A Simple Method for Decreasing the Liquid Junction Potential in a Flow-through-Type Differential pH Sensor Probe Consisting of pH-FETs by Exerting Spatiotemporal Control of the Liquid Junction

PubMed Central

Yamada, Akira; Mohri, Satoshi; Nakamura, Michihiro; Naruse, Keiji

2015-01-01

The liquid junction potential (LJP), the phenomenon that occurs when two electrolyte solutions of different composition come into contact, prevents accurate measurements in potentiometry. The effect of the LJP is usually remarkable in measurements of diluted solutions with low buffering capacities or low ion concentrations. Our group has constructed a simple method to eliminate the LJP by exerting spatiotemporal control of a liquid junction (LJ) formed between two solutions, a sample solution and a baseline solution (BLS), in a flow-through-type differential pH sensor probe. The method was contrived based on microfluidics. The sensor probe is a differential measurement system composed of two ion-sensitive field-effect transistors (ISFETs) and one Ag/AgCl electrode. With our new method, the border region of the sample solution and BLS is vibrated in order to mix solutions and suppress the overshoot after the sample solution is suctioned into the sensor probe. Compared to the conventional method without vibration, our method shortened the settling time from over two min to 15 s and reduced the measurement error by 86% to within 0.060 pH. This new method will be useful for improving the response characteristics and decreasing the measurement error of many apparatuses that use LJs. PMID:25835300

Vortex motion and dynamical states in Josephson arrays

NASA Astrophysics Data System (ADS)

Trias, Enrique

Underdamped Josephson junction arrays are used as model systems to study novel nonlinear effects. A combination of experiments, numerical simulations, and analytical analysis is used to probe different nonlinear behavior such as intrinsic localized modes, resonances in fully frustrated arrays, Meissner-like states, and vortex ratchets. Circuit models of Josephson networks are also developed, and applied to the design and measurement of parallel array oscillators. Ladder arrays have been used for an experimental study of intrinsic localized modes, or discrete breathers. Measurements of breather stability indicate that the maximum allowable bias current is proportional to the array depinning current while the minimum current is related to a junction retrapping mechanism. This retrapping instability usually leads to the formation of multi-site breathers. Collisions between the two nonlinear excitations in ladder arrays, discrete breathers and vortices, have also been numerically investigated. Discrete breathers act as pinning centers to vortex motion and the collisions can be modeled by an energy barrier activation process. When vortices are thermally induced over this barrier, a two-site breather is created. Experiments also reveal remarkable similarities among the do current-voltage characteristics of several kinds of square and triangular arrays, where two resonant voltages are observed. Simulations indicate that at full frustration a dynamical checkerboard state underlies these similarities. For such a traveling solution, the governing equations of the arrays are reduced to three coupled pendulum equations that have two characteristic resonant frequencies. Finally, a kink ratchet potential has been designed using a parallel array of Josephson junctions with alternating cell inductances and junctions areas. Experiments show that the depinning current depends on the direction of the applied current. Other properties of the depinning current versus applied field, such as a long period and a lack of reflection symmetry, have been observed and explained analytically. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139- 4307. Ph. 617-253-5668; Fax 617-253-1690.)

Pulse-voltammetric glucose detection at gold junction electrodes.

PubMed

Rassaei, Liza; Marken, Frank

2010-09-01

A novel glucose sensing concept based on the localized change or "modulation" in pH within a symmetric gold-gold junction electrode is proposed. A paired gold-gold junction electrode (average gap size ca. 500 nm) is prepared by simultaneous bipotentiostatic electrodeposition of gold onto two closely spaced platinum disk electrodes. For glucose detection in neutral aqueous solution, the potential of the "pH-modulator" electrode is set to -1.5 V vs saturated calomel reference electrode (SCE) to locally increase the pH, and simultaneously, either cyclic voltammetry or square wave voltammetry experiments are conducted at the sensor electrode. A considerable improvement in the sensor electrode response is observed when a normal pulse voltammetry sequence is applied to the modulator electrode (to generate "hydroxide pulses") and the glucose sensor electrode is operated with fixed bias at +0.5 V vs SCE (to eliminate capacitive charging currents). Preliminary data suggest good linearity for the glucose response in the medically relevant 1-10 mM concentration range (corresponding to 0.18-1.8 g L(-1)). Future electroanalytical applications of multidimensional pulse voltammetry in junction electrodes are discussed.

