aptamers preserve their ability to specifically bind target protein. Captured PfLDH retained enzymatic activity and protein-aptamer binding was observed dynamically using high-speed AFM. This work demonstrates the ability of DNA aptamers to recognise a malaria biomarker whilst being integrated within a supramolecular DNA scaffold, opening new possibilities for malaria diagnostic approaches based on DNA nanotechnology. PMID:26891622

Asymmetric Assembly of Merkel Cell Polyomavirus Large T-Antigen Origin Binding Domains at the Viral Origin

DOE Office of Scientific and Technical Information (OSTI.GOV)

C Harrison; G Meinke; H Kwun

2011-12-31

The double-stranded DNA polyomavirus Merkel cell polyomavirus (MCV) causes Merkel cell carcinoma, an aggressive but rare human skin cancer that most often affects immunosuppressed and elderly persons. As in other polyomaviruses, the large T-antigen of MCV recognizes the viral origin of replication by binding repeating G(A/G)GGC pentamers. The spacing, number, orientation, and necessity of repeats for viral replication differ, however, from other family members such as SV40 and murine polyomavirus. We report here the 2.9 {angstrom} crystal structure of the MCV large T-antigen origin binding domain (OBD) in complex with a DNA fragment from the MCV origin of replication. Consistentmore » with replication data showing that three of the G(A/G)GGC-like binding sites near the center of the origin are required for replication, the crystal structure contains three copies of the OBD. This stoichiometry was verified using isothermal titration calorimetry. The affinity for G(A/G)GGC-containing double-stranded DNA was found to be {approx} 740 nM, approximately 8-fold weaker than the equivalent domain in SV40 for the analogous region of the SV40 origin. The difference in affinity is partially attributable to DNA-binding residue Lys331 (Arg154 in SV40). In contrast to SV40, a small protein-protein interface is observed between MCV OBDs when bound to the central region of the origin. This protein-protein interface is reminiscent of that seen in bovine papilloma virus E1 protein. Mutational analysis indicates, however, that this interface contributes little to DNA binding energy.« less

Kinetics and Thermodynamics of Watson-Crick Base Pairing Driven DNA Origami Dimerization.

PubMed

Zenk, John; Tuntivate, Chanon; Schulman, Rebecca

2016-03-16

We investigate the kinetics and thermodynamics of DNA origami dimerization using flat rectangle origami components and different architectures of Watson-Crick complementary single-stranded DNA ("sticky end") linking strategies. We systematically vary the number of linkers, the length of the sticky ends on the linker, and linker architecture and measure the corresponding yields as well as forward and reverse reaction rate constants through fluorescence quenching assays. Yields were further verified using atomic force microscopy. We calculate values of H° and ΔS° for various interface designs and find nonlinear van't Hoff behavior, best described by two linear equations, suggesting distinct regimes of dimerization between those with and those without well-formed interfaces. We find that self-assembly reactions can be tuned by manipulating the interface architecture without suffering a loss in yield, even when yield is high, ∼75-80%. We show that the second-order forward reaction rate constant (k(on)) depends on both linker architecture and number of linkers used, with typical values on the order of 10(5)-10(6) (M·s)(-1), values that are similar to those of bimolecular association of small, complementary DNA strands. The k(on) values are generally non-Arrhenius, tending to increase with decreasing temperature. Finally, we use kinetic and thermodynamic information about the optimal linking architecture to extend the system to an infinite, two-component repeating lattice system and show that we can form micron-sized lattices, with well-formed structures up to 8 μm(2).

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE Office of Scientific and Technical Information (OSTI.GOV)

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE PAGES

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

A novel single-stranded DNA detection method based on organic semiconductor heterojunction

NASA Astrophysics Data System (ADS)

Gu, Wen; Liu, Hongbo; Zhang, Xia; Zhang, Hao; Chen, Xiong; Wang, Jun

2016-12-01

We demonstrate a novel DNA detection method with low-cost and disposable advantages by utilizing F16CuPc/CuPc planar organic heterojunction device. Single-stranded DNA (ssDNA) molecules have been well immobilized on the surface of CuPc film observed by atomic force microscopy, producing an obvious electrical response of the device. The conductivity of the organic heterojunction film was significantly increased by ssDNA immobilization because ssDNA molecules brought additional positive charges at heterojunction interface. Furthermore, the thickness dependence of CuPc upper layer on the electrical response was studied to optimize the sensitivity. This study will be helpful for the development of organic heterojunction based biosensors.

DNA materials: bridging nanotechnology and biotechnology.

PubMed

Yang, Dayong; Hartman, Mark R; Derrien, Thomas L; Hamada, Shogo; An, Duo; Yancey, Kenneth G; Cheng, Ru; Ma, Minglin; Luo, Dan

2014-06-17

CONSPECTUS: In recent decades, DNA has taken on an assortment of diverse roles, not only as the central genetic molecule in biological systems but also as a generic material for nanoscale engineering. DNA possesses many exceptional properties, including its biological function, biocompatibility, molecular recognition ability, and nanoscale controllability. Taking advantage of these unique attributes, a variety of DNA materials have been created with properties derived both from the biological functions and from the structural characteristics of DNA molecules. These novel DNA materials provide a natural bridge between nanotechnology and biotechnology, leading to far-ranging real-world applications. In this Account, we describe our work on the design and construction of DNA materials. Based on the role of DNA in the construction, we categorize DNA materials into two classes: substrate and linker. As a substrate, DNA interfaces with enzymes in biochemical reactions, making use of molecular biology's "enzymatic toolkit". For example, employing DNA as a substrate, we utilized enzymatic ligation to prepare the first bulk hydrogel made entirely of DNA. Using this DNA hydrogel as a structural scaffold, we created a protein-producing DNA hydrogel via linking plasmid DNA onto the hydrogel matrix through enzymatic ligation. Furthermore, to fully make use of the advantages of both DNA materials and polymerase chain reaction (PCR), we prepared thermostable branched DNA that could remain intact even under denaturing conditions, allowing for their use as modular primers for PCR. Moreover, via enzymatic polymerization, we have recently constructed a physical DNA hydrogel with unique internal structure and mechanical properties. As a linker, we have used DNA to interface with other functional moieties, including gold nanoparticles, clay minerals, proteins, and lipids, allowing for hybrid materials with unique properties for desired applications. For example, we recently designed a DNA-protein conjugate as a universal adapter for protein detection. We further demonstrate a diverse assortment of applications for these DNA materials including diagnostics, protein production, controlled drug release systems, the exploration of life evolution, and plasmonics. Although DNA has shown great potential as both substrate and linker in the construction of DNA materials, it is still in the initial stages of becoming a well-established and widely used material. Important challenges include the ease of design and fabrication, scaling-up, and minimizing cost. We envision that DNA materials will continue to bridge the gap between nanotechnology and biotechnology and will ultimately be employed for many real-world applications.

Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications.

PubMed

Henrich, Oliver; Gutiérrez Fosado, Yair Augusto; Curk, Tine; Ouldridge, Thomas E

2018-05-10

During the last decade coarse-grained nucleotide models have emerged that allow us to study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yao, Juan; Zhou, Yufan; Sui, Xiao

Switchable ionic liquids (SWIL) play an important role in green chemistry. Due to the nature of SWIL chemistry, such as air sensitivity and pressure and temperature dependence, it is difficult to characterize SWIL using vacuum-based surface techniques. The fully CO2 loaded and none-loaded DBU and hexanol mixtures, a SWIL system, were analyzed in situ by time-of-flight secondary ion mass spectrometry (ToF-SIMS) coupled with the System for Analysis at the Liquid Vacuum Interface (SALVI), respectively. The DBU/Hexanol/CO2 SWIL was injected into the microchannel before liquid SIMS analysis. Bi3+ primary ion beam was used. The positive and negative spectra of the SWILmore » chemical components are presented. The characteristic peaks m/z 153 (reduced DBU) in the positive mode and m/z 101 (oxidized hexanol) in negative mode were observed. In addition, ion pair peaks including m/z 253, 319, 305, 451 in the positive mode and m/z 145, 223, 257 in the negative mode are first observed using this approach. These results demonstrate that the SALVI microfluidic reactor enables the vacuum-based surface technique (i.e., ToF-SIMS) for in situ characterization of challenging liquid samples such as ionic liquids.« less

A universal DNA-based protein detection system.

PubMed

Tran, Thua N N; Cui, Jinhui; Hartman, Mark R; Peng, Songming; Funabashi, Hisakage; Duan, Faping; Yang, Dayong; March, John C; Lis, John T; Cui, Haixin; Luo, Dan

2013-09-25

Protein immune detection requires secondary antibodies which must be carefully selected in order to avoid interspecies cross-reactivity, and is therefore restricted by the limited availability of primary/secondary antibody pairs. Here we present a versatile DNA-based protein detection system using a universal adapter to interface between IgG antibodies and DNA-modified reporter molecules. As a demonstration of this capability, we successfully used DNA nano-barcodes, quantum dots, and horseradish peroxidase enzyme to detect multiple proteins using our DNA-based labeling system. Our system not only eliminates secondary antibodies but also serves as a novel method platform for protein detection with modularity, high capacity, and multiplexed capability.

A Universal DNA-Based Protein Detection System

PubMed Central

Tran, Thua N. N.; Cui, Jinhui; Hartman, Mark R.; Peng, Songming; Funabashi, Hisakage; Duan, Faping; Yang, Dayong; March, John C.; Lis, John T.; Cui, Haixin; Luo, Dan

2014-01-01

Protein immune detection requires secondary antibodies which must be carefully selected in order to avoid interspecies cross-reactivity, and is therefore restricted by the limited availability of primary/secondary antibody pairs. Here we present a versatile DNA-based protein detection system using a universal adapter to interface between IgG antibodies and DNA-modified reporter molecules. As a demonstration of this capability, we successfully used DNA nano-barcodes, quantum dots, and horseradish peroxidase enzyme to detect multiple proteins using our DNA-based labeling system. Our system not only eliminates secondary antibodies but also serves as a novel method platform for protein detection with modularity, high capacity, and multiplexed capability. PMID:23978265

Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution.

PubMed

Chen, Luan; Shi, Ke; Yin, Zhiqi; Aihara, Hideki

2013-01-07

Holliday junction (HJ) resolvases are structure-specific endonucleases that cleave four-way DNA junctions (HJs) generated during DNA recombination and repair. Bacterial RuvC, a prototypical HJ resolvase, functions as homodimer and nicks DNA strands precisely across the junction point. To gain insights into the mechanisms underlying symmetrical strand cleavages by RuvC, we performed crystallographic and biochemical analyses of RuvC from Thermus thermophilus (T.th. RuvC). The crystal structure of T.th. RuvC shows an overall protein fold similar to that of Escherichia coli RuvC, but T.th. RuvC has a more tightly associated dimer interface possibly reflecting its thermostability. The binding mode of a HJ-DNA substrate can be inferred from the shape/charge complementarity between the T.th. RuvC dimer and HJ-DNA, as well as positions of sulfate ions bound on the protein surface. Unexpectedly, the structure of T.th. RuvC homodimer refined at 1.28 Å resolution shows distinct asymmetry near the dimer interface, in the region harboring catalytically important aromatic residues. The observation suggests that the T.th. RuvC homodimer interconverts between two asymmetric conformations, with alternating subunits switched on for DNA strand cleavage. This model provides a structural basis for the 'nick-counter-nick' mechanism in HJ resolution, a mode of HJ processing shared by prokaryotic and eukaryotic HJ resolvases.

The crystal structure of the Sox4 HMG domain-DNA complex suggests a mechanism for positional interdependence in DNA recognition.

PubMed

Jauch, Ralf; Ng, Calista K L; Narasimhan, Kamesh; Kolatkar, Prasanna R

2012-04-01

It has recently been proposed that the sequence preferences of DNA-binding TFs (transcription factors) can be well described by models that include the positional interdependence of the nucleotides of the target sites. Such binding models allow for multiple motifs to be invoked, such as principal and secondary motifs differing at two or more nucleotide positions. However, the structural mechanisms underlying the accommodation of such variant motifs by TFs remain elusive. In the present study we examine the crystal structure of the HMG (high-mobility group) domain of Sox4 [Sry (sex-determining region on the Y chromosome)-related HMG box 4] bound to DNA. By comparing this structure with previously solved structures of Sox17 and Sox2, we observed subtle conformational differences at the DNA-binding interface. Furthermore, using quantitative electrophoretic mobility-shift assays we validated the positional interdependence of two nucleotides and the presence of a secondary Sox motif in the affinity landscape of Sox4. These results suggest that a concerted rearrangement of two interface amino acids enables Sox4 to accommodate primary and secondary motifs. The structural adaptations lead to altered dinucleotide preferences that mutually reinforce each other. These analyses underline the complexity of the DNA recognition by TFs and provide an experimental validation for the conceptual framework of positional interdependence and secondary binding motifs.

Superphobicity/philicity Janus Fabrics with Switchable, Spontaneous, Directional Transport Ability to Water and Oil Fluids

PubMed Central

Zhou, Hua; Wang, Hongxia; Niu, Haitao; Lin, Tong

2013-01-01

Herein we demonstrate that switchable, spontaneous, directional-transport ability to both water and oil fluids can be created on fabric materials through wet-chemistry coating and successive UV irradiation treatment. When the fabric showed directional transport to a liquid, it prevented liquids of higher surface tension from penetration, but allowed liquids of lower surface tension to permeate, from either side. The directional transport ability can be switched from one fluid to another simply by heating the fabric at an elevated temperature and then re-irradiating the fabric with UV light for required period of time. By attaching liquid drops vertically upwards to a horizontally-laid fabric, we further demonstrated that this novel directional fluid transport was an automatic process driven by surface property alone, irrespective of gravity's effect. This novel fabric may be useful for development of “smart” textiles and functional membranes for various applications. PMID:24129357

Switchable in-line monitor for multi-dimensional multiplexed photonic integrated circuit.

PubMed

Chen, Guanyu; Yu, Yu; Ye, Mengyuan; Zhang, Xinliang

2016-06-27

A flexible monitor suitable for the discrimination of on-chip transmitted mode division multiplexed (MDM) and wavelength division multiplexed (WDM) signals is proposed and fabricated. By selectively extracting part of the incoming signals through the tunable wavelength and mode dependent drop filter, the in-line and switchable monitor can discriminate the wavelength, mode and power information of the transmitted signals. Being different from a conventional mode and wavelength demultiplexer, the monitor is specifically designed to ensure a flexible in-line monitoring. For demonstration, three mode and three wavelength multiplexed signals are successfully processed. Assisted by the integrated photodetectors (PDs), both the measured photo currents and eye diagrams validate the performance of the proposed device. The bit error ratio (BER) measurement results show less than 0.4 dB power penalty between different modes and ~2 dB power penalty for single wavelength and WDM cases under 10^-9 BER level.

2D-3D switchable display based on a passive polymeric lenticular lens array and electrically suppressed ferroelectric liquid crystal.

PubMed

Shi, Liangyu; Srivastava, Abhishek Kumar; Wai Tam, Alwin Ming; Chigrinov, Vladimir Grigorievich; Kwok, Hoi Sing

2017-09-01

We reveal a 2D-3D switchable lens unit that is based on a polarization-sensitive microlens array and a polarization selector unit made of an electrically suppressed helix ferroelectric liquid crystal (ESHFLC) cell. The ESHFLCs offer a high contrast ratio (∼10k∶1) between the crossed polarizers at a low applied electric field (∼1.7  V/μm) with a small switching time (<50  μs). A special driving scheme, to switch between a 2D and 3D mode, has been developed to avoid unwanted issues related to DC accumulation in the ferroelectric liquid crystal without affecting its optical quality. The proposed lens unit is characterized by low power consumption, ultrafast response, and 3D crosstalk <5%, and can therefore find application in TVs, cell phones, etc.

Microsecond switchable thermal antenna

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ben-Abdallah, Philippe, E-mail: pba@institutoptique.fr; Benisty, Henri; Besbes, Mondher

2014-07-21

We propose a thermal antenna that can be actively switched on and off at the microsecond scale by means of a phase transition of a metal-insulator material, the vanadium dioxide (VO{sub 2}). This thermal source is made of a periodically patterned tunable VO{sub 2} nanolayer, which support a surface phonon-polariton in the infrared range in their crystalline phase. Using electrodes properly registered with respect to the pattern, the VO{sub 2} phase transition can be locally triggered by ohmic heating so that the surface phonon-polariton can be diffracted by the induced grating, producing a highly directional thermal emission. Conversely, when heatingmore » less, the VO{sub 2} layers cool down below the transition temperature, the surface phonon-polariton cannot be diffracted anymore so that thermal emission is inhibited. This switchable antenna could find broad applications in the domain of active thermal coatings or in those of infrared spectroscopy and sensing.« less

An Electrically Switchable Metal-Organic Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fernandez, CA; Martin, PC; Schaef, T

2014-08-19

Crystalline metal organic framework (MOF) materials containing interconnected porosity can be chemically modified to promote stimulus-driven (light, magnetic or electric fields) structural transformations that can be used in a number of devices. Innovative research strategies are now focused on understanding the role of chemical bond manipulation to reversibly alter the free volume in such structures of critical importance for electro-catalysis, molecular electronics, energy storage technologies, sensor devices and smart membranes. In this letter, we study the mechanism for which an electrically switchable MOF composed of Cu(TCNQ) (TCNQ = 7,7,8,8-tetracyanoquinodimethane) transitions from a high-resistance state to a conducting state in amore » reversible fashion by an applied potential. The actual mechanism for this reversible electrical switching is still not understood even though a number of reports are available describing the application of electric-field-induced switching of Cu(TCNQ) in device fabrication.« less

An Electrically Switchable Metal-Organic Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fernandez, Carlos A.; Martin, Paul F.; Schaef, Herbert T.

2014-08-19

Crystalline metal organic framework (MOF) materials containing interconnected porosity can be chemically modified to promote stimulus-driven (light, magnetic or electric fields) structural transformations that can be used in a number of devices. Innovative research strategies are now focused on understanding the role of chemical bond manipulation to reversibly alter the free volume in such structures of critical importance for electro-catalysis, molecular electronics, energy storage technologies, sensor devices and smart membranes. In this letter, we study the mechanism for which an electrically switchable MOF composed of Cu(TCNQ) (TCNQ 5 7,7,8,8-tetracyanoquinodimethane) transitions from a high-resistance state to a conducting state in amore » reversible fashion by an applied potential. The actual mechanism for this reversible electrical switching is still not understood even though a number of reports are available describing the application of electric-field-induced switching of Cu(TCNQ) in device fabrication.« less

Self-Assembly of a Tripodal Triszwitterion Forms a pH-Switchable Hydrogel that Can Reversibly Encapsulate Hydrophobic Guests in Water.

PubMed

Jana, Poulami; Schmuck, Carsten

2017-01-05

The development of supramolecular smart materials, which exhibit physicochemical structural changes in response to external stimuli is of current interest for various applications. Herein, we have developed the novel tripodal triszwitterion 1, derived from a C 3 -symmetric benzene-1,3,5-tricarboxamide (BTA) core, which forms a thermo-reversible and pH-switchable transparent hydrogel through intermolecular self-complementary zwitterionic interactions at a neutral pH value. The hierarchical supramolecular self-aggregation was fully analyzed by microscopy (AFM, field emission scanning electron microscopy (FESEM)), viscosity, dynamic light scattering (DLS), and rheology studies. Moreover, compound 1 enables to encapsulate hydrophobic guests, such as the dye Nile red in aqueous medium at pH 6, which makes it an interesting candidate for drug delivery and controlled release. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure-Function Study of Tertiary Amines as Switchable Polarity Solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aaron D. Wilson; Frederick F. Stewart

2014-02-01

A series of tertiary amines have been screened for their function as switchable polarity solvents (SPS). The relative ratios of tertiary amine and carbonate species as well as maximum possible concentration were determined through quantitative 1H and 13C NMR spectroscopy. The viscosities of the polar SPS solutions were measured and ranged from near water in dilute systems through to gel formation at high concentrations. The van't Hoff indices for SPS solutions were measured through freezing point depression studies as a proxy for osmotic pressures. A new form of SPS with an amine : carbonate ratio significantly greater than unity hasmore » been identified. Tertiary amines that function as SPS at ambient pressures appear to be limited to molecules with fewer than 12 carbons. The N,N-dimethyl-n-alkylamine structure has been identified as important to the function of an SPS.« less

Rational Design of a Green-Light-Mediated Unimolecular Platform for Fast Switchable Acidic Sensing.

PubMed

Zhou, Yunyun; Zou, Qi; Qiu, Jing; Wang, Linjun; Zhu, Liangliang

2018-02-01

A controllable sensing ability strongly connects to complex and precise events in diagnosis and treatment. However, imposing visible light into the molecular-scale mediation of sensing processes is restricted by the lack of structural relevance. To address this critical challenge, we present the rational design, synthesis, and in vitro studies of a novel cyanostyryl-modified azulene system for green-light-mediated fast switchable acidic sensing. The advantageous features of the design include a highly efficient green-light-driven Z/E-isomerization (a quantum yield up to 61.3%) for fast erasing chromatic and luminescent expressions and a superior compatibility with control of ratiometric protonation. Significantly, these merits of the design enable the development of a microfluidic system to perform a green-light-mediated reusable sensing function toward a gastric acid analyte in a miniaturized platform. The results may provide new insights for building future integrated green materials.

Switchable and tunable dual-wavelength Er-doped fiber ring laser with single-frequency lasing wavelengths

NASA Astrophysics Data System (ADS)

Zhang, Haiwei; Shi, Wei; Bai, Xiaolei; Sheng, Quan; Xue, Lifang; Yao, Jianquan

2018-02-01

We obtain a switchable and tunable dual-wavelength single-frequency Er-doped ring fiber laser. In order to realize single-longitudinal output, two saturable-absorber-based tracking narrow-band filters are formed in 3- meter-long unpumped Er-doped fiber to narrow the linewidth via using the PM-FBG as a reflection filter. The maximum output power is 2.11 mW centered at 1550.16 nm and 1550.54 nm when the fiber laser operates in dual-wavelength mode. The corresponding linewidths of those two wavelengths are measured to be 769 Hz and 673 Hz, respectively. When the temperature around the PM-FBG is changed from 15 °C to 55 °C, the dual-wavelength single-frequency fiber laser can be tuned from 1550.12 nm to 1550.52 nm and from 1550.49 nm to 1550.82 nm, respectively.

Achieving dynamic switchable filter based on a transmutable metasurface using SMA

NASA Astrophysics Data System (ADS)

Chen, Xin; Gao, Jinsong; Kang, Bonan

2017-09-01

We propose a switchable filter composed of transmutable array using shape memory alloys (SMA). It could exhibit a temperature induced morphology change spontaneously like the biological excitability, acting as a shutter that allows the incident energy to be selectively transmitted or reflected with in excess of 12dB isolation at the certain frequencies for both polarizations. Equivalent circuit models describe the operational principle qualitatively and the switching effect is underpinned by the full-wave analysis. A further physical mechanism is shown by contrasting the distributions of electric field and surface current on the surface at the same frequency for the two working modes. The experimental results consist with the theoretical simulations, indicating that the metasurface could serve as one innovative solution for manipulating the electromagnetic waves and enlighten the next generation of advanced electromagnetic materials with more freedom in the processes of design and manufacturing.

Switchable single-longitudinal-mode dual-wavelength erbium-doped fiber laser based on one polarization-maintaining fiber Bragg grating incorporating saturable absorber

NASA Astrophysics Data System (ADS)

Feng, Suchun; Xu, Ou; Lu, Shaohua; Chen, Ming; Jian, Shuisheng

2009-08-01

Switchable single-longitudinal-mode (SLM) dual-wavelength erbium-doped fiber laser at room temperature is demonstrated. One fiber Bragg grating (FBG) directly written in a polarization-maintaining and photosensitive erbiumdoped fiber (PMPEDF) as the wavelength-selective component is used in a linear laser cavity. Due to the polarization hole burning (PHB) enhanced by the polarization-maintaining fiber Bragg grating (PMFBG), the laser can be designed to operate in stable dual-wavelength or wavelength-switching modes with a wavelength spacing of 0.202 nm by adjusting a polarization controller (PC). The stable SLM operation is guaranteed by a saturable absorber (SA). The optical signal-tonoise ratio (OSNR) of the laser is over 40 dB. The amplitude variation in nearly one and half an hour is less than 0.5 dB for both wavelengths.

Study of true-remanent polarization using remanent hysteresis task and resistive leakage analysis in ferroelectric 0.64Pb(Mg1/3Nb2/3)O3-0.36PbTiO3 ceramics

NASA Astrophysics Data System (ADS)

Joseph, Abhilash J.; Kumar, Binay

2018-03-01

The conventionally reported value of remanent polarization (Pr) contains contribution from non-remanent components which are not usable for memory device applications. This report presents techniques which extract the true-remanent (intrinsic) component of polarization after eliminating the non-remanent component in ferroelectric ceramics. For this, "remanent hysteresis task" and "positive-up-negative-down technique" were performed which utilized the switchable properties of polarizations to nullify the contributions from the non-remanent (non-switchable) components. The report also addresses the time-dependent leakage behavior of the ceramics focusing on the presence of resistive leakage (a time-dependent parameter) present in the ceramics. The techniques presented here are especially useful for polycrystalline ceramics where leakage current leads to an erroneous estimation of Pr.

Energy requirements of the switchable polarity solvent forward osmosis (SPS-FO) water purification process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wendt, Daniel S.; Orme, Christopher J.; Mines, Gregory L.

A model was developed to estimate the process energy requirements of a switchable polarity solvent forward osmosis (SPS FO) system for water purification from aqueous NaCl feed solution concentrations ranging from 0.5 to 4.0 molal at an operational scale of 480 m3/day (feed stream). The model indicates recovering approximately 90% of the water from a feed solution with NaCl concentration similar to seawater using SPS FO would have total equivalent energy requirements between 2.4 and 4.3 kWh per m 3 of purified water product. The process is predicted to be competitive with current costs for disposal/treatment of produced water frommore » oil and gas drilling operations. As a result, once scaled up the SPS FO process may be a thermally driven desalination process that can compete with the cost of seawater reverse osmosis.« less

Programmable Phase Transitions in a Photonic Microgel System: Linking Soft Interactions to a Temporal pH Gradient.

PubMed

Go, Dennis; Rommel, Dirk; Chen, Lisa; Shi, Feng; Sprakel, Joris; Kuehne, Alexander J C

2017-02-28

Soft amphoteric microgel systems exhibit a rich phase behavior. Crystalline phases of these material systems are of interest because they exhibit photonic stop-gaps, giving rise to iridescent color. Such microgel systems are promising for applications in soft, switchable, and programmable photonic filters and devices. We here report a composite microgel system consisting of a hard and fluorescently labeled core and a soft, amphoteric microgel shell. At pH above the isoelectric point (IEP), these colloids easily crystallize into three-dimensional colloidal assemblies. By adding a cyclic lactone to the system, the temporal pH profile can be controlled, and the microgels can be programmed to melt, while they lose charge. When the microgels gain the opposite charge, they recrystallize into assemblies of even higher order. We provide a model system to study the dynamic phase behavior of soft particles and their switchable and programmable photonic effects.

Energy requirements of the switchable polarity solvent forward osmosis (SPS-FO) water purification process

DOE PAGES

Wendt, Daniel S.; Orme, Christopher J.; Mines, Gregory L.; ...

2015-08-01

A model was developed to estimate the process energy requirements of a switchable polarity solvent forward osmosis (SPS FO) system for water purification from aqueous NaCl feed solution concentrations ranging from 0.5 to 4.0 molal at an operational scale of 480 m3/day (feed stream). The model indicates recovering approximately 90% of the water from a feed solution with NaCl concentration similar to seawater using SPS FO would have total equivalent energy requirements between 2.4 and 4.3 kWh per m 3 of purified water product. The process is predicted to be competitive with current costs for disposal/treatment of produced water frommore » oil and gas drilling operations. As a result, once scaled up the SPS FO process may be a thermally driven desalination process that can compete with the cost of seawater reverse osmosis.« less

Dynamic control of chirality in phosphine ligands for enantioselective catalysis

PubMed Central

Zhao, Depeng; Neubauer, Thomas M.; Feringa, Ben L.

2015-01-01

Chirality plays a fundamental role in biology and chemistry and the precise control of chirality in a catalytic conversion is a key to modern synthesis most prominently seen in the production of pharmaceuticals. In enantioselective metal-based catalysis, access to each product enantiomer is commonly achieved through ligand design with chiral bisphosphines being widely applied as privileged ligands. Switchable phosphine ligands, in which chirality is modulated through an external trigger signal, might offer attractive possibilities to change enantioselectivity in a catalytic process in a non-invasive manner avoiding renewed ligand synthesis. Here we demonstrate that a photoswitchable chiral bisphosphine based on a unidirectional light-driven molecular motor, can be used to invert the stereoselectivity of a palladium-catalysed asymmetric transformation. It is shown that light-induced changes in geometry and helicity of the switchable ligand enable excellent selectivity towards the racemic or individual enantiomers of the product in a Pd-catalysed desymmetrization reaction. PMID:25806856

Superphobicity/philicity Janus Fabrics with Switchable, Spontaneous, Directional Transport Ability to Water and Oil Fluids

NASA Astrophysics Data System (ADS)

Zhou, Hua; Wang, Hongxia; Niu, Haitao; Lin, Tong

2013-10-01

Herein we demonstrate that switchable, spontaneous, directional-transport ability to both water and oil fluids can be created on fabric materials through wet-chemistry coating and successive UV irradiation treatment. When the fabric showed directional transport to a liquid, it prevented liquids of higher surface tension from penetration, but allowed liquids of lower surface tension to permeate, from either side. The directional transport ability can be switched from one fluid to another simply by heating the fabric at an elevated temperature and then re-irradiating the fabric with UV light for required period of time. By attaching liquid drops vertically upwards to a horizontally-laid fabric, we further demonstrated that this novel directional fluid transport was an automatic process driven by surface property alone, irrespective of gravity's effect. This novel fabric may be useful for development of ``smart'' textiles and functional membranes for various applications.

Switchable Hydrolase Based on Reversible Formation of Supramolecular Catalytic Site Using a Self-Assembling Peptide.

PubMed

Zhang, Chunqiu; Shafi, Ramim; Lampel, Ayala; MacPherson, Douglas; Pappas, Charalampos G; Narang, Vishal; Wang, Tong; Maldarelli, Charles; Ulijn, Rein V

2017-11-13

The reversible regulation of catalytic activity is a feature found in natural enzymes which is not commonly observed in artificial catalytic systems. Here, we fabricate an artificial hydrolase with pH-switchable activity, achieved by introducing a catalytic histidine residue at the terminus of a pH-responsive peptide. The peptide exhibits a conformational transition from random coil to β-sheet by changing the pH from acidic to alkaline. The β-sheet self-assembles to form long fibrils with the hydrophobic edge and histidine residues extending in an ordered array as the catalytic microenvironment, which shows significant esterase activity. Catalytic activity can be reversible switched by pH-induced assembly/disassembly of the fibrils into random coils. At higher concentrations, the peptide forms a hydrogel which is also catalytically active and maintains its reversible (de-)activation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

An Electrically Switchable Metal-Organic Framework

NASA Astrophysics Data System (ADS)

Fernandez, Carlos A.; Martin, Paul C.; Schaef, Todd; Bowden, Mark E.; Thallapally, Praveen K.; Dang, Liem; Xu, Wu; Chen, Xilin; McGrail, B. Peter

2014-08-01

Crystalline metal organic framework (MOF) materials containing interconnected porosity can be chemically modified to promote stimulus-driven (light, magnetic or electric fields) structural transformations that can be used in a number of devices. Innovative research strategies are now focused on understanding the role of chemical bond manipulation to reversibly alter the free volume in such structures of critical importance for electro-catalysis, molecular electronics, energy storage technologies, sensor devices and smart membranes. In this letter, we study the mechanism for which an electrically switchable MOF composed of Cu(TCNQ) (TCNQ = 7,7,8,8-tetracyanoquinodimethane) transitions from a high-resistance state to a conducting state in a reversible fashion by an applied potential. The actual mechanism for this reversible electrical switching is still not understood even though a number of reports are available describing the application of electric-field-induced switching of Cu(TCNQ) in device fabrication.

Guest-Induced Switchable Breathing Behavior in a Flexible Metal-Organic Framework with Pronounced Negative Gas Pressure.

PubMed

Shi, Yi-Xiang; Li, Wu-Xiang; Zhang, Wen-Hua; Lang, Jian-Ping

2018-06-29

Flexible metal-organic frameworks (MOFs) have attracted great interest for their dynamically structural transformability in response to external stimuli. Herein, we report a switchable "breathing" or "gate-opening" behavior associated with the phase transformation between a narrow pore (np) and a large pore (lp) in a flexible pillared-layered MOF, denoted as MOF-1 as, which is also confirmed by SCXRD and PXRD. The desolvated phase (MOF-1 des) features a unique stepwise adsorption isotherm for N 2 coupled with a pronounced negative gas adsorption pressure. For comparison, however, no appreciable CO 2 adsorption and gate-opening phenomenon with stepwise sorption can be observed. Furthermore, the polar micropore walls decorated with thiophene groups in MOF-1 des reveals the selective sorption of toluene over benzene and p-xylene associated with self-structural adjustment in spite of the markedly similar physicochemical properties of these vapor molecules.

Wavelength-switchable passively mode-locked fiber laser with mechanically exfoliated molybdenum ditelluride on side-polished fiber

NASA Astrophysics Data System (ADS)

Wang, Guomei

2017-11-01

We experimentally investigated the nonlinear saturable absorption characteristics of molybdenum ditelluride (MoTe2) and demonstrated a wavelength-switchable mode-locked erbium-doped fiber laser (EDFL) by using MoTe2 thin film on side-polished fiber (SPF) as saturable absorber. Here, the MoTe2 thin film was efficiently fabricated via mechanical exfoliation method and transferred onto the SPF with the assistance of polydimethylsiloxane (PDMS). MoTe2-covered SPF (MSPF) exhibits the nonlinear saturable absorption for pulses with different polarization states. Optical solitons with spectral bandwidth of 1.06 (1.31) nm centered at ∼1559 (∼1528) nm and pulse duration of 2.46 (2.04) ps can be obtained from the EDFL by adjusting the polarization controller (PC) properly. The time-bandwidth product (TBP) of the pulses was calculated as 0.322 (0.344).

Super-resolution photon-efficient imaging by nanometric double-helix point spread function localization of emitters (SPINDLE)

PubMed Central

Grover, Ginni; DeLuca, Keith; Quirin, Sean; DeLuca, Jennifer; Piestun, Rafael

2012-01-01

Super-resolution imaging with photo-activatable or photo-switchable probes is a promising tool in biological applications to reveal previously unresolved intra-cellular details with visible light. This field benefits from developments in the areas of molecular probes, optical systems, and computational post-processing of the data. The joint design of optics and reconstruction processes using double-helix point spread functions (DH-PSF) provides high resolution three-dimensional (3D) imaging over a long depth-of-field. We demonstrate for the first time a method integrating a Fisher information efficient DH-PSF design, a surface relief optical phase mask, and an optimal 3D localization estimator. 3D super-resolution imaging using photo-switchable dyes reveals the 3D microtubule network in mammalian cells with localization precision approaching the information theoretical limit over a depth of 1.2 µm. PMID:23187521

Low-cost, light-switched, forward-osmosis desalination system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warner, John C.

The looming water crisis is the second largest issue facing humanity after energy. In order to meet the increasing demand for clean water, new efficient and low-cost methods of water purification must be developed. A promising method for dry regions with sea borders is the desalination of seawater. While there remain many disadvantages to current desalination techniques, such as environmental pollution and high cost, there is a strong opportunity for new technology development in this area. In this Phase I program, the development of a light-switchable, low-cost desalination system was explored. The system requires photoselective switching of water solubility. Ninemore » new light-switchable spiropyran-based small molecule and polymeric materials were synthesized, and methods to evaluate their desalination potential were developed and utilized. Severable promising spiropyran analogues proved to be photoswitchable, but so far sufficient photoswitchablity of solubility for a commercial desalination system was not achieved. More development is required.« less

Nonspecific DNA Binding and Bending by HUαβ: Interfaces of the Three Binding Modes Characterized by Salt Dependent Thermodynamics

PubMed Central

Koh, Junseock; Shkel, Irina; Saecker, Ruth M.; Record, M. Thomas

2011-01-01

Previous ITC and FRET studies demonstrated that Escherichia coli HUαβ binds nonspecifically to duplex DNA in three different binding modes: a tighter-binding 34 bp mode which interacts with DNA in large (>34 bp) gaps between bound proteins, reversibly bending it 140° and thereby increasing its flexibility, and two weaker, modestly cooperative small-site-size modes (10 bp, 6 bp) useful for filling gaps between bound proteins shorter than 34 bp. Here we use ITC to determine the thermodynamics of these binding modes as a function of salt concentration, and deduce that DNA in the 34 bp mode is bent around but not wrapped on the body of HU, in contrast to specific binding of IHF. Analyses of binding isotherms (8, 15, 34 bp DNA) and initial binding heats (34, 38, 160 bp DNA) reveal that all three modes have similar log-log salt concentration derivatives of the binding constants (Ski) even though their binding site sizes differ greatly; most probable values of Ski on 34 bp or larger DNA are − 7.5 ± 0.5. From the similarity of Ski values, we conclude that binding interfaces of all three modes involve the same region of the arms and saddle of HU. All modes are entropy-driven, as expected for nonspecific binding driven by the polyelectrolyte effect. The bent-DNA 34 bp mode is most endothermic, presumably because of the cost of HU-induced DNA bending, while the 6 bp mode is modestly exothermic at all salt concentrations examined. Structural models consistent with the observed Ski values are proposed. PMID:21513716

(CAG)(n)-hairpin DNA binds to Msh2-Msh3 and changes properties of mismatch recognition.

PubMed

Owen, Barbara A L; Yang, Zungyoon; Lai, Maoyi; Gajec, Maciej; Gajek, Maciez; Badger, John D; Hayes, Jeffrey J; Edelmann, Winfried; Kucherlapati, Raju; Wilson, Teresa M; McMurray, Cynthia T

2005-08-01

Cells have evolved sophisticated DNA repair systems to correct damaged DNA. However, the human DNA mismatch repair protein Msh2-Msh3 is involved in the process of trinucleotide (CNG) DNA expansion rather than repair. Using purified protein and synthetic DNA substrates, we show that Msh2-Msh3 binds to CAG-hairpin DNA, a prime candidate for an expansion intermediate. CAG-hairpin binding inhibits the ATPase activity of Msh2-Msh3 and alters both nucleotide (ADP and ATP) affinity and binding interfaces between protein and DNA. These changes in Msh2-Msh3 function depend on the presence of A.A mispaired bases in the stem of the hairpin and on the hairpin DNA structure per se. These studies identify critical functional defects in the Msh2-Msh3-CAG hairpin complex that could misdirect the DNA repair process.

Structural basis of human PCNA sliding on DNA

NASA Astrophysics Data System (ADS)

de March, Matteo; Merino, Nekane; Barrera-Vilarmau, Susana; Crehuet, Ramon; Onesti, Silvia; Blanco, Francisco J.; de Biasio, Alfredo

2017-01-01

Sliding clamps encircle DNA and tether polymerases and other factors to the genomic template. However, the molecular mechanism of clamp sliding on DNA is unknown. Using crystallography, NMR and molecular dynamics simulations, here we show that the human clamp PCNA recognizes DNA through a double patch of basic residues within the ring channel, arranged in a right-hand spiral that matches the pitch of B-DNA. We propose that PCNA slides by tracking the DNA backbone via a `cogwheel' mechanism based on short-lived polar interactions, which keep the orientation of the clamp invariant relative to DNA. Mutation of residues at the PCNA-DNA interface has been shown to impair the initiation of DNA synthesis by polymerase δ (pol δ). Therefore, our findings suggest that a clamp correctly oriented on DNA is necessary for the assembly of a replication-competent PCNA-pol δ holoenzyme.