Low Level Pro-inflammatory Cytokines Decrease Connexin36 Gap Junction Coupling in Mouse and Human Islets through Nitric Oxide-mediated Protein Kinase Cδ.

PubMed

Farnsworth, Nikki L; Walter, Rachelle L; Hemmati, Alireza; Westacott, Matthew J; Benninger, Richard K P

2016-02-12

Pro-inflammatory cytokines contribute to the decline in islet function during the development of diabetes. Cytokines can disrupt insulin secretion and calcium dynamics; however, the mechanisms underlying this are poorly understood. Connexin36 gap junctions coordinate glucose-induced calcium oscillations and pulsatile insulin secretion across the islet. Loss of gap junction coupling disrupts these dynamics, similar to that observed during the development of diabetes. This study investigates the mechanisms by which pro-inflammatory cytokines mediate gap junction coupling. Specifically, as cytokine-induced NO can activate PKCδ, we aimed to understand the role of PKCδ in modulating cytokine-induced changes in gap junction coupling. Isolated mouse and human islets were treated with varying levels of a cytokine mixture containing TNF-α, IL-1β, and IFN-γ. Islet dysfunction was measured by insulin secretion, calcium dynamics, and gap junction coupling. Modulators of PKCδ and NO were applied to determine their respective roles in modulating gap junction coupling. High levels of cytokines caused cell death and decreased insulin secretion. Low levels of cytokine treatment disrupted calcium dynamics and decreased gap junction coupling, in the absence of disruptions to insulin secretion. Decreases in gap junction coupling were dependent on NO-regulated PKCδ, and altered membrane organization of connexin36. This study defines several mechanisms underlying the disruption to gap junction coupling under conditions associated with the development of diabetes. These mechanisms will allow for greater understanding of islet dysfunction and suggest ways to ameliorate this dysfunction during the development of diabetes. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Myosin II Controls Junction Fluctuations to Guide Epithelial Tissue Ordering.

PubMed

Curran, Scott; Strandkvist, Charlotte; Bathmann, Jasper; de Gennes, Marc; Kabla, Alexandre; Salbreux, Guillaume; Baum, Buzz

2017-11-20

Under conditions of homeostasis, dynamic changes in the length of individual adherens junctions (AJs) provide epithelia with the fluidity required to maintain tissue integrity in the face of intrinsic and extrinsic forces. While the contribution of AJ remodeling to developmental morphogenesis has been intensively studied, less is known about AJ dynamics in other circumstances. Here, we study AJ dynamics in an epithelium that undergoes a gradual increase in packing order, without concomitant large-scale changes in tissue size or shape. We find that neighbor exchange events are driven by stochastic fluctuations in junction length, regulated in part by junctional actomyosin. In this context, the developmental increase of isotropic junctional actomyosin reduces the rate of neighbor exchange, contributing to tissue order. We propose a model in which the local variance in tension between junctions determines whether actomyosin-based forces will inhibit or drive the topological transitions that either refine or deform a tissue. Copyright © 2017. Published by Elsevier Inc.

Dynamic current susceptibility as a probe of Majorana bound states in nanowire-based Josephson junctions

NASA Astrophysics Data System (ADS)

Trif, Mircea; Dmytruk, Olesia; Bouchiat, Hélène; Aguado, Ramón; Simon, Pascal

2018-02-01

We theoretically study a Josephson junction based on a semiconducting nanowire subject to a time-dependent flux bias. We establish a general density-matrix approach for the dynamical response of the Majorana junction and calculate the resulting flux-dependent susceptibility using both microscopic and effective low-energy descriptions for the nanowire. We find that the diagonal component of the susceptibility, associated with the dynamics of the Majorana state populations, dominates over the standard Kubo contribution for a wide range of experimentally relevant parameters. The diagonal term, explored, in this Rapid Communication, in the context of Majorana physics, allows probing accurately the presence of Majorana bound states in the junction.