Micropatterning stretched and aligned DNA using microfluidics and surface patterning for applications in hybridization-mediated templated assembly of nanostructures

NASA Astrophysics Data System (ADS)

Carbeck, Jeffrey; Petit, Cecilia

2004-03-01

Current efforts in nanotechnology use one of two basic approaches: top-down fabrication and bottom-up assembly. Top-down strategies use lithography and contact printing to create patterned surfaces and microfluidic channels that, in turn, can corral and organize nanoscale structures. Bottom-up approaches use templates to direct the assembly of atoms, molecules, and nanoparticles through molecular recognition. The goal of this work is to integrate these strategies by first patterning and orienting DNA molecules through top-down tools so that single DNA chains can then serve as templates for the bottom-up construction of hetero-structures composed of proteins and nanoparticles, both metallic and semi-conducting. The first part of this talk focuses on the top-down strategies used to create microscopic patterns of stretched and aligned molecules of DNA. Specifically, it presents a new method in which molecular combing -- a process by which molecules are deposited and stretched onto a surface by the passage of an air-water interface -- is performed in microchannels. This approach demonstrates that the shape and motion of this interface serve as an effective local field directing the chains dynamically as they are stretched onto the surface. The geometry of the microchannel directs the placement of the DNA molecules, while the geometry of the air-water interface directs the local orientation and curvature of the molecules. This ability to control both the placement and orientation of chains has implication for the use of this technique in genetic analysis and in the bottom up approach to nanofabrication.The second half of this talk presents our bottom-up strategy, which allows placement of nanoparticles along individual DNA chains with a theoretical resolution of less than 1 nm. Specifically, we demonstrate the sequence-specific patterning of nanoparticles via the hybridization of functionalized complementary probes to surface-bound chains of double-stranded DNA. Using this technique, we demonstrate the ability to assemble metals, semiconductors, and a composite of both on a single molecule.

Platinated DNA oligonucleotides: new probes forming ultrastable conjugates with graphene oxide

NASA Astrophysics Data System (ADS)

Wang, Feng; Liu, Juewen

2014-05-01

Metal containing polymers have expanded the property of polymers by involving covalently associated metal complexes. DNA is a special block copolymer. While metal ions are known to influence DNA, little is explored on its polymer property when strong metal complexes are associated. In this work, we study cisplatin modified DNA as a new polymer and probe. Out of the complexes formed between cisplatin-A15, HAuCl4-A15, Hg2+-T15 and Ag+-C15, only the cisplatin adduct is stable under the denaturing gel electrophoresis condition. Each Pt-nucleobase bond gives a positive charge and thus makes DNA a zwitterionic polymer. This allows ultrafast adsorption of DNA by graphene oxide (GO) and the adsorbed complex is highly stable. Non-specific DNA, protein, surfactants and thiolated compounds cannot displace platinated DNA from GO, while non-modified DNA is easily displaced in most cases. The stable GO/DNA conjugate is further tested for surface hybridization. This is the first demonstration of using metallated DNA as a polymeric material for interfacing with nanoscale materials.Metal containing polymers have expanded the property of polymers by involving covalently associated metal complexes. DNA is a special block copolymer. While metal ions are known to influence DNA, little is explored on its polymer property when strong metal complexes are associated. In this work, we study cisplatin modified DNA as a new polymer and probe. Out of the complexes formed between cisplatin-A15, HAuCl4-A15, Hg2+-T15 and Ag+-C15, only the cisplatin adduct is stable under the denaturing gel electrophoresis condition. Each Pt-nucleobase bond gives a positive charge and thus makes DNA a zwitterionic polymer. This allows ultrafast adsorption of DNA by graphene oxide (GO) and the adsorbed complex is highly stable. Non-specific DNA, protein, surfactants and thiolated compounds cannot displace platinated DNA from GO, while non-modified DNA is easily displaced in most cases. The stable GO/DNA conjugate is further tested for surface hybridization. This is the first demonstration of using metallated DNA as a polymeric material for interfacing with nanoscale materials. Electronic supplementary information (ESI) available: Methods, additional gels, kinetics, mass spectrum. See DOI: 10.1039/c4nr00867g

Mechanisms of Surface-Mediated DNA Hybridization

PubMed Central

2015-01-01

Single-molecule total internal reflection fluorescence microscopy was employed in conjunction with resonance energy transfer (RET) to observe the dynamic behavior of donor-labeled ssDNA at the interface between aqueous solution and a solid surface decorated with complementary acceptor-labeled ssDNA. At least 100 000 molecular trajectories were determined for both complementary strands and negative control ssDNA. RET was used to identify trajectory segments corresponding to the hybridized state. The vast majority of molecules from solution adsorbed nonspecifically to the surface, where a brief two-dimensional search was performed with a 7% chance of hybridization. Successful hybridization events occurred with a characteristic search time of ∼0.1 s, and unsuccessful searches resulted in desorption from the surface, ultimately repeating the adsorption and search process. Hybridization was reversible, and two distinct modes of melting (i.e., dehybridization) were observed, corresponding to long-lived (∼15 s) and short-lived (∼1.4 s) hybridized time intervals. A strand that melted back onto the surface could rehybridize after a brief search or desorb from the interface. These mechanistic observations provide guidance for technologies that involve DNA interactions in the near-surface region, suggesting a need to design surfaces that both enhance the complex multidimensional search process and stabilize the hybridized state. PMID:24708278

Visual ModuleOrganizer: a graphical interface for the detection and comparative analysis of repeat DNA modules

PubMed Central

2014-01-01

Background DNA repeats, such as transposable elements, minisatellites and palindromic sequences, are abundant in sequences and have been shown to have significant and functional roles in the evolution of the host genomes. In a previous study, we introduced the concept of a repeat DNA module, a flexible motif present in at least two occurences in the sequences. This concept was embedded into ModuleOrganizer, a tool allowing the detection of repeat modules in a set of sequences. However, its implementation remains difficult for larger sequences. Results Here we present Visual ModuleOrganizer, a Java graphical interface that enables a new and optimized version of the ModuleOrganizer tool. To implement this version, it was recoded in C++ with compressed suffix tree data structures. This leads to less memory usage (at least 120-fold decrease in average) and decreases by at least four the computation time during the module detection process in large sequences. Visual ModuleOrganizer interface allows users to easily choose ModuleOrganizer parameters and to graphically display the results. Moreover, Visual ModuleOrganizer dynamically handles graphical results through four main parameters: gene annotations, overlapping modules with known annotations, location of the module in a minimal number of sequences, and the minimal length of the modules. As a case study, the analysis of FoldBack4 sequences clearly demonstrated that our tools can be extended to comparative and evolutionary analyses of any repeat sequence elements in a set of genomic sequences. With the increasing number of sequences available in public databases, it is now possible to perform comparative analyses of repeated DNA modules in a graphic and friendly manner within a reasonable time period. Availability Visual ModuleOrganizer interface and the new version of the ModuleOrganizer tool are freely available at: http://lcb.cnrs-mrs.fr/spip.php?rubrique313. PMID:24678954

Switchable Underwater Bubble Wettability on Laser-Induced Titanium Multiscale Micro-/Nanostructures by Vertically Crossed Scanning.

PubMed

Jiao, Yunlong; Li, Chuanzong; Wu, Sizhu; Hu, Yanlei; Li, Jiawen; Yang, Liang; Wu, Dong; Chu, Jiaru

2018-05-16

We present here a kind of novel multiscale TiO 2 square micropillar arrays on titanium sheets through vertically crossed scanning of femtosecond laser. This multiscale micro-/nanostructure is ascribed to the combination of laser ablation/shock compression/debris self-deposition, which shows superaerophobicity in water with a very small sliding angle. The laser-induced sample displays switchable bubble wettability in water via heating in a dark environment and ultraviolet (UV) irradiation in alcohol. After heating in a dark environment (0.5 h), the ablated titanium surface shows superaerophilicity in water with a bubble contact angle (BCA) of ∼4°, which has a great ability of capturing bubbles in water. After UV irradiation in alcohol (1 h), the sample recovered its superaerophobicity in water and the BCA turns into 156°. The mechanism of reversible switching is believed as the chemical conversion between Ti-OH and Ti-O. It is worth noting that our proposed switching strategy is time-saving and the switch wetting cycle costs only 1.5 h. Then we repeat five switching cycles on the reversibility and the method shows excellent reproducibility and stability. Moreover, laser-induced samples with different scanning spacing (50-120 μm) are fabricated and all of them show switchable underwater bubble wettability via the above tunable methods. Finally, we fabricate hybrid-patterned microstructures to show different patterned bubbles in water on the heated samples. We believe the original works will provide some new insights to researchers in bubble manipulation and gas collection fields.

Dual switchable CRET-induced luminescence of CdSe/ZnS quantum dots (QDs) by the hemin/G-quadruplex-bridged aggregation and deaggregation of two-sized QDs.

PubMed

Hu, Lianzhe; Liu, Xiaoqing; Cecconello, Alessandro; Willner, Itamar

2014-10-08

The hemin/G-quadruplex-catalyzed generation of chemiluminescence through the oxidation of luminol by H2O2 stimulates the chemiluminescence resonance energy transfer (CRET) to CdSe/ZnS quantum dots (QDs), resulting in the luminescence of the QDs. By the cyclic K(+)-ion-induced formation of the hemin/G-quadruplex linked to the QDs, and the separation of the G-quadruplex in the presence of 18-crown-6-ether, the ON-OFF switchable CRET-induced luminescence of the QDs is demonstrated. QDs were modified with nucleic acids consisting of the G-quadruplex subunits sequences and of programmed domains that can be cross-linked through hybridization, using an auxiliary scaffold. In the presence of K(+)-ions, the QDs aggregate through the cooperative stabilization of K(+)-ion-stabilized G-quadruplex bridges and duplex domains between the auxiliary scaffold and the nucleic acids associated with the QDs. In the presence of 18-crown-6-ether, the K(+)-ions are eliminated from the G-quadruplex units, leading to the separation of the aggregated QDs. By the cyclic treatment of the QDs with K(+)-ions/18-crown-6-ether, the reversible aggregation/deaggregation of the QDs is demonstrated. The incorporation of hemin into the K(+)-ion-stabilized G-quadruplex leads to the ON-OFF switchable CRET-stimulated luminescence of the QDs. By the mixing of appropriately modified two-sized QDs, emitting at 540 and 610 nm, the dual ON-OFF activation of the luminescence of the QDs is demonstrated.

Temperature-Triggered Switchable Helix-Helix Inversion of Poly(phenylacetylene) Bearing l-Valine Ethyl Ester Pendants and Its Chiral Recognition Ability.

PubMed

Zhou, Yanli; Zhang, Chunhong; Qiu, Yuan; Liu, Lijia; Yang, Taotao; Dong, Hongxing; Satoh, Toshifumi; Okamoto, Yoshio

2016-11-21

A phenylacetylene containing the l-valine ethyl ester pendant (PAA-Val) was synthesized and polymerized by an organorhodium catalyst (Rh(nbd)BPh₄) to produce the corresponding one-handed helical cis -poly(phenylacetylene) (PPAA-Val). PPAA-Val showed a unique temperature-triggered switchable helix-sense in chloroform, while it was not observed in highly polar solvents, such as N , N '-dimethylformamide (DMF). By heating the solution of PPAA-Val in chloroform, the sign of the CD absorption became reversed, but recovered after cooling the solution to room temperature. Even after six cycles of the heating-cooling treatment, the helix sense of the PPAA-Val's backbone was still switchable without loss of the CD intensity. The PPAA-Val was then coated on silica gel particles to produce novel chiral stationary phases (CSPs) for high-performance liquid chromatography (HPLC). These novel PPAA-Val based CSPs showed a high chiral recognition ability for racemic mandelonitrile ( α = 2.18) and racemic trans - N , N '-diphenylcyclohexane-1,2-dicarboxamide ( α = 2.60). Additionally, the one-handed helical cis -polyene backbone of PPAA-Val was irreversibly destroyed to afford PPAA-Val-H by heating in dimethyl sulfoxide (DMSO) accompanied by the complete disappearance of the Cotton effect. Although PPAA-Val-H had the same l-valine ethyl ester pendants as its cis -isomer PPAA-Val, it showed no chiral recognition. It was concluded that the one-handed helical cis -polyene backbone of PPAA-Val plays an important role in the chiral recognition ability.

Detection of sub-femtomolar DNA based on double potential electrodeposition of electrocatalytic platinum nanoparticles.

PubMed

Spain, Elaine; McArdle, Hazel; Keyes, Tia E; Forster, Robert J

2013-08-07

Suspensions of electrocatalytic platinum nanoparticles with radii as small as 78.9 ± 3.5 nm that are functionalised with DNA only in one region have been created using templated electrodeposition. The integrity of the bound DNA following nanoparticle desorption from the electrode is demonstrated by detecting attomolar concentrations of DNA without the need for molecular, e.g., PCR or NASBA, amplification. Double potential step approaches coupled with interface engineering via nucleation sites allows PtNPs to be created with controlled particle size and density in a facile and reproducible manner.

The Dimeric Architecture of Checkpoint Kinases Mec1ATR and Tel1ATM Reveal a Common Structural Organization.

PubMed

Sawicka, Marta; Wanrooij, Paulina H; Darbari, Vidya C; Tannous, Elias; Hailemariam, Sarem; Bose, Daniel; Makarova, Alena V; Burgers, Peter M; Zhang, Xiaodong

2016-06-24

The phosphatidylinositol 3-kinase-related protein kinases are key regulators controlling a wide range of cellular events. The yeast Tel1 and Mec1·Ddc2 complex (ATM and ATR-ATRIP in humans) play pivotal roles in DNA replication, DNA damage signaling, and repair. Here, we present the first structural insight for dimers of Mec1·Ddc2 and Tel1 using single-particle electron microscopy. Both kinases reveal a head to head dimer with one major dimeric interface through the N-terminal HEAT (named after Huntingtin, elongation factor 3, protein phosphatase 2A, and yeast kinase TOR1) repeat. Their dimeric interface is significantly distinct from the interface of mTOR complex 1 dimer, which oligomerizes through two spatially separate interfaces. We also observe different structural organizations of kinase domains of Mec1 and Tel1. The kinase domains in the Mec1·Ddc2 dimer are located in close proximity to each other. However, in the Tel1 dimer they are fully separated, providing potential access of substrates to this kinase, even in its dimeric form. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Xiaoming; Gelinas, Amy D.; von Carlowitz, Ira

IL-1α is an essential cytokine that contributes to inflammatory responses and is implicated in various forms of pathogenesis and cancer. Here we report a naphthyl modified DNA aptamer that specifically binds IL-1α and inhibits its signaling pathway. By solving the crystal structure of the IL-1α/aptamer, we provide a high-resolution structure of this critical cytokine and we reveal its functional interaction interface with high-affinity ligands. The non-helical aptamer, which represents a highly compact nucleic acid structure, contains a wealth of new conformational features, including an unknown form of G-quadruplex. The IL-1α/aptamer interface is composed of unusual polar and hydrophobic elements, alongmore » with an elaborate hydrogen bonding network that is mediated by sodium ion. IL-1α uses the same interface to interact with both the aptamer and its cognate receptor IL-1RI, thereby suggesting a novel route to immunomodulatory therapeutics.« less

Logic Gate Operation by DNA Translocation through Biological Nanopores.

PubMed

Yasuga, Hiroki; Kawano, Ryuji; Takinoue, Masahiro; Tsuji, Yutaro; Osaki, Toshihisa; Kamiya, Koki; Miki, Norihisa; Takeuchi, Shoji

2016-01-01

Logical operations using biological molecules, such as DNA computing or programmable diagnosis using DNA, have recently received attention. Challenges remain with respect to the development of such systems, including label-free output detection and the rapidity of operation. Here, we propose integration of biological nanopores with DNA molecules for development of a logical operating system. We configured outputs "1" and "0" as single-stranded DNA (ssDNA) that is or is not translocated through a nanopore; unlabeled DNA was detected electrically. A negative-AND (NAND) operation was successfully conducted within approximately 10 min, which is rapid compared with previous studies using unlabeled DNA. In addition, this operation was executed in a four-droplet network. DNA molecules and associated information were transferred among droplets via biological nanopores. This system would facilitate linking of molecules and electronic interfaces. Thus, it could be applied to molecular robotics, genetic engineering, and even medical diagnosis and treatment.

Logic Gate Operation by DNA Translocation through Biological Nanopores

PubMed Central

Takinoue, Masahiro; Tsuji, Yutaro; Osaki, Toshihisa; Kamiya, Koki; Miki, Norihisa; Takeuchi, Shoji

2016-01-01

Logical operations using biological molecules, such as DNA computing or programmable diagnosis using DNA, have recently received attention. Challenges remain with respect to the development of such systems, including label-free output detection and the rapidity of operation. Here, we propose integration of biological nanopores with DNA molecules for development of a logical operating system. We configured outputs “1” and “0” as single-stranded DNA (ssDNA) that is or is not translocated through a nanopore; unlabeled DNA was detected electrically. A negative-AND (NAND) operation was successfully conducted within approximately 10 min, which is rapid compared with previous studies using unlabeled DNA. In addition, this operation was executed in a four-droplet network. DNA molecules and associated information were transferred among droplets via biological nanopores. This system would facilitate linking of molecules and electronic interfaces. Thus, it could be applied to molecular robotics, genetic engineering, and even medical diagnosis and treatment. PMID:26890568

Patscanui: an intuitive web interface for searching patterns in DNA and protein data.

PubMed

Blin, Kai; Wohlleben, Wolfgang; Weber, Tilmann

2018-05-02

Patterns in biological sequences frequently signify interesting features in the underlying molecule. Many tools exist to search for well-known patterns. Less support is available for exploratory analysis, where no well-defined patterns are known yet. PatScanUI (https://patscan.secondarymetabolites.org/) provides a highly interactive web interface to the powerful generic pattern search tool PatScan. The complex PatScan-patterns are created in a drag-and-drop aware interface allowing researchers to do rapid prototyping of the often complicated patterns useful to identifying features of interest.

Human Chromosome Y and Haplogroups; introducing YDHS Database.

PubMed

Tiirikka, Timo; Moilanen, Jukka S

2015-12-01

As the high throughput sequencing efforts generate more biological information, scientists from different disciplines are interpreting the polymorphisms that make us unique. In addition, there is an increasing trend in general public to research their own genealogy, find distant relatives and to know more about their biological background. Commercial vendors are providing analyses of mitochondrial and Y-chromosomal markers for such purposes. Clearly, an easy-to-use free interface to the existing data on the identified variants would be in the interest of general public and professionals less familiar with the field. Here we introduce a novel metadatabase YDHS that aims to provide such an interface for Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants. The database uses ISOGG Y-DNA tree as the source of mutations and haplogroups and by using genomic positions of the mutations the database links them to genes and other biological entities. YDHS contains analysis tools for deeper Y-SNP analysis. YDHS addresses the shortage of Y-DNA related databases. We have tested our database using a set of different cases from literature ranging from infertility to autism. The database is at http://www.semanticgen.net/ydhs Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants have not been in the scientific limelight, excluding certain specialized fields like forensics, mainly because there is not much freely available information or it is scattered in different sources. However, as we have demonstrated Y-SNPs do play a role in various cases on the haplogroup level and it is possible to create a free Y-DNA dedicated bioinformatics resource.

FragIdent--automatic identification and characterisation of cDNA-fragments.

PubMed

Seelow, Dominik; Goehler, Heike; Hoffmann, Katrin

2009-03-02

Many genetic studies and functional assays are based on cDNA fragments. After the generation of cDNA fragments from an mRNA sample, their content is at first unknown and must be assigned by sequencing reactions or hybridisation experiments. Even in characterised libraries, a considerable number of clones are wrongly annotated. Furthermore, mix-ups can happen in the laboratory. It is therefore essential to the relevance of experimental results to confirm or determine the identity of the employed cDNA fragments. However, the manual approach for the characterisation of these fragments using BLAST web interfaces is not suited for larger number of sequences and so far, no user-friendly software is publicly available. Here we present the development of FragIdent, an application for the automatic identification of open reading frames (ORFs) within cDNA-fragments. The software performs BLAST analyses to identify the genes represented by the sequences and suggests primers to complete the sequencing of the whole insert. Gene-specific information as well as the protein domains encoded by the cDNA fragment are retrieved from Internet-based databases and included in the output. The application features an intuitive graphical interface and is designed for researchers without any bioinformatics skills. It is suited for projects comprising up to several hundred different clones. We used FragIdent to identify 84 cDNA clones from a yeast two-hybrid experiment. Furthermore, we identified 131 protein domains within our analysed clones. The source code is freely available from our homepage at http://compbio.charite.de/genetik/FragIdent/.

Mechanism of opening a sliding clamp

PubMed Central

Douma, Lauren G.; Yu, Kevin K.; England, Jennifer K.

2017-01-01

Abstract Clamp loaders load ring-shaped sliding clamps onto DNA where the clamps serve as processivity factors for DNA polymerases. In the first stage of clamp loading, clamp loaders bind and stabilize clamps in an open conformation, and in the second stage, clamp loaders place the open clamps around DNA so that the clamps encircle DNA. Here, the mechanism of the initial clamp opening stage is investigated. Mutations were introduced into the Escherichia coli β-sliding clamp that destabilize the dimer interface to determine whether the formation of an open clamp loader–clamp complex is dependent on spontaneous clamp opening events. In other work, we showed that mutation of a positively charged Arg residue at the β-dimer interface and high NaCl concentrations destabilize the clamp, but neither facilitates the formation of an open clamp loader–clamp complex in experiments presented here. Clamp opening reactions could be fit to a minimal three-step ‘bind-open-lock’ model in which the clamp loader binds a closed clamp, the clamp opens, and subsequent conformational rearrangements ‘lock’ the clamp loader–clamp complex in a stable open conformation. Our results support a model in which the E. coli clamp loader actively opens the β-sliding clamp. PMID:28973453

Modulating the DNA affinity of Elk-1 with computationally selected mutations.

PubMed

Park, Sheldon; Boder, Eric T; Saven, Jeffery G

2005-04-22

In order to regulate gene expression, transcription factors must first bind their target DNA sequences. The affinity of this binding is determined by both the network of interactions at the interface and the entropy change associated with the complex formation. To study the role of structural fluctuation in fine-tuning DNA affinity, we performed molecular dynamics simulations of two highly homologous proteins, Elk-1 and SAP-1, that exhibit different sequence specificity. Simulation studies show that several residues in Elk have significantly higher main-chain root-mean-square deviations than their counterparts in SAP. In particular, a single residue, D69, may contribute to Elk's lower DNA affinity for P(c-fos) by structurally destabilizing the carboxy terminus of the recognition helix. While D69 does not contact DNA directly, the increased mobility in the region may contribute to its weaker binding. We measured the ability of single point mutants of Elk to bind P(c-fos) in a reporter assay, in which D69 of wild-type Elk has been mutated to other residues with higher helix propensity in order to stabilize the local conformation. The gains in transcriptional activity and the free energy of binding suggested from these measurements correlate well with stability gains computed from helix propensity and charge-macrodipole interactions. The study suggests that residues that are distal to the binding interface may indirectly modulate the binding affinity by stabilizing the protein scaffold required for efficient DNA interaction.

DNA nanotechnology from the test tube to the cell.

PubMed

Chen, Yuan-Jyue; Groves, Benjamin; Muscat, Richard A; Seelig, Georg

2015-09-01

The programmability of Watson-Crick base pairing, combined with a decrease in the cost of synthesis, has made DNA a widely used material for the assembly of molecular structures and dynamic molecular devices. Working in cell-free settings, researchers in DNA nanotechnology have been able to scale up system complexity and quantitatively characterize reaction mechanisms to an extent that is infeasible for engineered gene circuits or other cell-based technologies. However, the most intriguing applications of DNA nanotechnology - applications that best take advantage of the small size, biocompatibility and programmability of DNA-based systems - lie at the interface with biology. Here, we review recent progress in the transition of DNA nanotechnology from the test tube to the cell. We highlight key successes in the development of DNA-based imaging probes, prototypes of smart therapeutics and drug delivery systems, and explore the future challenges and opportunities for cellular DNA nanotechnology.

j5 DNA assembly design automation.

PubMed

Hillson, Nathan J

2014-01-01

Modern standardized methodologies, described in detail in the previous chapters of this book, have enabled the software-automated design of optimized DNA construction protocols. This chapter describes how to design (combinatorial) scar-less DNA assembly protocols using the web-based software j5. j5 assists biomedical and biotechnological researchers construct DNA by automating the design of optimized protocols for flanking homology sequence as well as type IIS endonuclease-mediated DNA assembly methodologies. Unlike any other software tool available today, j5 designs scar-less combinatorial DNA assembly protocols, performs a cost-benefit analysis to identify which portions of an assembly process would be less expensive to outsource to a DNA synthesis service provider, and designs hierarchical DNA assembly strategies to mitigate anticipated poor assembly junction sequence performance. Software integrated with j5 add significant value to the j5 design process through graphical user-interface enhancement and downstream liquid-handling robotic laboratory automation.

Investigations of the CLOCK and BMAL1 Proteins Binding to DNA: A Molecular Dynamics Simulation Study.

PubMed

Xue, Tuo; Song, Chunnian; Wang, Qing; Wang, Yan; Chen, Guangju

2016-01-01

The circadian locomotor output cycles kaput (CLOCK), and brain and muscle ARNT-like 1 (BMAL1) proteins are important transcriptional factors of the endogenous circadian clock. The CLOCK and BMAL1 proteins can regulate the transcription-translation activities of the clock-related genes through the DNA binding. The hetero-/homo-dimerization and DNA combination of the CLOCK and BMAL1 proteins play a key role in the positive and negative transcriptional feedback processes. In the present work, we constructed a series of binary and ternary models for the bHLH/bHLH-PAS domains of the CLOCK and BMAL1 proteins, and the DNA molecule, and carried out molecular dynamics simulations, free energy calculations and conformational analysis to explore the interaction properties of the CLOCK and BMAL1 proteins with DNA. The results show that the bHLH domains of CLOCK and BMAL1 can favorably form the heterodimer of the bHLH domains of CLOCK and BMAL1 and the homodimer of the bHLH domains of BMAL1. And both dimers could respectively bind to DNA at its H1-H1 interface. The DNA bindings of the H1 helices in the hetero- and homo-bHLH dimers present the rectangular and diagonal binding modes, respectively. Due to the function of the α-helical forceps in these dimers, the tight gripping of the H1 helices to the major groove of DNA would cause the decrease of interactions at the H1-H2 interfaces in the CLOCK and BMAL1 proteins. The additional PAS domains in the CLOCK and BMAL1 proteins affect insignificantly the interactions of the CLOCK and BMAL1 proteins with the DNA molecule due to the flexible and long loop linkers located at the middle of the PAS and bHLH domains. The present work theoretically explains the interaction mechanisms of the bHLH domains of the CLOCK and BMAL1 proteins with DNA.

Computer-assisted design for scaling up systems based on DNA reaction networks.

PubMed

Aubert, Nathanaël; Mosca, Clément; Fujii, Teruo; Hagiya, Masami; Rondelez, Yannick

2014-04-06

In the past few years, there have been many exciting advances in the field of molecular programming, reaching a point where implementation of non-trivial systems, such as neural networks or switchable bistable networks, is a reality. Such systems require nonlinearity, be it through signal amplification, digitalization or the generation of autonomous dynamics such as oscillations. The biochemistry of DNA systems provides such mechanisms, but assembling them in a constructive manner is still a difficult and sometimes counterintuitive process. Moreover, realistic prediction of the actual evolution of concentrations over time requires a number of side reactions, such as leaks, cross-talks or competitive interactions, to be taken into account. In this case, the design of a system targeting a given function takes much trial and error before the correct architecture can be found. To speed up this process, we have created DNA Artificial Circuits Computer-Assisted Design (DACCAD), a computer-assisted design software that supports the construction of systems for the DNA toolbox. DACCAD is ultimately aimed to design actual in vitro implementations, which is made possible by building on the experimental knowledge available on the DNA toolbox. We illustrate its effectiveness by designing various systems, from Montagne et al.'s Oligator or Padirac et al.'s bistable system to new and complex networks, including a two-bit counter or a frequency divider as well as an example of very large system encoding the game Mastermind. In the process, we highlight a variety of behaviours, such as enzymatic saturation and load effect, which would be hard to handle or even predict with a simpler model. We also show that those mechanisms, while generally seen as detrimental, can be used in a positive way, as functional part of a design. Additionally, the number of parameters included in these simulations can be large, especially in the case of complex systems. For this reason, we included the possibility to use CMA-ES, a state-of-the-art optimization algorithm that will automatically evolve parameters chosen by the user to try to match a specified behaviour. Finally, because all possible functionality cannot be captured by a single software, DACCAD includes the possibility to export a system in the synthetic biology markup language, a widely used language for describing biological reaction systems. DACCAD can be downloaded online at http://www.yannick-rondelez.com/downloads/.

Taking Orders from Light: Photo-Switchable Working/Inactive Smart Surfaces for Protein and Cell Adhesion.

PubMed

Zhang, Junji; Ma, Wenjing; He, Xiao-Peng; Tian, He

2017-03-15

Photoresponsive smart surfaces are promising candidates for a variety of applications in optoelectronics and sensing devices. The use of light as an order signal provides advantages of remote and noninvasive control with high temporal and spatial resolutions. Modification of the photoswitches with target biomacromolecules, such as peptides, DNA, and small molecules including folic acid derivatives and sugars, has recently become a popular strategy to empower the smart surfaces with an improved detection efficiency and specificity. Herein, we report the construction of photoswitchable self-assembled monolayers (SAMs) based on sugar (galactose/mannose)-decorated azobenzene derivatives and determine their photoswitchable, selective protein/cell adhesion performances via electrochemistry. Under alternate UV/vis irradiation, interconvertible high/low recognition and binding affinity toward selective lectins (proteins that recognize sugars) and cells that highly express sugar receptors are achieved. Furthermore, the cis-SAMs with a low binding affinity toward selective proteins and cells also exhibit minimal response toward unselective protein and cell samples, which offers the possibility in avoiding unwanted contamination and consumption of probes prior to functioning for practical applications. Besides, the electrochemical technique used facilitates the development of portable devices based on the smart surfaces for on-demand disease diagnosis.

Signal-Switchable Electrochemiluminescence System Coupled with Target Recycling Amplification Strategy for Sensitive Mercury Ion and Mucin 1 Assay.

PubMed

Jiang, Xinya; Wang, Huijun; Wang, Haijun; Yuan, Ruo; Chai, Yaqin

2016-09-20

In the present work, we first found that mercury ion (Hg(2+)) has an efficient quenching effect on the electrochemiluminescence (ECL) of N-(aminobutyl)-N-(ethylisoluminol) (ABEI). Since we were inspired by this discovery, an aptamer-based ECL sensor was fabricated based on a Hg(2+) triggered signal switch coupled with an exonuclease I (Exo I)-stimulated target recycling amplification strategy for ultrasensitive determination of Hg(2+) and mucin 1 (MUC1). Concretely, the ECL intensity of ABEI-functionalized silver nanoparticles decorated graphene oxide nanocomposite (GO-AgNPs-ABEI) was initially enhanced by ferrocene labeled ssDNA (Fc-S1) (first signal switch "on" state) in the existence of H2O2. With the aid of aptamer, assistant ssDNA (S2) and full thymine (T) bases ssDNA (S3) modified Au nanoparticles (AuNPs-S2-S3) were immobilized on the sensing surface through the hybridization reaction. Then, via the strong and stable T-Hg(2+)-T interaction, an abundance of Hg(2+) was successfully captured on the AuNPs-S2-S3 and effectively inhibited the ECL reaction of ABEI (signal switch "off" state). Finally, the signal switch "on" state was executed by utilizing MUC1 as an aptamer-specific target to bind aptamer, leading to the large decrease of the captured Hg(2+). To further improve the sensitivity of the aptasensor, Exo I was implemented to digest the binded aptamer, which resulted in the release of MUC1 for achieving target recycling with strong detectable ECL signal even in a low level of MUC1. By integrating the quenching effect of Hg(2+) to reduce the background signal and target recycling for signal amplification, this proposed ECL aptasensor was successfully used to detect Hg(2+) and MUC1 sensitively with a wide linear response.

Vacuum compatible, high-speed, 2-D mirror tilt stage

DOEpatents

Denham; Paul E.

2007-09-25

A compact and vacuum compatible magnetic-coil driven tiltable stage that is equipped with a high efficiency reflective coating can be employed as a scanner in EUV applications. The drive electronics for the scanner is fully in situ programmable and rapidly switchable.

Developments in Molecular Recognition and Sensing at Interfaces

PubMed Central

Ariga, Katsuhiko; Hill, Jonathan P.; Endo, Hiroshi

2007-01-01

In biological systems, molecular recognition events occur mostly within interfacial environments such as at membrane surfaces, enzyme reaction sites, or at the interior of the DNA double helix. Investigation of molecular recognition at model interfaces provides great insights into biological phenomena. Molecular recognition at interfaces not only has relevance to biological systems but is also important for modern applications such as high sensitivity sensors. Selective binding of guest molecules in solution to host molecules located at solid surfaces is crucial for electronic or photonic detection of analyte substances. In response to these demands, molecular recognition at interfaces has been investigated extensively during the past two decades using Langmuir monolayers, self-assembled monolayers, and lipid assemblies as recognition media. In this review, advances of molecular recognition at interfaces are briefly summarized.

Amino Acid Interaction (INTAA) web server.

PubMed

Galgonek, Jakub; Vymetal, Jirí; Jakubec, David; Vondrášek, Jirí

2017-07-03

Large biomolecules-proteins and nucleic acids-are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.cas.cz/INTAA/). INTAA offers the calculation of the residue Interaction Energy Matrix for any protein structure (deposited in Protein Data Bank or submitted by the user) and a comprehensive analysis of the interfaces in protein-DNA complexes. The Interaction Energy Matrix web application aims to identify key residues within protein structures which contribute significantly to the stability of the protein. The application provides an interactive user interface enhanced by 3D structure viewer for efficient visualization of pairwise and net interaction energies of individual amino acids, side chains and backbones. The protein-DNA interaction analysis part of the web server allows the user to view the relative abundance of various configurations of amino acid-deoxyribonucleotide pairs found at the protein-DNA interface and the interaction energies corresponding to these configurations calculated using a molecular mechanical force field. The effects of the sugar-phosphate moiety and of the dielectric properties of the solvent on the interaction energies can be studied for the various configurations. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Switchable adhesion for wafer-handling based on dielectric elastomer stack transducers

NASA Astrophysics Data System (ADS)

Grotepaß, T.; Butz, J.; Förster-Zügel, F.; Schlaak, H. F.

2016-04-01

Vacuum grippers are often used for the handling of wafers and small devices. In order to evacuate the gripper, a gas flow is created that can harm the micro structures on the wafer. A promising alternative to vacuum grippers could be adhesive grippers with switchable adhesion. There have been some publications of gecko-inspired adhesive devices. Most of these former works consist of a structured surface which adheres to the object manipulated and an actuator for switching the adhesion. Until now different actuator principles have been investigated, like smart memory alloys and pneumatics. In this work for the first time dielectric elastomer stack transducers (DEST) are combined with a structured surface. DESTs are a promising new transducer technology with many applications in different industry sectors like medical devices, human-machine-interaction and soft robotics. Stacked dielectric elastomer transducers show thickness contraction originating from the electromechanical pressure of two compliant electrodes compressing an elastomeric dielectric when a voltage is applied. Since DESTs and the adhesive surfaces previously described are made of elastomers, it is self-evident to combine both systems in one device. The DESTs are fabricated by a spin coating process. If the flat surface of the spinning carrier is substituted for example by a perforated one, the structured elastomer surface and the DEST can be fabricated in one process. By electrical actuation the DEST contracts and laterally expands which causes the gecko-like cilia to adhere on the object to manipulate. This work describes the assembly and the experimental results of such a device using switchable adhesion. It is intended to be used for the handling of glass wafers.

Tying Knots in DNA with Holographic Optical Tweezers

NASA Astrophysics Data System (ADS)

Miles, Mervyn; Foster, David; Seddon, Annela; Phillips, David; Carberry, David; Padgett, Miles; Dennis, Mark

It has been demonstrated that holographic optical tweezers can be used to tie a trefoil knot in double-stranded DNA. We have developed an advanced holographic optical tweezers system with several types of intuitive control interfaces. It has been used in a range of research projects including the characterization and assembly of structures. Here the process of tying increasingly complex knots with holographic tweezers will be described. The DNA is of the order of 50 μ m in length and is fluorescently labeled, in order that it can be visualized in the optical microscope of the tweezers system. With a knot was tied, the effect of increasing the persistence length of the DNA by partial methylation of the DNA molecule was investigated. Leverhulme Trust.

Interfacing DNA nanodevices with biology: challenges, solutions and perspectives

NASA Astrophysics Data System (ADS)

Vinther, Mathias; Kjems, Jørgen

2016-08-01

The cellular machinery performs millions of complex reactions with extreme precision at nanoscale. From studying these reactions, scientists have become inspired to build artificial nanosized molecular devices with programmed functions. One of the fundamental tools in designing and creating these nanodevices is molecular self-assembly. In nature, deoxyribonucleic acid (DNA) is inarguably one of the most remarkable self-assembling molecules. Governed by the Watson-Crick base-pairing rules, DNA assembles with a structural reliability and predictability based on sequence composition unlike any other complex biological polymer. This consistency has enabled rational design of hundreds of two- and three-dimensional shapes with a molecular precision and homogeneity not preceded by any other known technology at the nanometer scale. During the last two decades, DNA nanotechnology has undergone a rapid evolution pioneered by the work of Nadrian Seeman (Kallenbach et al 1983 Nature 205 829-31). Especially the introduction of the versatile DNA Origami technique by Rothemund (2006 Nature 440 297-302) led to an efflorescence of new DNA-based self-assembled nanostructures (Andersen et al 2009 Nature 459 73-6, Douglas et al 2009 Nature 459 414-8, Dietz et al 2009 Science 325 725-30, Han et al 2011 Science 332 342-6, Iinuma et al 2014 Science 344 65-9), and variations of this technique have contributed to an increasing repertoire of DNA nanostructures (Wei et al 2012 Nature 485 623-6, Ke et al 2012 Science 338 1177-83, Benson et al 2015 Nature 523 441-4, Zhang et al 2015 Nat. Nanotechnol. 10 779-84, Scheible et al 2015 Small 11 5200-5). These advances have naturally triggered the question: What can these DNA nanostructures be used for? One of the leading proposals of use for DNA nanotechnology has been in biology and biomedicine acting as a molecular ‘nanorobot’ or smart drug interacting with the cellular machinery. In this review, we will explore and examine the perspective of DNA nanotechnology for such use. We summarize which requirements DNA nanostructures must fulfil to function in cellular environments and inside living organisms. In addition, we highlight recent advances in interfacing DNA nanostructures with biology.

SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data from 200 samples of a healthy aging cohort.

PubMed

Rueda, Manuel; Torkamani, Ali

2017-08-18

Whole genome and exome sequencing usually include reads containing mitochondrial DNA (mtDNA). Yet, state-of-the-art pipelines and services for human nuclear genome variant calling and annotation do not handle mitochondrial genome data appropriately. As a consequence, any researcher desiring to add mtDNA variant analysis to their investigations is forced to explore the literature for mtDNA pipelines, evaluate them, and implement their own instance of the desired tool. This task is far from trivial, and can be prohibitive for non-bioinformaticians. We have developed SG-ADVISER mtDNA, a web server to facilitate the analysis and interpretation of mtDNA genomic data coming from next generation sequencing (NGS) experiments. The server was built in the context of our SG-ADVISER framework and on top of the MtoolBox platform (Calabrese et al., Bioinformatics 30(21):3115-3117, 2014), and includes most of its functionalities (i.e., assembly of mitochondrial genomes, heteroplasmic fractions, haplogroup assignment, functional and prioritization analysis of mitochondrial variants) as well as a back-end and a front-end interface. The server has been tested with unpublished data from 200 individuals of a healthy aging cohort (Erikson et al., Cell 165(4):1002-1011, 2016) and their data is made publicly available here along with a preliminary analysis of the variants. We observed that individuals over ~90 years old carried low levels of heteroplasmic variants in their genomes. SG-ADVISER mtDNA is a fast and functional tool that allows for variant calling and annotation of human mtDNA data coming from NGS experiments. The server was built with simplicity in mind, and builds on our own experience in interpreting mtDNA variants in the context of sudden death and rare diseases. Our objective is to provide an interface for non-bioinformaticians aiming to acquire (or contrast) mtDNA annotations via MToolBox. SG-ADVISER web server is freely available to all users at https://genomics.scripps.edu/mtdna .

Identification of the Dimer Exchange Interface of the Bacterial DNA Damage Response Protein UmuD.

PubMed

Murison, David A; Timson, Rebecca C; Koleva, Bilyana N; Ordazzo, Michael; Beuning, Penny J

2017-09-12

The Escherichia coli SOS response, an induced DNA damage response pathway, confers survival on bacterial cells by providing accurate repair mechanisms as well as the potentially mutagenic pathway translesion synthesis (TLS). The umuD gene products are upregulated after DNA damage and play roles in both nonmutagenic and mutagenic aspects of the SOS response. Full-length UmuD is expressed as a homodimer of 139-amino-acid subunits, which eventually cleaves its N-terminal 24 amino acids to form UmuD'. The cleavage product UmuD' and UmuC form the Y-family polymerase DNA Pol V (UmuD' 2 C) capable of performing TLS. UmuD and UmuD' exist as homodimers, but their subunits can readily exchange to form UmuDD' heterodimers preferentially. Heterodimer formation is an essential step in the degradation pathway of UmuD'. The recognition sequence for ClpXP protease is located within the first 24 amino acids of full-length UmuD, and the partner of full-length UmuD, whether UmuD or UmuD', is degraded by ClpXP. To better understand the mechanism by which UmuD subunits exchange, we measured the kinetics of exchange of a number of fluorescently labeled single-cysteine UmuD variants as detected by Förster resonance energy transfer. Labeling sites near the dimer interface correlate with increased rates of exchange, indicating that weakening the dimer interface facilitates exchange, whereas labeling sites on the exterior decrease the rate of exchange. In most but not all cases, homodimer and heterodimer exchange exhibit similar rates, indicating that somewhat different molecular surfaces mediate homodimer exchange and heterodimer formation.