The precipitation of aluminum, iron and manganese at the junction of Deer Creek with the Snake River in Summit County, Colorado

USGS Publications Warehouse

Theobald, P.K.; Lakin, H.W.; Hawkins, D.B.

1963-01-01

The oxidation of disseminated pyrite in relatively acid schists and gneisses of the Snake River drainage basin provides abundant iron sulfate and sulfuric acid to ground and surface water. This acid water dissolves large quantities of many elements, particularly aluminum and surprisingly large quantities of elements, such as magnesium and zinc, not expected to be abundant in the drainage basin. The adjoining drainage to the west, Deer Creek, is underlain by basic rocks, from which the water inherits a high pH. Despite the presence of base- and precious- metal veins in the drainage basin of Deer Creek, it carries less metal than the Snake River. The principal precipitate on the bed of the Snake River is hydrated iron oxide with small quantities of the other metals. In Deer Creek manganese oxide is precipitated with iron oxide and large quantities of other metals are carried down with this precipitate. Below the junction of these streams the pH stabilizes at a near-neutral value. Iron is removed from the Snake River water at the junction, and aluminum is precipitated for some distance downstream. The aluminum precipitate carries down other metals in concentrations slightly less than that in the manganese precipitate on Deer Creek. The natural processes observed in this junction if carried to a larger scale could provide the mechanism described by Ansheles (1927) for the formation of bauxite. In the environment described, geochemical exploration by either water or stream sediment techniques is difficult because of (1) the extreme pH differential between the streams above their junction and (2) the difference in the precipitates formed on the streambeds. ?? 1963.

Observing Holliday junction branch migration one step at a time

NASA Astrophysics Data System (ADS)

Ha, Taekjip

2004-03-01

During genetic recombination, two homologous DNA molecules undergo strand exchange to form a four-way DNA (Holliday) junction and the recognition and processing of this species by branch migration and junction resolving enzymes determine the outcome. We have used single molecule fluorescence techniques to study two intrinsic structural dynamics of the Holliday junction, stacking conformer transitions and spontaneous branch migration. Our studies show that the dynamics of branch migration, resolved with one base pair resolution, is determined by the stability of conformers which in turn depends on the local DNA sequences. Therefore, the energy landscape of Holliday junction branch migation is not uniform, but is rugged.

Measure synchronization in a spin-orbit-coupled bosonic Josephson junction

NASA Astrophysics Data System (ADS)

Wang, Wen-Yuan; Liu, Jie; Fu, Li-Bin

2015-11-01

We present measure synchronization (MS) in a bosonic Josephson junction with spin-orbit coupling. The two atomic hyperfine states are coupled by a Raman dressing scheme, and they are regarded as two orientations of a pseudo-spin-1 /2 system. A feature specific to a spin-orbit-coupled (SOC) bosonic Josephson junction is that the transition from non-MS to MS dynamics can be modulated by Raman laser intensity, even in the absence of interspin atomic interaction. A phase diagram of non-MS and MS dynamics as functions of Raman laser intensity and Josephson tunneling amplitude is presented. Taking into account interspin atomic interactions, the system exhibits MS breaking dynamics resulting from the competition between intraspin and interspin atomic interactions. When interspin atomic interactions dominate in the competition, the system always exhibits MS dynamics. For interspin interaction weaker than intraspin interaction, a window for non-MS dynamics is present. Since SOC Bose-Einstein condensates provide a powerful platform for studies on physical problems in various fields, the study of MS dynamics is valuable in researching the collective coherent dynamical behavior in a spin-orbit-coupled bosonic Josephson junction.

Neogenin recruitment of the WAVE regulatory complex maintains adherens junction stability and tension

PubMed Central

Lee, Natalie K.; Fok, Ka Wai; White, Amanda; Wilson, Nicole H.; O'Leary, Conor J.; Cox, Hayley L.; Michael, Magdalene; Yap, Alpha S.; Cooper, Helen M.