Optoelectronic switch matrix as a look-up table for residue arithmetic.

PubMed

Macdonald, R I

1987-10-01

The use of optoelectronic matrix switches to perform look-up table functions in residue arithmetic processors is proposed. In this application, switchable detector arrays give the advantage of a greatly reduced requirement for optical sources by comparison with previous optoelectronic residue processors.

Electrochromic devices and related products and methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Snow, Timothy; McFadden, Judith; Tenent, Robert

2018-01-30

An electrochromic device may be switchable between a transparent state and at least one reflective state. A lithium-containing reflective feature may form when the electrochromic device is switched from the transparent state to the reflective state. Various products and methods may involve the electrochromic device.

Generic concept to program the time domain of self-assemblies with a self-regulation mechanism.

PubMed

Heuser, Thomas; Steppert, Ann-Kathrin; Lopez, Catalina Molano; Zhu, Baolei; Walther, Andreas

2015-04-08

Nature regulates complex structures in space and time via feedback loops, kinetically controlled transformations, and under energy dissipation to allow non-equilibrium processes. Although man-made static self-assemblies realize excellent control over hierarchical structures via molecular programming, managing their temporal destiny by self-regulation is a largely unsolved challenge. Herein, we introduce a generic concept to control the time domain by programming the lifetimes of switchable self-assemblies in closed systems. We conceive dormant deactivators that, in combination with fast promoters, enable a unique kinetic balance to establish an autonomously self-regulating, transient pH-state, whose duration can be programmed over orders of magnitude-from minutes to days. Coupling this non-equilibrium state to pH-switchable self-assemblies allows predicting their assembly/disassembly fate in time, similar to a precise self-destruction mechanism. We demonstrate a platform approach by programming self-assembly lifetimes of block copolymers, nanoparticles, and peptides, enabling dynamic materials with a self-regulation functionality.

Switchable Scattering Meta-Surfaces for Broadband Terahertz Modulation

PubMed Central

Unlu, M.; Hashemi, M. R.; Berry, C. W.; Li, S.; Yang, S.-H.; Jarrahi, M.

2014-01-01

Active tuning and switching of electromagnetic properties of materials is of great importance for controlling their interaction with electromagnetic waves. In spite of their great promise, previously demonstrated reconfigurable metamaterials are limited in their operation bandwidth due to their resonant nature. Here, we demonstrate a new class of meta-surfaces that exhibit electrically-induced switching in their scattering parameters at room temperature and over a broad range of frequencies. Structural configuration of the subwavelength meta-molecules determines their electromagnetic response to an incident electromagnetic radiation. By reconfiguration of the meta-molecule structure, the strength of the induced electric field and magnetic field in the opposite direction to the incident fields are varied and the scattering parameters of the meta-surface are altered, consequently. We demonstrate a custom-designed meta-surface with switchable scattering parameters at a broad range of terahertz frequencies, enabling terahertz intensity modulation with record high modulation depths and modulation bandwidths through a fully integrated, voltage-controlled device platform at room temperature. PMID:25028123

Switchable Pickering Emulsions Stabilized by Awakened TiO2 Nanoparticle Emulsifiers Using UV/Dark Actuation.

PubMed

Zhang, Qing; Bai, Rui-Xue; Guo, Ting; Meng, Tao

2015-08-26

In this work, switchable Pickering emulsions that utilize UV/dark manipulation employ a type of smart TiO2 nanoparticle as emulsifiers. The emulsifiers can be awakened when needed via UV-induced degradation of grafted silanes on TiO2 nanoparticles. By tuning the surface wettability of TiO2 nanoparticles in situ via UV/dark actuation, emulsions stabilized by the nanoparticles can be reversibly switched between the water-in-oil (W/O) type and oil-in-water (O/W) type for several cycles. Due to the convertible wettability, the smart nanoparticle emulsifiers can be settled in either the oil phase or the water phase as desired during phase separation, making it convenient for recycling. The present work provides a facile and noninvasive method to freely manipulate the formation, breakage, and switching of the emulsion; this method has promising potential as a powerful technique for use in energy-efficient and environmentally friendly industries.

Chitosan-Gated Magnetic-Responsive Nanocarrier for Dual-Modal Optical Imaging, Switchable Drug Release, and Synergistic Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hui; Mu, Qingxin; Revia, Richard

In this study, we present a multifunctional yet structurally simple nanocarrier that has a high drug loading capacity, releases drug in response to onset of an AC magnetic field, and can serve as a long-term imaging contrast agent and effectively kills cancer cells by synergistic action. This nanocarrier (HMMC-NC) has a spherical shell structure with a center cavity of 80 nm in diameter. The shell is comprised of two layers: an inner layer of magnetite that exhibits superparamagnetism and an outer layer of mesoporous carbon embedded with carbon dots that exhibit photoluminescence property. Thus in addition to being a drugmore » carrier, HMMC-NC is also a contrast agent for bioimaging. The switchable drug release is enabled by the chitosan molecules attached on the nanocarrier as the switching material which turns on or off the drug release in response to the application or withdrawal of an AC magnetic field.« less

Produced Water Treatment Using the Switchable Polarity Solvent Forward Osmosis (SPS FO) Desalination Process: Preliminary Engineering Design Basis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wendt, Daniel; Adhikari, Birendra; Orme, Christopher

Switchable Polarity Solvent Forward Osmosis (SPS FO) is a semi-permeable membrane-based water treatment technology. INL is currently advancing SPS FO technology such that a prototype unit can be designed and demonstrated for the purification of produced water from oil and gas production operations. The SPS FO prototype unit will used the thermal energy in the produced water as a source of process heat, thereby reducing the external process energy demands. Treatment of the produced water stream will reduce the volume of saline wastewater requiring disposal via injection, an activity that is correlated with undesirable seismic events, as well as generatemore » a purified product water stream with potential beneficial uses. This paper summarizes experimental data that has been collected in support of the SPS FO scale-up effort, and describes how this data will be used in the sizing of SPS FO process equipment. An estimate of produced water treatment costs using the SPS FO process is also provided.« less

Designing switchable near room-temperature multiferroics via the discovery of a novel magnetoelectric coupling

NASA Astrophysics Data System (ADS)

Feng, J. S.; Xu, Ke; Bellaiche, Laurent; Xiang, H. J.

2018-05-01

Magnetoelectric (ME) coupling is the key ingredient for realizing the cross-control of magnetism and ferroelectricity in multiferroics. However, multiferroics are not only rare, especially at room-temperature, in nature but also the overwhelming majority of known multiferroics do not exhibit highly-desired switching of the direction of magnetization when the polarization is reversed by an electric field. Here, we report group theory analysis and ab initio calculations demonstrating, and revealing the origin of, the existence of a novel form of ME coupling term in a specific class of materials that does allow such switching. This term naturally explains the previously observed electric field control of magnetism in the first known multiferroics, i.e., the Ni–X boracite family. It is also presently used to design a switchable near room-temperature multiferroic (namely, LaSrMnOsO6 perovskite) having rather large ferroelectric polarization and spontaneous magnetization, as well as strong ME coupling.

REDOX-SWITCHABLE CALIX[6]ARENE-BASED ISOMERIC ROTAXANES.

PubMed

Zanichelli, Valeria; Bazzoni, Margherita; Arduini, Arturo; Franchi, Paola; Lucarini, Marco; Ragazzon, Giulio; Secchi, Andrea; Silvi, Serena

2018-04-16

Operating molecular machines are based on switchable systems, whose components can be set in motion in a controllable fashion. The presence of non-symmetric elements is a mandatory requirement to obtain and demonstrate the unidirectionality of motion. Calixarene-based macrocycles have proven very efficient hosts in the design of oriented rotaxanes and of pseudorotaxanes with a strict control on the direction of complexation. We have synthesized and characterized a series of two-station rotaxanes based on bypiridinium-ammonium axles. We have exploited a recently reported supramolecular-assisted strategy for the synthesis of different orientational isomers and we identified the ammonium unit as a proper secondary station for the calixarene. We were able to trigger the displacement of the macrocycle upon electrochemical reduction of the bipyridinium primary station and we demonstrated that the shuttling is influenced both by the length of the chain of the axle component and by the position of the secondary station with respect to the calixarene rims. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intermolecular Structural Change for Thermoswitchable Polymeric Photosensitizer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Wooram; Park, Sin-Jung; Cho, Soojeong

2016-08-17

A switchable photosensitizer (PS), which can be activated at a spe-cific condition beside light, has tremendous advantages for photo-dynamic therapy (PDT). Herein, we developed a thermo-switchable polymeric photosensitizer (T-PPS) by conjugating PS (Pheophor-bide-a, PPb-a) to a temperature-responsive polymer backbone of biocompatible hydroxypropyl cellulose (HPC). Self-quenched PS molecules linked in close proximity by pi-pi stacking in T-PPS were easily transited to an active monomeric state by the tempera-ture induced phase transition of polymer backbones. The tempera-ture responsive inter-molecular interaction changes of PS molecules in T-PPS were demonstrated in synchrotron small-angle X-ray scattering (SAXS) and UV-Vis spectrophotometer analysis. The T-PPS allowed switchablemore » activation and synergistically enhanced cancer cell killing effect at the hyperthermia temperature (45 °C). Our developed T-PPS has the considerable potential not only as a new class of photomedicine in clinics but also as a biosensor based on temperature responsiveness.« less

Photo-manipulated photonic bandgap devices based on optically tristable chiral-tilted homeotropic nematic liquid crystal.

PubMed

Huang, Kuan-Chung; Hsiao, Yu-Cheng; Timofeev, Ivan V; Zyryanov, Victor Ya; Lee, Wei

2016-10-31

We report on the spectral properties of an optically switchable tristable chiral-tilted homeotropic nematic liquid crystal (LC) incorporated as a tunable defect layer in one-dimensional photonic crystal. By varying the polarization angle of the incident light and modulating the light intensity ratio between UV and green light, various transmission characteristics of the composite were obtained. The hybrid structure realizes photo-tunability in transmission of defect-mode peaks within the photonic bandgap in addition to optical switchability among three distinct sets of defect modes via photoinduced tristable state transitions. Because the fabrication process is easier and less critical in terms of cell parameters or sample preparation conditions and the LC layer itself possesses an extra stable state compared with the previously reported bistable counterpart operating on the basis of biased-voltage dual-frequency switching, it has much superior potential for photonic applications such as a low-power-consumption multichannel filter and an optically controllable intensity modulator.

Warm/cool-tone switchable thermochromic material for smart windows by orthogonally integrating properties of pillar[6]arene and ferrocene.

PubMed

Wang, Sai; Xu, Zuqiang; Wang, Tingting; Xiao, Tangxin; Hu, Xiao-Yu; Shen, Ying-Zhong; Wang, Leyong

2018-04-30

Functional materials play a vital role in the fabrication of smart windows, which can provide a more comfortable indoor environment for humans to enjoy a better lifestyle. Traditional materials for smart windows tend to possess only a single functionality with the purpose of regulating the input of solar energy. However, different color tones also have great influences on human emotions. Herein, a strategy for orthogonal integration of different properties is proposed, namely the thermo-responsiveness of ethylene glycol-modified pillar[6]arene (EGP6) and the redox-induced reversible color switching of ferrocene/ferrocenium groups are orthogonally integrated into one system. This gives rise to a material with cooperative and non-interfering dual functions, featuring both thermochromism and warm/cool tone-switchability. Consequently, the obtained bifunctional material for fabricating smart windows can not only regulate the input of solar energy but also can provide a more comfortable color tone to improve the feelings and emotions of people in indoor environments.

Self-assembly of colloid-cholesteric composites provides a possible route to switchable optical materials

NASA Astrophysics Data System (ADS)

Stratford, K.; Henrich, O.; Lintuvuori, J. S.; Cates, M. E.; Marenduzzo, D.

2014-06-01

Colloidal particles dispersed in liquid crystals can form new materials with tunable elastic and electro-optic properties. In a periodic ‘blue phase’ host, particles should template into colloidal crystals with potential uses in photonics, metamaterials and transformational optics. Here we show by computer simulation that colloid/cholesteric mixtures can give rise to regular crystals, glasses, percolating gels, isolated clusters, twisted rings and undulating colloidal ropes. This structure can be tuned via particle concentration, and by varying the surface interactions of the cholesteric host with both the particles and confining walls. Many of these new materials are metastable: two or more structures can arise under identical thermodynamic conditions. The observed structure depends not only on the formulation protocol but also on the history of an applied electric field. This new class of soft materials should thus be relevant to design of switchable, multistable devices for optical technologies such as smart glass and e-paper.

Novel Driving Method for Two-Dimensional and Three-Dimensional Switchable Active Matrix Organic Light-Emitting Diode Displays for Emission and Programming Time Extension

NASA Astrophysics Data System (ADS)

In, Hai-Jung; Kwon, Oh-Kyong

2012-03-01

A novel driving method for two-dimensional (2D) and three-dimensional (3D) switchable active matrix organic light-emitting diode (AMOLED) displays is proposed to extend emission time and data programming time during 3D display operation. The proposed pixel consists of six thin-film transistors (TFTs) and two capacitors, and the aperture ratio of the pixel is 45.8% under 40-in. full-high-definition television condition. By increasing emission time and programming time, the flicker problem can be reduced and the lifetime of AMOLED displays can be extended owing to the decrease in emission current density. Simulation results show that the emission current error range from -0.4 to 1.6% is achieved when the threshold voltage variation of driving TFTs is in the range from -1.0 to 1.0 V, and the emission current error is 1.0% when the power line IR-drop is 2.0 V.

Generation of switchable domain wall and Cubic-Quintic nonlinear Schrödinger equation dark pulse

NASA Astrophysics Data System (ADS)

Tiu, Z. C.; Suthaskumar, M.; Zarei, A.; Tan, S. J.; Ahmad, H.; Harun, S. W.

2015-10-01

A switchable domain-wall (DW) and Cubic-Quintic nonlinear Schrödinger equation (CQNLSE) dark soliton pulse generation are demonstrated in Erbium-doped fiber laser (EDFL) for the first time. The DW pulse train operates at 1575 nm with a fundamental repetition rate of 1.52 MHz and pulse width of 203 ns as the pump power is increased above the threshold pump power of 80 mW. The highest pulse energy of 2.24 nJ is obtained at the maximum pump power of 140 mW. CQNLSE pulse can also be realized from the same cavity by adjusting the polarization state but at a higher threshold pump power of 104 mW. The repetition rate and pulse width of the CQNLSE dark pulses are obtained at 1.52 MHz and 219 ns, respectively. The highest energy of 0.58 nJ is obtained for the CQNLSE pulse at pump power of 140 mW.

Reversible optical switching of highly confined phonon-polaritons with an ultrathin phase-change material

NASA Astrophysics Data System (ADS)

Li, Peining; Yang, Xiaosheng; Maß, Tobias W. W.; Hanss, Julian; Lewin, Martin; Michel, Ann-Katrin U.; Wuttig, Matthias; Taubner, Thomas

2016-08-01

Surface phonon-polaritons (SPhPs), collective excitations of photons coupled with phonons in polar crystals, enable strong light-matter interaction and numerous infrared nanophotonic applications. However, as the lattice vibrations are determined by the crystal structure, the dynamical control of SPhPs remains challenging. Here, we realize the all-optical, non-volatile, and reversible switching of SPhPs by controlling the structural phase of a phase-change material (PCM) employed as a switchable dielectric environment. We experimentally demonstrate optical switching of an ultrathin PCM film (down to 7 nm, <λ/1,200) with single laser pulses and detect ultra-confined SPhPs (polariton wavevector kp > 70k0, k0 = 2π/λ) in quartz. Our proof of concept allows the preparation of all-dielectric, rewritable SPhP resonators without the need for complex fabrication methods. With optimized materials and parallelized optical addressing we foresee application potential for switchable infrared nanophotonic elements, for example, imaging elements such as superlenses and hyperlenses, as well as reconfigurable metasurfaces and sensors.

Spectral study on conformation switchable cationic calix[4]carbazole serving as curcumin container, stabilizer and sustained-delivery carrier

NASA Astrophysics Data System (ADS)

Zhao, Liang; Kang, Le; Chen, Yan; Li, Gang; Wang, Lan; Hu, Chun; Yang, Peng

2018-03-01

A fluorescent 2,7-dimethoxy-substituted calix[4]carbazole (1) is facilely synthesized. The spectral behaviors of both the guest-induced switchable conformation of 1 and its abilities serving as the stabilizer and molecular carrier of curcumin are investigated. UV-vis, fluorescence and NMR spectral results show that upon binding to curcumin, the 1,3-alternate conformation of 1 is converted to be the cone one. The relative high association constant (6.4 × 106 M- 1) of 1 binding to curcumin enables it to stabilize the curcumin, to suppress its degradation, and to sustainably deliver it into the EYPC vesicles within 20 h. Moreover, the cytotoxicity assay shows that 1 does not interfere the antiproliferative activities of curcumin. All these properties endow 1 the potential capability of serving as the molecular drug carrier. Our current result may pave the way looking for more efficient fluorescent calixcarbazoles and thereof spectral utilities.

Semiconductor activated terahertz metamaterials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Hou-Tong

Metamaterials have been developed as a new class of artificial effective media realizing many exotic phenomena and unique properties not normally found in nature. Metamaterials enable functionality through structure design, facilitating applications by addressing the severe material issues in the terahertz frequency range. Consequently, prototype functional terahertz devices have been demonstrated, including filters, antireflection coatings, perfect absorbers, polarization converters, and arbitrary wavefront shaping devices. Further integration of functional materials into metamaterial structures have enabled actively and dynamically switchable and frequency tunable terahertz metamaterials through the application of external stimuli. The enhanced light-matter interactions in active terahertz metamaterials may result inmore » unprecedented control and manipulation of terahertz radiation, forming the foundation of many terahertz applications. In this paper, we review the progress during the past few years in this rapidly growing research field. We particularly focus on the design principles and realization of functionalities using single-layer and few-layer terahertz planar metamaterials, and active terahertz metamaterials through the integration of semiconductors to achieve switchable and frequency-tunable response.« less

Semiconductor activated terahertz metamaterials

DOE PAGES

Chen, Hou-Tong

2014-08-01

Metamaterials have been developed as a new class of artificial effective media realizing many exotic phenomena and unique properties not normally found in nature. Metamaterials enable functionality through structure design, facilitating applications by addressing the severe material issues in the terahertz frequency range. Consequently, prototype functional terahertz devices have been demonstrated, including filters, antireflection coatings, perfect absorbers, polarization converters, and arbitrary wavefront shaping devices. Further integration of functional materials into metamaterial structures have enabled actively and dynamically switchable and frequency tunable terahertz metamaterials through the application of external stimuli. The enhanced light-matter interactions in active terahertz metamaterials may result inmore » unprecedented control and manipulation of terahertz radiation, forming the foundation of many terahertz applications. In this paper, we review the progress during the past few years in this rapidly growing research field. We particularly focus on the design principles and realization of functionalities using single-layer and few-layer terahertz planar metamaterials, and active terahertz metamaterials through the integration of semiconductors to achieve switchable and frequency-tunable response.« less

Time-Dependent Liquid Transport on a Biomimetic Topological Surface.

PubMed

Yu, Cunlong; Li, Chuxin; Gao, Can; Dong, Zhichao; Wu, Lei; Jiang, Lei

2018-05-02

Liquid drops impacting on a solid surface is a familiar phenomenon. On rainy days, it is quite important for leaves to drain off impacting raindrops. Water can bounce off or flow down a water-repellent leaf easily, but with difficulty on a hydrophilic leaf. Here, we show an interesting phenomenon in which impacting drops on the hydrophilic pitcher rim of Nepenthes alata can spread outward to prohibit water filling the pitcher tank. We mimic the peristome surface through a designed 3D printing and replicating way and report a time-dependently switchable liquid transport based on biomimetic topological structures, where surface curvature can work synergistically with the surface microtextures to manipulate the switchable spreading performance. Motived by this strange behavior, we construct a large-scaled peristome-mimetic surface in a 3D profile, demonstrating the ability to reduce the need to mop or to squeegee drops that form during the drop impacting process on pipes or other curved surfaces in food processing, moisture transfer, heat management, etc.

New generation ICG-based contrast agents for ultrasound-switchable fluorescence imaging

PubMed Central

Yu, Shuai; Cheng, Bingbing; Yao, Tingfeng; Xu, Cancan; Nguyen, Kytai T.; Hong, Yi; Yuan, Baohong

2016-01-01

Recently, we developed a new technology, ultrasound-switchable fluorescence (USF), for high-resolution imaging in centimeter-deep tissues via fluorescence contrast. The success of USF imaging highly relies on excellent contrast agents. ICG-encapsulated poly(N-isopropylacrylamide) nanoparticles (ICG-NPs) are one of the families of the most successful near-infrared (NIR) USF contrast agents. However, the first-generation ICG-NPs have a short shelf life (<1 month). This work significantly increases the shelf life of the new-generation ICG-NPs (>6 months). In addition, we have conjugated hydroxyl or carboxyl function groups on the ICG-NPs for future molecular targeting. Finally, we have demonstrated the effect of temperature-switching threshold (Tth) and the background temperature (TBG) on the quality of USF images. We estimated that the Tth of the ICG-NPs should be controlled at ~38–40 °C (slightly above the body temperature of 37 °C) for future in vivo USF imaging. Addressing these challenges further reduces the application barriers of USF imaging. PMID:27775014

Photo-switchable bistable twisted nematic liquid crystal optical switch.

PubMed

Wang, Chun-Ta; Wu, Yueh-Chi; Lin, Tsung-Hsien

2013-02-25

This work demonstrates a photo-switchable bistable optical switch that is based on an azo-chiral doped liquid crystal (ACDLC). The photo-induced isomerization of the azo-chiral dopant can change the chirality of twisted nematic liquid crystal and the gap/pitch ratio of an ACDLC device, enabling switching between 0° and 180° twist states in a homogeneous aligned cell. The bistable 180° and 0° twist states of the azo-chiral doped liquid crystal between crossed polarizers correspond to the ON and OFF states of a light shutter, respectively, and they can be maintained stably for tens of hours. Rapid switching between 180° and 0° twist states can be carried out using 408 and 532 nm addressing light. Such a photo-controllable optical switch requires no specific asymmetric alignment layer or precise control of the cell gap/pitch ratio, so it is easily fabricated and has the potential for use in optical systems.

Smart windows with functions of reflective display and indoor temperature-control

NASA Astrophysics Data System (ADS)

Lee, I.-Hui; Chao, Yu-Ching; Hsu, Chih-Cheng; Chang, Liang-Chao; Chiu, Tien-Lung; Lee, Jiunn-Yih; Kao, Fu-Jen; Lee, Chih-Kung; Lee, Jiun-Haw

2010-02-01

In this paper, a switchable window based on cholestreric liquid crystal (CLC) was demonstrated. Under different applied voltages, incoming light at visible and infrared wavelengths was modulated, respectively. A mixture of CLC with a nematic liquid crystal and a chiral dopant selectively reflected infrared light without bias, which effectively reduced the indoor temperature under sunlight illumination. At this time, transmission at visible range was kept at high and the windows looked transparent. With increasing the voltage to 15V, CLC changed to focal conic state and can be used as a reflective display, a privacy window, or a screen for projector. Under a high voltage (30V), homeotropic state was achieved. At this time, both infrared and visible light can transmit which acted as a normal window, which permitted infrared spectrum of winter sunlight to enter the room so as to reduce the heating requirement. Such a device can be used as a switchable window in smart buildings, green houses and windshields.

DNATCO: assignment of DNA conformers at dnatco.org.

PubMed

Černý, Jiří; Božíková, Paulína; Schneider, Bohdan

2016-07-08

The web service DNATCO (dnatco.org) classifies local conformations of DNA molecules beyond their traditional sorting to A, B and Z DNA forms. DNATCO provides an interface to robust algorithms assigning conformation classes called NTC: to dinucleotides extracted from DNA-containing structures uploaded in PDB format version 3.1 or above. The assigned dinucleotide NTC: classes are further grouped into DNA structural alphabet NTA: , to the best of our knowledge the first DNA structural alphabet. The results are presented at two levels: in the form of user friendly visualization and analysis of the assignment, and in the form of a downloadable, more detailed table for further analysis offline. The website is free and open to all users and there is no login requirement. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Programmable cells: Interfacing natural and engineered gene networks

NASA Astrophysics Data System (ADS)

Kobayashi, Hideki; Kærn, Mads; Araki, Michihiro; Chung, Kristy; Gardner, Timothy S.; Cantor, Charles R.; Collins, James J.

2004-06-01

Novel cellular behaviors and characteristics can be obtained by coupling engineered gene networks to the cell's natural regulatory circuitry through appropriately designed input and output interfaces. Here, we demonstrate how an engineered genetic circuit can be used to construct cells that respond to biological signals in a predetermined and programmable fashion. We employ a modular design strategy to create Escherichia coli strains where a genetic toggle switch is interfaced with: (i) the SOS signaling pathway responding to DNA damage, and (ii) a transgenic quorum sensing signaling pathway from Vibrio fischeri. The genetic toggle switch endows these strains with binary response dynamics and an epigenetic inheritance that supports a persistent phenotypic alteration in response to transient signals. These features are exploited to engineer cells that form biofilms in response to DNA-damaging agents and cells that activate protein synthesis when the cell population reaches a critical density. Our work represents a step toward the development of "plug-and-play" genetic circuitry that can be used to create cells with programmable behaviors. heterologous gene expression | synthetic biology | Escherichia coli

Architecture with GIDEON, A Program for Design in Structural DNA Nanotechnology

PubMed Central

Birac, Jeffrey J.; Sherman, William B.; Kopatsch, Jens; Constantinou, Pamela E.; Seeman, Nadrian C.

2012-01-01

We present geometry based design strategies for DNA nanostructures. The strategies have been implemented with GIDEON – a Graphical Integrated Development Environment for OligoNucleotides. GIDEON has a highly flexible graphical user interface that facilitates the development of simple yet precise models, and the evaluation of strains therein. Models are built on a simple model of undistorted B-DNA double-helical domains. Simple point and click manipulations of the model allow the minimization of strain in the phosphate-backbone linkages between these domains and the identification of any steric clashes that might occur as a result. Detailed analysis of 3D triangles yields clear predictions of the strains associated with triangles of different sizes. We have carried out experiments that confirm that 3D triangles form well only when their geometrical strain is less than 4% deviation from the estimated relaxed structure. Thus geometry-based techniques alone, without energetic considerations, can be used to explain general trends in DNA structure formation. We have used GIDEON to build detailed models of double crossover and triple crossover molecules, evaluating the non-planarity associated with base tilt and junction mis-alignments. Computer modeling using a graphical user interface overcomes the limited precision of physical models for larger systems, and the limited interaction rate associated with earlier, command-line driven software. PMID:16630733

Ubiquitin recognition by FAAP20 expands the complex interface beyond the canonical UBZ domain

PubMed Central

Wojtaszek, Jessica L.; Wang, Su; Kim, Hyungjin; Wu, Qinglin; D'Andrea, Alan D.; Zhou, Pei

2014-01-01

FAAP20 is an integral component of the Fanconi anemia core complex that mediates the repair of DNA interstrand crosslinks. The ubiquitin-binding capacity of the FAAP20 UBZ is required for recruitment of the Fanconi anemia complex to interstrand DNA crosslink sites and for interaction with the translesion synthesis machinery. Although the UBZ–ubiquitin interaction is thought to be exclusively encapsulated within the ββα module of UBZ, we show that the FAAP20–ubiquitin interaction extends beyond such a canonical zinc-finger motif. Instead, ubiquitin binding by FAAP20 is accompanied by transforming a disordered tail C-terminal to the UBZ of FAAP20 into a rigid, extended β-loop that latches onto the complex interface of the FAAP20 UBZ and ubiquitin, with the invariant C-terminal tryptophan emanating toward I44Ub for enhanced binding specificity and affinity. Substitution of the C-terminal tryptophan with alanine in FAAP20 not only abolishes FAAP20–ubiquitin binding in vitro, but also causes profound cellular hypersensitivity to DNA interstrand crosslink lesions in vivo, highlighting the indispensable role of the C-terminal tail of FAAP20, beyond the compact zinc finger module, toward ubiquitin recognition and Fanconi anemia complex-mediated DNA interstrand crosslink repair. PMID:25414354

DNAproDB: an interactive tool for structural analysis of DNA–protein complexes

PubMed Central

Sagendorf, Jared M.

2017-01-01

Abstract Many biological processes are mediated by complex interactions between DNA and proteins. Transcription factors, various polymerases, nucleases and histones recognize and bind DNA with different levels of binding specificity. To understand the physical mechanisms that allow proteins to recognize DNA and achieve their biological functions, it is important to analyze structures of DNA–protein complexes in detail. DNAproDB is a web-based interactive tool designed to help researchers study these complexes. DNAproDB provides an automated structure-processing pipeline that extracts structural features from DNA–protein complexes. The extracted features are organized in structured data files, which are easily parsed with any programming language or viewed in a browser. We processed a large number of DNA–protein complexes retrieved from the Protein Data Bank and created the DNAproDB database to store this data. Users can search the database by combining features of the DNA, protein or DNA–protein interactions at the interface. Additionally, users can upload their own structures for processing privately and securely. DNAproDB provides several interactive and customizable tools for creating visualizations of the DNA–protein interface at different levels of abstraction that can be exported as high quality figures. All functionality is documented and freely accessible at http://dnaprodb.usc.edu. PMID:28431131

Terminating DNA Tile Assembly with Nanostructured Caps.

PubMed

Agrawal, Deepak K; Jiang, Ruoyu; Reinhart, Seth; Mohammed, Abdul M; Jorgenson, Tyler D; Schulman, Rebecca

2017-10-24

Precise control over the nucleation, growth, and termination of self-assembly processes is a fundamental tool for controlling product yield and assembly dynamics. Mechanisms for altering these processes programmatically could allow the use of simple components to self-assemble complex final products or to design processes allowing for dynamic assembly or reconfiguration. Here we use DNA tile self-assembly to develop general design principles for building complexes that can bind to a growing biomolecular assembly and terminate its growth by systematically characterizing how different DNA origami nanostructures interact with the growing ends of DNA tile nanotubes. We find that nanostructures that present binding interfaces for all of the binding sites on a growing facet can bind selectively to growing ends and stop growth when these interfaces are presented on either a rigid or floppy scaffold. In contrast, nucleation of nanotubes requires the presentation of binding sites in an arrangement that matches the shape of the structure's facet. As a result, it is possible to build nanostructures that can terminate the growth of existing nanotubes but cannot nucleate a new structure. The resulting design principles for constructing structures that direct nucleation and termination of the growth of one-dimensional nanostructures can also serve as a starting point for programmatically directing two- and three-dimensional crystallization processes using nanostructure design.

Multiscale and Multifunctional Emulsions by Host–Guest Interaction-Mediated Self-Assembly

PubMed Central

2018-01-01

Emulsions are widely used in numerous fields. Therefore, there has been increasing interest in the development of new emulsification strategies toward emulsions with advanced functions. Herein we report the formation of diverse emulsions by host–guest interaction-mediated interfacial self-assembly under mild conditions. In this strategy, a hydrophilic diblock copolymer with one block containing β-cyclodextrin (β-CD) can assemble at the oil/water interface when its aqueous solution is mixed with an oil phase of benzyl alcohol (BA), by host–guest interactions between β-CD and BA. This results in significantly reduced interfacial tension and the formation of switchable emulsions with easily tunable droplet sizes. Furthermore, nanoemulsions with excellent stability are successfully prepared simply via vortexing. The self-assembled oil-in-water emulsions also show catastrophic phase inversion, which can generate stable bicontinuous phase and water-in-oil emulsions, thereby further extending phase structures that can be realized by this host–guest self-assembly approach. Moreover, the host–guest nanoemulsions are able to engineer different nanoparticles and microstructures as well as solubilize a diverse array of hydrophobic drugs and dramatically enhance their oral bioavailability. The host–guest self-assembly emulsification is facile, energetically friendly, and fully translatable to industry, therefore representing a conceptually creative approach toward advanced emulsions. PMID:29806006

Enzyme-Based Logic Gates and Networks with Output Signals Analyzed by Various Methods.

PubMed

Katz, Evgeny

2017-07-05

The paper overviews various methods that are used for the analysis of output signals generated by enzyme-based logic systems. The considered methods include optical techniques (optical absorbance, fluorescence spectroscopy, surface plasmon resonance), electrochemical techniques (cyclic voltammetry, potentiometry, impedance spectroscopy, conductivity measurements, use of field effect transistor devices, pH measurements), and various mechanoelectronic methods (using atomic force microscope, quartz crystal microbalance). Although each of the methods is well known for various bioanalytical applications, their use in combination with the biomolecular logic systems is rather new and sometimes not trivial. Many of the discussed methods have been combined with the use of signal-responsive materials to transduce and amplify biomolecular signals generated by the logic operations. Interfacing of biocomputing logic systems with electronics and "smart" signal-responsive materials allows logic operations be extended to actuation functions; for example, stimulating molecular release and switchable features of bioelectronic devices, such as biofuel cells. The purpose of this review article is to emphasize the broad variability of the bioanalytical systems applied for signal transduction in biocomputing processes. All bioanalytical systems discussed in the article are exemplified with specific logic gates and multi-gate networks realized with enzyme-based biocatalytic cascades. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhanced electrical properties in bilayered ferroelectric thin films

NASA Astrophysics Data System (ADS)

Zhang, Hao; Long, WeiJie; Chen, YaQing; Guo, DongJie

2013-03-01

Sr2Bi4Ti5O18 (SBTi) single layered and Sr2Bi4Ti5O18/Pb(Zr0.53Ti0.47)O3 (SBTi/PZT) bilayered thin films have been prepared on Pt/TiO2/SiO2/Si substrates by pulsed-laser deposition (PLD). The related structural characterizations and electrical properties have been comparatively investigated. X-ray diffraction reveals that both films have crystallized into perovskite phases and scanning electron microscopy shows the sharp interfaces. Both films show well-saturated ferroelectric hysteresis loops, however, compared with the single layered SBTi films, the SBTi/PZT bilayered films have significantly increased remnant polarization ( P r) and decreased coercive field ( E c), with the applied field of 260 kV/cm. The measured P r and E c of SBTi and SBTi/PZT films were 7.9 μC/cm2, 88.1 kV/cm and 13.0 μC/cm2, 51.2 kV/cm, respectively. In addition, both films showed good fatigue-free characteristics, the switchable polarization decreased by 9% and 11% of the initial values after 2.2×109 switching cycles for the SBTi single layered films and the SBTi/PZT bilayered films, respectively. Our results may provide some guidelines for further optimization of multilayered ferroelectric thin films.

Relational databases: a transparent framework for encouraging biology students to think informatically.

PubMed

Rice, Michael; Gladstone, William; Weir, Michael

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills.

Relational Databases: A Transparent Framework for Encouraging Biology Students To Think Informatically

PubMed Central

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills. PMID:15592597

A facile route to steady redox-modulated nitroxide spin-labeled surfaces based on diazonium chemistry.

PubMed

Cougnon, Charles; Boisard, Séverine; Cador, Olivier; Dias, Marylène; Levillain, Eric; Breton, Tony

2013-05-18

A TEMPO derivative was covalently grafted onto carbon and gold surfaces via the diazonium chemistry. The acid-dependent redox properties of the nitroxyl group were exploited to elaborate electro-switchable magnetic surfaces. ESR characterization demonstrated the reversible and permanent magnetic character of the material.

Nanoporous membranes with electrochemically switchable, chemically stabilized ionic selectivity

NASA Astrophysics Data System (ADS)

Small, Leo J.; Wheeler, David R.; Spoerke, Erik D.

2015-10-01

Nanopore size, shape, and surface charge all play important roles in regulating ionic transport through nanoporous membranes. The ability to control these parameters in situ provides a means to create ion transport systems tunable in real time. Here, we present a new strategy to address this challenge, utilizing three unique electrochemically switchable chemistries to manipulate the terminal functional group and control the resulting surface charge throughout ensembles of gold plated nanopores in ion-tracked polycarbonate membranes 3 cm2 in area. We demonstrate the diazonium mediated surface functionalization with (1) nitrophenyl chemistry, (2) quinone chemistry, and (3) previously unreported trimethyl lock chemistry. Unlike other works, these chemistries are chemically stabilized, eliminating the need for a continuously applied gate voltage to maintain a given state and retain ionic selectivity. The effect of surface functionalization and nanopore geometry on selective ion transport through these functionalized membranes is characterized in aqueous solutions of sodium chloride at pH = 5.7. The nitrophenyl surface allows for ionic selectivity to be irreversibly switched in situ from cation-selective to anion-selective upon reduction to an aminophenyl surface. The quinone-terminated surface enables reversible changes between no ionic selectivity and a slight cationic selectivity. Alternatively, the trimethyl lock allows ionic selectivity to be reversibly switched by up to a factor of 8, approaching ideal selectivity, as a carboxylic acid group is electrochemically revealed or hidden. By varying the pore shape from cylindrical to conical, it is demonstrated that a controllable directionality can be imparted to the ionic selectivity. Combining control of nanopore geometry with stable, switchable chemistries facilitates superior control of molecular transport across the membrane, enabling tunable ion transport systems.Nanopore size, shape, and surface charge all play important roles in regulating ionic transport through nanoporous membranes. The ability to control these parameters in situ provides a means to create ion transport systems tunable in real time. Here, we present a new strategy to address this challenge, utilizing three unique electrochemically switchable chemistries to manipulate the terminal functional group and control the resulting surface charge throughout ensembles of gold plated nanopores in ion-tracked polycarbonate membranes 3 cm2 in area. We demonstrate the diazonium mediated surface functionalization with (1) nitrophenyl chemistry, (2) quinone chemistry, and (3) previously unreported trimethyl lock chemistry. Unlike other works, these chemistries are chemically stabilized, eliminating the need for a continuously applied gate voltage to maintain a given state and retain ionic selectivity. The effect of surface functionalization and nanopore geometry on selective ion transport through these functionalized membranes is characterized in aqueous solutions of sodium chloride at pH = 5.7. The nitrophenyl surface allows for ionic selectivity to be irreversibly switched in situ from cation-selective to anion-selective upon reduction to an aminophenyl surface. The quinone-terminated surface enables reversible changes between no ionic selectivity and a slight cationic selectivity. Alternatively, the trimethyl lock allows ionic selectivity to be reversibly switched by up to a factor of 8, approaching ideal selectivity, as a carboxylic acid group is electrochemically revealed or hidden. By varying the pore shape from cylindrical to conical, it is demonstrated that a controllable directionality can be imparted to the ionic selectivity. Combining control of nanopore geometry with stable, switchable chemistries facilitates superior control of molecular transport across the membrane, enabling tunable ion transport systems. Electronic supplementary information (ESI) available: Experimental procedures, synthesis, and characterization of molecules 1, 2 and 3. Explanation of the electrochemical method for approximating nanopore diameter. Additional XPS spectra. See DOI: 10.1039/C5NR02939B

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.

PubMed

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. http://www.cemb.edu.pk/sw.html RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.

Structure of the FANCI-FANCD2 Complex: Insights into the Fanconi Anemia DNA Repair Pathway

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joo, Woo; Xu, Guozhou; Persky, Nicole S.

2011-08-29

Fanconi anemia is a cancer predisposition syndrome caused by defects in the repair of DNA interstrand cross-links (ICLs). Central to this pathway is the Fanconi anemia I-Fanconi anemia D2 (FANCI-FANCD2) (ID) complex, which is activated by DNA damage-induced phosphorylation and monoubiquitination. The 3.4 angstrom crystal structure of the {approx}300 kilodalton ID complex reveals that monoubiquitination and regulatory phosphorylation sites map to the I-D interface, suggesting that they occur on monomeric proteins or an opened-up complex and that they may serve to stabilize I-D heterodimerization. The 7.8 angstrom electron-density map of FANCI-DNA crystals and in vitro data show that each proteinmore » has binding sites for both single- and double-stranded DNA, suggesting that the ID complex recognizes DNA structures that result from the encounter of replication forks with an ICL.« less

Structure of the FANCI-FANCD2 Complex: Insights into the Fanconi Anemia DNA Repair Pathway

DOE Office of Scientific and Technical Information (OSTI.GOV)

W Joo; G Xu; n Persky

2011-12-31

Fanconi anemia is a cancer predisposition syndrome caused by defects in the repair of DNA interstrand cross-links (ICLs). Central to this pathway is the Fanconi anemia I-Fanconi anemia D2 (FANCI-FANCD2) (ID) complex, which is activated by DNA damage-induced phosphorylation and monoubiquitination. The 3.4 angstrom crystal structure of the {approx}300 kilodalton ID complex reveals that monoubiquitination and regulatory phosphorylation sites map to the I-D interface, suggesting that they occur on monomeric proteins or an opened-up complex and that they may serve to stabilize I-D heterodimerization. The 7.8 angstrom electron-density map of FANCI-DNA crystals and in vitro data show that each proteinmore » has binding sites for both single- and double-stranded DNA, suggesting that the ID complex recognizes DNA structures that result from the encounter of replication forks with an ICL.« less

Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase

PubMed Central

Roberts, Victoria A.; Pique, Michael E.; Hsu, Simon; Li, Sheng; Slupphaug, Geir; Rambo, Robert P.; Jamison, Jonathan W.; Liu, Tong; Lee, Jun H.; Tainer, John A.; Ten Eyck, Lynn F.; Woods, Virgil L.

2012-01-01

X-ray crystallography provides excellent structural data on protein–DNA interfaces, but crystallographic complexes typically contain only small fragments of large DNA molecules. We present a new approach that can use longer DNA substrates and reveal new protein–DNA interactions even in extensively studied systems. Our approach combines rigid-body computational docking with hydrogen/deuterium exchange mass spectrometry (DXMS). DXMS identifies solvent-exposed protein surfaces; docking is used to create a 3-dimensional model of the protein–DNA interaction. We investigated the enzyme uracil-DNA glycosylase (UNG), which detects and cleaves uracil from DNA. UNG was incubated with a 30 bp DNA fragment containing a single uracil, giving the complex with the abasic DNA product. Compared with free UNG, the UNG–DNA complex showed increased solvent protection at the UNG active site and at two regions outside the active site: residues 210–220 and 251–264. Computational docking also identified these two DNA-binding surfaces, but neither shows DNA contact in UNG–DNA crystallographic structures. Our results can be explained by separation of the two DNA strands on one side of the active site. These non-sequence-specific DNA-binding surfaces may aid local uracil search, contribute to binding the abasic DNA product and help present the DNA product to APE-1, the next enzyme on the DNA-repair pathway. PMID:22492624

MethLAB: a graphical user interface package for the analysis of array-based DNA methylation data.

PubMed

Kilaru, Varun; Barfield, Richard T; Schroeder, James W; Smith, Alicia K; Conneely, Karen N

2012-03-01

Recent evidence suggests that DNA methylation changes may underlie numerous complex traits and diseases. The advent of commercial, array-based methods to interrogate DNA methylation has led to a profusion of epigenetic studies in the literature. Array-based methods, such as the popular Illumina GoldenGate and Infinium platforms, estimate the proportion of DNA methylated at single-base resolution for thousands of CpG sites across the genome. These arrays generate enormous amounts of data, but few software resources exist for efficient and flexible analysis of these data. We developed a software package called MethLAB (http://genetics.emory.edu/conneely/MethLAB) using R, an open source statistical language that can be edited to suit the needs of the user. MethLAB features a graphical user interface (GUI) with a menu-driven format designed to efficiently read in and manipulate array-based methylation data in a user-friendly manner. MethLAB tests for association between methylation and relevant phenotypes by fitting a separate linear model for each CpG site. These models can incorporate both continuous and categorical phenotypes and covariates, as well as fixed or random batch or chip effects. MethLAB accounts for multiple testing by controlling the false discovery rate (FDR) at a user-specified level. Standard output includes a spreadsheet-ready text file and an array of publication-quality figures. Considering the growing interest in and availability of DNA methylation data, there is a great need for user-friendly open source analytical tools. With MethLAB, we present a timely resource that will allow users with no programming experience to implement flexible and powerful analyses of DNA methylation data.

Programming Cell Adhesion for On-Chip Sequential Boolean Logic Functions.

PubMed

Qu, Xiangmeng; Wang, Shaopeng; Ge, Zhilei; Wang, Jianbang; Yao, Guangbao; Li, Jiang; Zuo, Xiaolei; Shi, Jiye; Song, Shiping; Wang, Lihua; Li, Li; Pei, Hao; Fan, Chunhai

2017-08-02

Programmable remodelling of cell surfaces enables high-precision regulation of cell behavior. In this work, we developed in vitro constructed DNA-based chemical reaction networks (CRNs) to program on-chip cell adhesion. We found that the RGD-functionalized DNA CRNs are entirely noninvasive when interfaced with the fluidic mosaic membrane of living cells. DNA toehold with different lengths could tunably alter the release kinetics of cells, which shows rapid release in minutes with the use of a 6-base toehold. We further demonstrated the realization of Boolean logic functions by using DNA strand displacement reactions, which include multi-input and sequential cell logic gates (AND, OR, XOR, and AND-OR). This study provides a highly generic tool for self-organization of biological systems.

Reduced Synchronization Persistence in Neural Networks Derived from Atm-Deficient Mice

PubMed Central

Levine-Small, Noah; Yekutieli, Ziv; Aljadeff, Jonathan; Boccaletti, Stefano; Ben-Jacob, Eshel; Barzilai, Ari

2011-01-01

Many neurodegenerative diseases are characterized by malfunction of the DNA damage response. Therefore, it is important to understand the connection between system level neural network behavior and DNA. Neural networks drawn from genetically engineered animals, interfaced with micro-electrode arrays allowed us to unveil connections between networks’ system level activity properties and such genome instability. We discovered that Atm protein deficiency, which in humans leads to progressive motor impairment, leads to a reduced synchronization persistence compared to wild type synchronization, after chemically imposed DNA damage. Not only do these results suggest a role for DNA stability in neural network activity, they also establish an experimental paradigm for empirically determining the role a gene plays on the behavior of a neural network. PMID:21519382

ProbeDesigner: for the design of probesets for branched DNA (bDNA) signal amplification assays.

PubMed

Bushnell, S; Budde, J; Catino, T; Cole, J; Derti, A; Kelso, R; Collins, M L; Molino, G; Sheridan, P; Monahan, J; Urdea, M

1999-05-01

The sensitivity and specificity of branched DNA (bDNA) assays are derived in part through the judicious design of the capture and label extender probes. To minimize non-specific hybridization (NSH) events, which elevate assay background, candidate probes must be computer screened for complementarity with generic sequences present in the assay. We present a software application which allows for rapid and flexible design of bDNA probesets for novel targets. It includes an algorithm for estimating the magnitude of NSH contribution to background, a mechanism for removing probes with elevated contributions, a methodology for the simultaneous design of probesets for multiple targets, and a graphical user interface which guides the user through the design steps. The program is available as a commercial package through the Pharmaceutical Drug Discovery program at Chiron Diagnostics.

MFP1 is a thylakoid-associated, nucleoid-binding protein with a coiled-coil structure

PubMed Central

Jeong, Sun Yong; Rose, Annkatrin; Meier, Iris

2003-01-01

Plastid DNA, like bacterial and mitochondrial DNA, is organized into protein–DNA complexes called nucleoids. Plastid nucleoids are believed to be associated with the inner envelope in developing plastids and the thylakoid membranes in mature chloroplasts, but the mechanism for this re-localization is unknown. Here, we present the further characterization of the coiled-coil DNA-binding protein MFP1 as a protein associated with nucleoids and with the thylakoid membranes in mature chloroplasts. MFP1 is located in plastids in both suspension culture cells and leaves and is attached to the thylakoid membranes with its C-terminal DNA-binding domain oriented towards the stroma. It has a major DNA-binding activity in mature Arabidopsis chloroplasts and binds to all tested chloroplast DNA fragments without detectable sequence specificity. Its expression is tightly correlated with the accumulation of thylakoid membranes. Importantly, it is associated in vivo with nucleoids, suggesting a function for MFP1 at the interface between chloroplast nucleoids and the developing thylakoid membrane system. PMID:12930969

Studying the orientation of bio-objects by nematic liquid crystals

NASA Astrophysics Data System (ADS)

Zubtsova, Yu. A.; Kamanin, A. A.; Kamanina, N. V.

2017-05-01

We have studied the ability of a liquid-crystal (LC) matrix to visualize and orient DNA molecules. It is established that the relief of the interface between the LC mesophase and conducting contact can be improved without using an additional high-ohmic polymer layer. Spectroscopic and ellipsometric techniques revealed changes in the refractive properties and structure of composites. The obtained results can be used in creating devices for rapid DNA testing with retained form of biostructures.

DeviceEditor visual biological CAD canvas

PubMed Central

2012-01-01

Background Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs. PMID:22373390

The structure of (CENP-A-H4) 2 reveals physical features that mark centromeres

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sekulic, Nikolina; Bassett, Emily A; Rogers, Danielle J

2010-09-20

Centromeres are specified epigenetically, and the histone H3 variant CENP-A is assembled into the chromatin of all active centromeres. Divergence from H3 raises the possibility that CENP-A generates unique chromatin features to mark physically centromere location. Here we report the crystal structure of a subnucleosomal heterotetramer, human (CENP-A-H4) 2, that reveals three distinguishing properties encoded by the residues that comprise the CENP-A targeting domain (CATD; ref. 2): (1) a CENP-A-CENP-A interface that is substantially rotated relative to the H3-H3 interface; (2) a protruding loop L1 of the opposite charge as that on H3; and (3) strong hydrophobic contacts that rigidifymore » the CENP-A-H4 interface. Residues involved in the CENP-A-CENP-A rotation are required for efficient incorporation into centromeric chromatin, indicating specificity for an unconventional nucleosome shape. DNA topological analysis indicates that CENP-A-containing nucleosomes are octameric with conventional left-handed DNA wrapping, in contrast to other recent proposals. Our results indicate that CENP-A marks centromere location by restructuring the nucleosome from within its folded histone core.« less

Electrical manipulation of oligonucleotides grafted to charged surfaces.

PubMed

Rant, Ulrich; Arinaga, Kenji; Fujita, Shozo; Yokoyama, Naoki; Abstreiter, Gerhard; Tornow, Marc

2006-09-21

The electrical manipulation of short DNA molecules on surfaces offers novel functionalities with fascinating possibilities in the field of bio-interfaces. Here we present systematic investigations of the electrical interactions which govern the structure of oligonucleotides on charged gold surfaces. Successively, we address influences of the applied field strength, the role of DC electrode potentials, in particular for polycrystalline surfaces, as well as screening effects of the surrounding electrolyte solution. Data obtained for single and double stranded DNA exhibit differences which can be attributed to the dissimilar flexibility of the different molecular conformations. A comparison of the experimental results with a basic model shows how the alignment of the molecules adjusts according to a balance between electrically induced ordering and stochastic thermal motions. The presented conclusions are expected to be of general relevance for the behaviour of polyelectrolytes exposed to localized electric fields at interfaces.

Anomalous Dynamics of Water Confined in Protein-Protein and Protein-DNA Interfaces.

PubMed

Chong, Song-Ho; Ham, Sihyun

2016-10-06

Confined water often exhibits anomalous properties not observable in the bulk phase. Although water in hydrophobic confinement has been the focus of intense investigation, the behavior of water confined between hydrophilic surfaces, which are more frequently found in biological systems, has not been fully explored. Here, we investigate using molecular dynamics simulations dynamical properties of the water confined in hydrophilic protein-protein and protein-DNA interfaces. We find that the interfacial water exhibits glassy slow relaxations even at 300 K. In particular, the rotational dynamics show a logarithmic decay that was observed in glass-forming liquids at deeply supercooled states. We argue that such slow water dynamics are indeed induced by the hydrophilic binding surfaces, which is in opposition to the picture that the hydration water slaves protein motions. Our results will significantly impact the view on the role of water in biomolecular interactions.

Two-dimensional enzyme diffusion in laterally confined DNA monolayers.

PubMed

Castronovo, Matteo; Lucesoli, Agnese; Parisse, Pietro; Kurnikova, Anastasia; Malhotra, Aseem; Grassi, Mario; Grassi, Gabriele; Scaggiante, Bruna; Casalis, Loredana; Scoles, Giacinto

2011-01-01

Addressing the effects of confinement and crowding on biomolecular function may provide insight into molecular mechanisms within living organisms, and may promote the development of novel biotechnology tools. Here, using molecular manipulation methods, we investigate restriction enzyme reactions with double-stranded (ds)DNA oligomers confined in relatively large (and flat) brushy matrices of monolayer patches of controlled, variable density. We show that enzymes from the contacting solution cannot access the dsDNAs from the top-matrix interface, and instead enter at the matrix sides to diffuse two-dimensionally in the gap between top- and bottom-matrix interfaces. This is achieved by limiting lateral access with a barrier made of high-density molecules that arrest enzyme diffusion. We put forward, as a possible explanation, a simple and general model that relates these data to the steric hindrance in the matrix, and we briefly discuss the implications and applications of this strikingly new phenomenon.

Near-Infrared Ag2S Quantum Dots-Based DNA Logic Gate Platform for miRNA Diagnostics.

PubMed

Miao, Peng; Tang, Yuguo; Wang, Bidou; Meng, Fanyu

2016-08-02

Dysregulation of miRNA expression is correlated with the development and progression of many diseases. These miRNAs are regarded as promising biomarkers. However, it is challenging to measure these low abundant molecules without employing time-consuming radioactive labeling or complex amplification strategies. Here, we present a DNA logic gate platform for miRNA diagnostics with fluorescence outputs from near-infrared (NIR) Ag2S quantum dots (QDs). Carefully designed toehold exchange-mediated strand displacements with different miRNA inputs occur on a solid-state interface, which control QDs release from solid-state interface to solution, responding to multiplex information on initial miRNAs. Excellent fluorescence emission properties of NIR Ag2S QDs certify the great prospect for amplification-free and sensitive miRNA assay. We demonstrate the potential of this platform by achieving femtomolar level miRNA analysis and the versatility of a series of logic circuits computation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yao, Juan; Zhou, Yufan; Sui, Xiao

The identification of a number of mass peaks in the switchable ionic liquid (SWIL) observed in ToF-SIMS is updated based on the most likely chemical formation pathways. The revised identification better reflects the chemical interactions in the SWIL consisting of DBU, 1-hexanol and CO2. A companion paper illustrates the formation mechanism of these updated species is currently under review.

Threshold-Switchable Particles (TSPs) to Control Internal Hemorrhage

DTIC Science & Technology

2015-12-01

Many nudix-type phosphatases are clinically important enzymes and their overexpression can be markers of disease. Nudt2 (Apah1), for example, is an Ap4A ...hydrolase that, when overexpressed in breast cancer, correlates with poor prognosis.26 In addition to processing Ap4A , Nudt2 can hydrolyze long-chain

Switchable thulium-doped fiber laser from polarization rotation vector to scalar soliton

NASA Astrophysics Data System (ADS)

Wu, Zhichao; Fu, Songnian; Jiang, Kai; Song, Jue; Li, Huizi; Tang, Ming; Shum, Ping; Liu, Deming

2016-10-01

We experimentally demonstrate switchable temporal soliton generation from a thulium-doped fiber laser (TDFL), using carbon nanotubes as the mode-locker. With the help of residual polarization dependent loss of a wavelength division multiplexer, a weak nonlinear polarization rotation (NPR) effect can be achieved within the laser cavity, which may provide joint contribution for passive mode-locking operation. By finely adjusting the polarization to alter the strength of NPR-based saturable absorption, the TDFL either approaches the operation regime of scalar soliton with strong NPR effect, or generates polarization rotation locked vector soliton (PRLVS) with weak NPR effect. The scalar solitons and PRLVSs possess 3-dB optical spectrum bandwidth of 2.2 nm and 2 nm, pulse-width of 1.8 ps and 2 ps, respectively. Moreover, the PRLVSs demonstrate a typical energy exchange between two polarized components on optical spectra and a period-doubling feature in time domain. Such operation principle can also be used in 1550 nm band fiber lasers and other nonlinear systems.

Switchable thulium-doped fiber laser from polarization rotation vector to scalar soliton

PubMed Central

Wu, Zhichao; Fu, Songnian; Jiang, Kai; Song, Jue; Li, Huizi; Tang, Ming; Shum, Ping; Liu, Deming

2016-01-01

We experimentally demonstrate switchable temporal soliton generation from a thulium-doped fiber laser (TDFL), using carbon nanotubes as the mode-locker. With the help of residual polarization dependent loss of a wavelength division multiplexer, a weak nonlinear polarization rotation (NPR) effect can be achieved within the laser cavity, which may provide joint contribution for passive mode-locking operation. By finely adjusting the polarization to alter the strength of NPR-based saturable absorption, the TDFL either approaches the operation regime of scalar soliton with strong NPR effect, or generates polarization rotation locked vector soliton (PRLVS) with weak NPR effect. The scalar solitons and PRLVSs possess 3-dB optical spectrum bandwidth of 2.2 nm and 2 nm, pulse-width of 1.8 ps and 2 ps, respectively. Moreover, the PRLVSs demonstrate a typical energy exchange between two polarized components on optical spectra and a period-doubling feature in time domain. Such operation principle can also be used in 1550 nm band fiber lasers and other nonlinear systems. PMID:27708427

Switchable thulium-doped fiber laser from polarization rotation vector to scalar soliton.

PubMed

Wu, Zhichao; Fu, Songnian; Jiang, Kai; Song, Jue; Li, Huizi; Tang, Ming; Shum, Ping; Liu, Deming

2016-10-06

We experimentally demonstrate switchable temporal soliton generation from a thulium-doped fiber laser (TDFL), using carbon nanotubes as the mode-locker. With the help of residual polarization dependent loss of a wavelength division multiplexer, a weak nonlinear polarization rotation (NPR) effect can be achieved within the laser cavity, which may provide joint contribution for passive mode-locking operation. By finely adjusting the polarization to alter the strength of NPR-based saturable absorption, the TDFL either approaches the operation regime of scalar soliton with strong NPR effect, or generates polarization rotation locked vector soliton (PRLVS) with weak NPR effect. The scalar solitons and PRLVSs possess 3-dB optical spectrum bandwidth of 2.2 nm and 2 nm, pulse-width of 1.8 ps and 2 ps, respectively. Moreover, the PRLVSs demonstrate a typical energy exchange between two polarized components on optical spectra and a period-doubling feature in time domain. Such operation principle can also be used in 1550 nm band fiber lasers and other nonlinear systems.

Charge Modulation in Graphitic Carbon Nitride as a Switchable Approach to High-Capacity Hydrogen Storage.

PubMed

Tan, Xin; Kou, Liangzhi; Tahini, Hassan A; Smith, Sean C

2015-11-01

Electrical charging of graphitic carbon nitride nanosheets (g-C4 N3 and g-C3 N4 ) is proposed as a strategy for high-capacity and electrocatalytically switchable hydrogen storage. Using first-principle calculations, we found that the adsorption energy of H2 molecules on graphitic carbon nitride nanosheets is dramatically enhanced by injecting extra electrons into the adsorbent. At full hydrogen coverage, the negatively charged graphitic carbon nitride achieves storage capacities up to 6-7 wt %. In contrast to other hydrogen storage approaches, the storage/release occurs spontaneously once extra electrons are introduced or removed, and these processes can be simply controlled by switching on/off the charging voltage. Therefore, this approach promises both facile reversibility and tunable kinetics without the need of specific catalysts. Importantly, g-C4 N3 has good electrical conductivity and high electron mobility, which can be a very good candidate for electron injection/release. These predictions may prove to be instrumental in searching for a new class of high-capacity hydrogen storage materials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Polymeric microcapsules with switchable mechanical properties for self-healing concrete: synthesis, characterisation and proof of concept

NASA Astrophysics Data System (ADS)

Kanellopoulos, A.; Giannaros, P.; Palmer, D.; Kerr, A.; Al-Tabbaa, A.

2017-04-01

Microcapsules, with sodium silicate solution as core, were produced using complex coacervation in a double, oil-in-water-in oil, emulsion system. The shell material was a gelatin-acacia gum crosslinked coacervate and the produced microcapsules had diameters ranging from 300 to 700 μm. The shell material designed with switchable mechanical properties. When it is hydrated exhibits soft and ‘rubbery’ behaviour and, when dried, transitions to a stiff and ‘glassy’ material. The microcapsules survived drying and rehydrating cycles and preserved their structural integrity when exposed to highly alkaline solutions that mimic the pH environment of concrete. Microscopy revealed that the shell thickness of the microcapsules varies across their perimeter from 5 to 20 μm. Thermal analysis showed that the produced microcapsules were very stable up to 190 °C. Proof of concept investigation has demonstrated that the microcapsules successfully survive and function when exposed to a cement-based matrix. Observations showed that the microcapsules survive mixing with cement and rupture successfully upon crack formation releasing the encapsulated sodium silicate solution.

Ferroelectric self-assembled molecular materials showing both rectifying and switchable conductivity

PubMed Central

Gorbunov, Andrey V.; Garcia Iglesias, Miguel; Guilleme, Julia; Cornelissen, Tim D.; Roelofs, W. S. Christian; Torres, Tomas; González-Rodríguez, David; Meijer, E. W.; Kemerink, Martijn

2017-01-01

Advanced molecular materials that combine two or more physical properties are typically constructed by combining different molecules, each being responsible for one of the properties required. Ideally, single molecules could take care of this combined functionality, provided they are self-assembled correctly and endowed with different functional subunits whose strong electronic coupling may lead to the emergence of unprecedented and exciting properties. We present a class of disc-like semiconducting organic molecules that are functionalized with strong dipolar side groups. Supramolecular organization of these materials provides long-range polar order that supports collective ferroelectric behavior of the side groups as well as charge transport through the stacked semiconducting cores. The ferroelectric polarization in these supramolecular polymers is found to couple to the charge transport and leads to a bulk conductivity that is both switchable and rectifying. An intuitive model is developed and found to quantitatively reproduce the experimental observations. In a larger perspective, these results highlight the possibility of modulating material properties using the large electric fields associated with ferroelectric polarization. PMID:28975150

Self-assembly of block copolymers into sieve-like particles with arrayed switchable channels and as scaffolds to guide the arrangement of gold nanoparticles.

PubMed

He, Yun; Zhang, Yan; Yan, Nan; Zhu, Yutian; Jiang, Wei; Shi, Dean

2017-10-12

Well-defined polymeric particles with not only a controllable shape and internal nanostructures but also stimuli-responsive functions have attracted intensive attention because of their great potential in various fields. Herein, we created unique sieve-like particles with lattice arrayed switchable channels via the confined self-assembly of poly(4-vinylpyridine)-b-polystyrene-b-poly(4-vinylpyridine) (P4VP-b-PS-b-P4VP) triblock copolymers within the emulsion droplets and the subsequent swelling treatment in ethanol. It is worth noting that the hexagonally packed P4VP channels in the sieve-like particles are switched on and off by changing the solvent type, i.e., P4VP channels are switched on in ethanol and switched off in water, which can operate as a solvent-controlled chemical gate. Moreover, the well-defined sieve-like particles can be further used as scaffolds to guide the spatial arrangement of gold nanoparticles, which generates hybrid nanomaterials with controllable morphology and ordered spatial arrangement of AuNPs.

Electrically switchable metadevices via graphene

PubMed Central

Balci, Osman; Kakenov, Nurbek; Karademir, Ertugrul; Balci, Sinan; Cakmakyapan, Semih; Polat, Emre O.; Caglayan, Humeyra; Özbay, Ekmel; Kocabas, Coskun

2018-01-01

Metamaterials bring subwavelength resonating structures together to overcome the limitations of conventional materials. The realization of active metadevices has been an outstanding challenge that requires electrically reconfigurable components operating over a broad spectrum with a wide dynamic range. However, the existing capability of metamaterials is not sufficient to realize this goal. By integrating passive metamaterials with active graphene devices, we demonstrate a new class of electrically controlled active metadevices working in microwave frequencies. The fabricated active metadevices enable efficient control of both amplitude (>50 dB) and phase (>90°) of electromagnetic waves. In this hybrid system, graphene operates as a tunable Drude metal that controls the radiation of the passive metamaterials. Furthermore, by integrating individually addressable arrays of metadevices, we demonstrate a new class of spatially varying digital metasurfaces where the local dielectric constant can be reconfigured with applied bias voltages. In addition, we reconfigure resonance frequency of split-ring resonators without changing its amplitude by damping one of the two coupled metasurfaces via graphene. Our approach is general enough to implement various metamaterial systems that could yield new applications ranging from electrically switchable cloaking devices to adaptive camouflage systems. PMID:29322094

Correlative transmission electron microscopy and electrical properties study of switchable phase-change random access memory line cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oosthoek, J. L. M.; Kooi, B. J., E-mail: B.J.Kooi@rug.nl; Voogt, F. C.

2015-02-14

Phase-change memory line cells, where the active material has a thickness of 15 nm, were prepared for transmission electron microscopy (TEM) observation such that they still could be switched and characterized electrically after the preparation. The result of these observations in comparison with detailed electrical characterization showed (i) normal behavior for relatively long amorphous marks, resulting in a hyperbolic dependence between SET resistance and SET current, indicating a switching mechanism based on initially long and thin nanoscale crystalline filaments which thicken gradually, and (ii) anomalous behavior, which holds for relatively short amorphous marks, where initially directly a massive crystalline filament ismore » formed that consumes most of the width of the amorphous mark only leaving minor residual amorphous regions at its edges. The present results demonstrate that even in (purposely) thick TEM samples, the TEM sample preparation hampers the probability to observe normal behavior and it can be debated whether it is possible to produce electrically switchable TEM specimen in which the memory cells behave the same as in their original bulk embedded state.« less

Concentration Dependent Speciation and Mass Transport Properties of Switchable Polarity Solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aaron D. Wilson; Christopher J. Orme

2014-12-01

Tertiary amine switchable polarity solvents (SPS) consisting of predominantly water, tertiary amine, and tertiary ammonium and bicarbonate ions were produced at various concentrations for three different amines: N,N-dimethylcyclohexylamine, N,N-dimethyloctylamine, and 1 cyclohexylpiperidine. For all concentrations, physical properties were measured including viscosity, molecular diffusion coefficients, freezing point depression, and density. Based on these measurements a variation on the Mark Houwink equation was developed to predict the viscosity of any tertiary amine SPS as a function of concentration using the amine’s molecular mass. The observed physical properties allowed the identification of solution state speciation of non-osmotic SPS, where the amine to carbonicmore » acid ratio is significantly greater than one. These results indicate that at most concentrations the stoichiometric excess amine is involved in solvating a proton with two amines. The physical properties of osmotic SPS have consistent concentration dependence behavior over a wide range of concentrations; this consistence suggests osmotic pressures based on low concentrations freezing point studies can be reliably extrapolated to higher concentrations.« less

A fast pH-switchable and self-healing supramolecular hydrogel carrier for guided, local catheter injection in the infarcted myocardium.

PubMed

Bastings, Maartje M C; Koudstaal, Stefan; Kieltyka, Roxanne E; Nakano, Yoko; Pape, A C H; Feyen, Dries A M; van Slochteren, Frebus J; Doevendans, Pieter A; Sluijter, Joost P G; Meijer, E W; Chamuleau, Steven A J; Dankers, Patricia Y W

2014-01-01

Minimally invasive intervention strategies after myocardial infarction use state-of-the-art catheter systems that are able to combine mapping of the infarcted area with precise, local injection of drugs. To this end, catheter delivery of drugs that are not immediately pumped out of the heart is still challenging, and requires a carrier matrix that in the solution state can be injected through a long catheter, and instantaneously gelates at the site of injection. To address this unmet need, a pH-switchable supramolecular hydrogel is developed. The supramolecular hydrogel is switched into a liquid at pH > 8.5, with a viscosity low enough to enable passage through a 1-m long catheter while rapidly forming a hydrogel in contact with tissue. The hydrogel has self-healing properties taking care of adjustment to the injection site. Growth factors are delivered from the hydrogel thereby clearly showing a reduction of infarct scar in a pig myocardial infarction model. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interplay of hot electrons from localized and propagating plasmons.

PubMed

Hoang, Chung V; Hayashi, Koki; Ito, Yasuo; Gorai, Naoki; Allison, Giles; Shi, Xu; Sun, Quan; Cheng, Zhenzhou; Ueno, Kosei; Goda, Keisuke; Misawa, Hiroaki

2017-10-03

Plasmon-induced hot-electron generation has recently received considerable interest and has been studied to develop novel applications in optoelectronics, photovoltaics and green chemistry. Such hot electrons are typically generated from either localized plasmons in metal nanoparticles or propagating plasmons in patterned metal nanostructures. Here we simultaneously generate these heterogeneous plasmon-induced hot electrons and exploit their cooperative interplay in a single metal-semiconductor device to demonstrate, as an example, wavelength-controlled polarity-switchable photoconductivity. Specifically, the dual-plasmon device produces a net photocurrent whose polarity is determined by the balance in population and directionality between the hot electrons from localized and propagating plasmons. The current responsivity and polarity-switching wavelength of the device can be varied over the entire visible spectrum by tailoring the hot-electron interplay in various ways. This phenomenon may provide flexibility to manipulate the electrical output from light-matter interaction and offer opportunities for biosensors, long-distance communications, and photoconversion applications.Plasmon-induced hot electrons have potential applications spanning photodetection and photocatalysis. Here, Hoang et al. study the interplay between hot electrons generated by localized and propagating plasmons, and demonstrate wavelength-controlled polarity-switchable photoconductivity.

Correlative transmission electron microscopy and electrical properties study of switchable phase-change random access memory line cells

NASA Astrophysics Data System (ADS)

Oosthoek, J. L. M.; Voogt, F. C.; Attenborough, K.; Verheijen, M. A.; Hurkx, G. A. M.; Gravesteijn, D. J.; Kooi, B. J.

2015-02-01

Phase-change memory line cells, where the active material has a thickness of 15 nm, were prepared for transmission electron microscopy (TEM) observation such that they still could be switched and characterized electrically after the preparation. The result of these observations in comparison with detailed electrical characterization showed (i) normal behavior for relatively long amorphous marks, resulting in a hyperbolic dependence between SET resistance and SET current, indicating a switching mechanism based on initially long and thin nanoscale crystalline filaments which thicken gradually, and (ii) anomalous behavior, which holds for relatively short amorphous marks, where initially directly a massive crystalline filament is formed that consumes most of the width of the amorphous mark only leaving minor residual amorphous regions at its edges. The present results demonstrate that even in (purposely) thick TEM samples, the TEM sample preparation hampers the probability to observe normal behavior and it can be debated whether it is possible to produce electrically switchable TEM specimen in which the memory cells behave the same as in their original bulk embedded state.

Vortex-assisted switchable liquid-liquid microextraction for the preconcentration of cadmium in environmental samples prior to its determination with flame atomic absorption spectrometry.

PubMed

Fırat, Merve; Bodur, Süleyman; Tışlı, Büşra; Özlü, Cansu; Chormey, Dotse Selali; Turak, Fatma; Bakırdere, Sezgin

2018-06-12

In this study, a switchable solvent was used to preconcentrate trace amounts of Cd from aqueous solution for its determination by flame atomic absorption spectrometry (FAAS). Protonation of N,N-dimethylbenzylamine by dry ice (solid CO 2 ) made it water soluble, and addition of sodium hydroxide converted it back to its original nonionic state for phase separation and subsequent extraction of Cd. A slotted quartz tube (SQT) was attached to the flame burner head to increase the residence time of Cd atoms in the light path. Under the optimum conditions, limits of detection and quantification were determined as 0.7 and 2.6 μg L -1 , respectively. Low relative standard deviations calculated from seven replicate measurements of the lowest concentration indicated high precision. Accuracy of the developed method was checked by using a standard reference material (SRM 1633c). Spiked recovery tests were also performed on lake water and wastewater samples at different concentrations to check the applicability of the developed method, and the results obtained (90-103%) established high recovery.

Switchable transport strategy to deposit active Fe/Fe3C cores into hollow microporous carbons for efficient chromium removal.

PubMed

Liu, Dong-Hai; Guo, Yue; Zhang, Lu-Hua; Li, Wen-Cui; Sun, Tao; Lu, An-Hui

2013-11-25

Magnetic hollow structures with microporous shell and highly dispersed active cores (Fe/Fe3 C nanoparticles) are rationally designed and fabricated by solution-phase switchable transport of active iron species combined with a solid-state thermolysis technique, thus allowing selective encapsulation of functional Fe/Fe3 C nanoparticles in the interior cavity. These engineered functional materials show high loading (≈54 wt%) of Fe, excellent chromium removal capability (100 mg g(-1)), fast adsorption rate (8766 mL mg(-1) h(-1)), and easy magnetic separation property (63.25 emu g(-1)). During the adsorption process, the internal highly dispersed Fe/Fe3 C nanoparticles supply a driving force for facilitating Cr(VI) diffusion inward, thus improving the adsorption rate and the adsorption capacity. At the same time, the external microporous carbon shell can also efficiently trap guest Cr(VI) ions and protect Fe/Fe3 C nanoparticles from corrosion and subsequent leaching problems. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photoaligning and photopatterning technology: applications in displays and photonics

NASA Astrophysics Data System (ADS)

Chigrinov, Vladimir

2016-03-01

The advantages of LC photoalignment technology in comparison with common "rubbing" alignment methods tend to the continuation of the research in this field. Almost all the criteria of perfect LC alignment are met in case of azo-dye layers. Nowadays azo-dye alignment materials can be already used in LCD manufacturing, e.g. for the alignment of monomers in LCP films for new generations of photonics and optics devices. Recently the new application of photoaligned technology for the tunable LC lenses with a variable focal distance was proposed. New optically rewritable (ORW) liquid crystal display and photonics devices with a light controllable structure may include LC E-paper screens, LC lenses with a variable focal distance etc. Fast ferroelectric liquid crystal devices (FLCD) are achieved through the application of nano-scale photo aligning (PA) layers in FLC cells. The novel photoaligned FLC devices may include field sequential color (FSC) FLC with a high resolution, high brightness, low power consumption and extended color gamut to be used for PCs, PDAs, switchable goggles, and new generation of switchable 2D/3D LCD TVs, as well as photonics elements.

Photo-switchable tweezers illuminate pore-opening motions of an ATP-gated P2X ion channel

PubMed Central

Habermacher, Chloé; Martz, Adeline; Calimet, Nicolas; Lemoine, Damien; Peverini, Laurie; Specht, Alexandre; Cecchini, Marco; Grutter, Thomas

2016-01-01

P2X receptors function by opening a transmembrane pore in response to extracellular ATP. Recent crystal structures solved in apo and ATP-bound states revealed molecular motions of the extracellular domain following agonist binding. However, the mechanism of pore opening still remains controversial. Here we use photo-switchable cross-linkers as ‘molecular tweezers’ to monitor a series of inter-residue distances in the transmembrane domain of the P2X2 receptor during activation. These experimentally based structural constraints combined with computational studies provide high-resolution models of the channel in the open and closed states. We show that the extent of the outer pore expansion is significantly reduced compared to the ATP-bound structure. Our data further reveal that the inner and outer ends of adjacent pore-lining helices come closer during opening, likely through a hinge-bending motion. These results provide new insight into the gating mechanism of P2X receptors and establish a versatile strategy applicable to other membrane proteins. DOI: http://dx.doi.org/10.7554/eLife.11050.001 PMID:26808983

Ferroelectric based catalysis: Switchable surface chemistry

NASA Astrophysics Data System (ADS)

Kakekhani, Arvin; Ismail-Beigi, Sohrab

2015-03-01

We describe a new class of catalysts that uses an epitaxial monolayer of a transition metal oxide on a ferroelectric substrate. The ferroelectric polarization switches the surface chemistry between strongly adsorptive and strongly desorptive regimes, circumventing difficulties encountered on non-switchable catalytic surfaces where the Sabatier principle dictates a moderate surface-molecule interaction strength. This method is general and can, in principle, be applied to many reactions, and for each case the choice of the transition oxide monolayer can be optimized. Here, as a specific example, we show how simultaneous NOx direct decomposition (into N2 and O2) and CO oxidation can be achieved efficiently on CrO2 terminated PbTiO3, while circumventing oxygen (and sulfur) poisoning issues. One should note that NOx direct decomposition has been an open challenge in automotive emission control industry. Our method can expand the range of catalytically active elements to those which are not conventionally considered for catalysis and which are more economical, e.g., Cr (for NOx direct decomposition and CO oxidation) instead of canonical precious metal catalysts. Primary support from Toyota Motor Engineering and Manufacturing, North America, Inc.

Effective Control of Bioelectricity Generation from a Microbial Fuel Cell by Logical Combinations of pH and Temperature

PubMed Central

Tang, Jiahuan; Liu, Ting; Yuan, Yong

2014-01-01

In this study, a microbial fuel cell (MFC) with switchable power release is designed, which can be logically controlled by combinations of the most physiologically important parameters such as “temperature” and “pH.” Changes in voltage output in response to temperature and pH changes were significant in which voltage output decreased sharply when temperature was lowered from 30°C to 10°C or pH was decreased from 7.0 to 5.0. The switchability of the MFC comes from the microbial anode whose activity is affected by the combined medium temperature and pH. Changes in temperature and pH cause reversible activation-inactivation of the bioanode, thus affecting the activity of the entire MFC. With temperature and pH as input signals, an AND logic operation is constructed for the MFC whose power density is controlled. The developed system has the potential to meet the requirement of power supplies producing electrical power on-demand for self-powered biosensors or biomedical devices. PMID:24741343

Proof-of-concept switchable hydrophobic/hydrophilic patterned surfaces from thermo-mechanically tailored acrylate systems

NASA Astrophysics Data System (ADS)

Laursen, Christopher M.

A novel, proof-of-concept, switchable hydrophobic/hydrophilic structured surface targeted to assist in antifouling of materials in aqueous environments was created through the development of a multi-tiered platform. The understructure consists of a thermo-mechanically tailored acrylate based polymer patterned in a pillared array, which was then overlaid with spatially tailored hydrophobic/hydrophilic surface chemistry treatments. Development focused on the synthesis of a ternary acrylate system displaying proper thermo-mechanical behavior in submerged conditions for the understructure, creation of a sufficient soft molding technique, and methods to chemically alter water-surface wetting interactions. The final acrylate based polymer constituents were chosen based on expected low-toxicity and the ability to be photopolymerized, while the final system displayed appropriate mechanical toughness, water absorption, and material stiffness over a select temperature window. This was important as alteration in wettability characteristics relied upon a stark transition in the polymeric materials stiffness within a narrow temperature range. The material qualitatively displayed a more hydrophobic state with the pillared surface structures erect, and a more hydrophilic state with the pillars bent over.

Charge-controlled switchable CO adsorption on FeN4 cluster embedded in graphene

NASA Astrophysics Data System (ADS)

Omidvar, Akbar

2018-02-01

Electrical charging of an FeN4 cluster embedded in graphene (FeN4G) is proposed as an approach for electrocatalytically switchable carbon monoxide (CO) adsorption. Using density functional theory (DFT), we found that the CO molecule is strongly adsorbed on the uncharged FeN4G cluster. Our results show that the adsorption energy of a CO molecule on the FeN4G cluster is dramatically decreased by introducing extra electrons into the cluster. Once the charges are removed, the CO molecule is spontaneously adsorbed on the FeN4G absorbent. In the framework of frontier molecular orbital (FMO) analysis, the enhanced sensitivity and reactivity of the FeN4G cluster towards the CO molecule can be interpreted in terms of interaction between the HOMO of CO molecule and the LUMO of FeN4G cluster. Therefore, this approach promises both facile reversibility and tunable kinetics without the need of specific catalysts. Our study indicates that the FeN4G nanomaterial is an excellent absorbent for controllable and reversible capture and release of the CO.

A Dual-Modality System for Both Multi-Color Ultrasound-Switchable Fluorescence and Ultrasound Imaging

PubMed Central

Kandukuri, Jayanth; Yu, Shuai; Cheng, Bingbing; Bandi, Venugopal; D’Souza, Francis; Nguyen, Kytai T.; Hong, Yi; Yuan, Baohong

2017-01-01

Simultaneous imaging of multiple targets (SIMT) in opaque biological tissues is an important goal for molecular imaging in the future. Multi-color fluorescence imaging in deep tissues is a promising technology to reach this goal. In this work, we developed a dual-modality imaging system by combining our recently developed ultrasound-switchable fluorescence (USF) imaging technology with the conventional ultrasound (US) B-mode imaging. This dual-modality system can simultaneously image tissue acoustic structure information and multi-color fluorophores in centimeter-deep tissue with comparable spatial resolutions. To conduct USF imaging on the same plane (i.e., x-z plane) as US imaging, we adopted two 90°-crossed ultrasound transducers with an overlapped focal region, while the US transducer (the third one) was positioned at the center of these two USF transducers. Thus, the axial resolution of USF is close to the lateral resolution, which allows a point-by-point USF scanning on the same plane as the US imaging. Both multi-color USF and ultrasound imaging of a tissue phantom were demonstrated. PMID:28165390