2016-01-01

To maintain tissue integrity during epithelial morphogenesis, adherens junctions (AJs) must resist the mechanical stresses exerted by dynamic tissue movements. Junctional stability is dependent on actomyosin contractility within the actin ring. Here we describe a novel function for the axon guidance receptor, Neogenin, as a key component of the actin nucleation machinery governing junctional stability. Loss of Neogenin perturbs AJs and attenuates junctional tension. Neogenin promotes actin nucleation at AJs by recruiting the Wave regulatory complex (WRC) and Arp2/3. A direct interaction between the Neogenin WIRS domain and the WRC is crucial for the spatially restricted recruitment of the WRC to the junction. Thus, we provide the first example of a functional WIRS–WRC interaction in epithelia. We further show that Neogenin regulates cadherin recycling at the AJ. In summary, we identify Neogenin as a pivotal component of the AJ, where it influences both cadherin dynamics and junctional tension. PMID:27029596

Quantifying cadherin mechanotransduction machinery assembly/disassembly dynamics using fluorescence covariance analysis.

PubMed

Vedula, Pavan; Cruz, Lissette A; Gutierrez, Natasha; Davis, Justin; Ayee, Brian; Abramczyk, Rachel; Rodriguez, Alexis J

2016-06-30

Quantifying multi-molecular complex assembly in specific cytoplasmic compartments is crucial to understand how cells use assembly/disassembly of these complexes to control function. Currently, biophysical methods like Fluorescence Resonance Energy Transfer and Fluorescence Correlation Spectroscopy provide quantitative measurements of direct protein-protein interactions, while traditional biochemical approaches such as sub-cellular fractionation and immunoprecipitation remain the main approaches used to study multi-protein complex assembly/disassembly dynamics. In this article, we validate and quantify multi-protein adherens junction complex assembly in situ using light microscopy and Fluorescence Covariance Analysis. Utilizing specific fluorescently-labeled protein pairs, we quantified various stages of adherens junction complex assembly, the multiprotein complex regulating epithelial tissue structure and function following de novo cell-cell contact. We demonstrate: minimal cadherin-catenin complex assembly in the perinuclear cytoplasm and subsequent localization to the cell-cell contact zone, assembly of adherens junction complexes, acto-myosin tension-mediated anchoring, and adherens junction maturation following de novo cell-cell contact. Finally applying Fluorescence Covariance Analysis in live cells expressing fluorescently tagged adherens junction complex proteins, we also quantified adherens junction complex assembly dynamics during epithelial monolayer formation.

Temporo-Parietal Junction Activity in Theory-of-Mind Tasks: Falseness, Beliefs, or Attention

ERIC Educational Resources Information Center

Aichhorn, Markus; Perner, Josef; Weiss, Benjamin; Kronbichler, Martin; Staffen, Wolfgang; Ladurner, Gunther

2009-01-01

By combining the false belief (FB) and photo (PH) vignettes to identify theory-of-mind areas with the false sign (FS) vignettes, we re-establish the functional asymmetry between the left and right temporo-parietal junction (TPJ). The right TPJ (TPJ-R) is specially sensitive to processing belief information, whereas the left TPJ (TPJ-L) is equally…

Unfolding of a branched double-helical DNA three-way junction with triple-helical ends.

PubMed

Hüsler, P L; Klump, H H

1994-08-15

We have designed three oligonucleotides (33 mers) which when mixed in a 1:1:1 ratio form double-helical DNA three-way junctions with triple helical ends in the pH interval pH 4 to 5.5. The triplex to coil transition is initiated by raising the temperature and was recorded by temperature gradient gel electrophoresis, uv melting, and differential scanning calorimetry. The transitions can be deconvoluted into three subtransitions representing the independent thermal denaturation of each of the arms. We have proposed a model for the unfolding pathway and give the thermodynamic parameters for each step as calculated using the formalism outlined in the appendix.

10.4% Efficient triple organic solar cells containing near infrared absorbers

NASA Astrophysics Data System (ADS)

Meerheim, Rico; Körner, Christian; Oesen, Benjamin; Leo, Karl

2016-03-01

The efficiency of organic solar cells can be increased by serially stacked subcells with spectrally different absorber materials. For the triple junction devices presented here, we use the small molecule donor materials DCV5T-Me for the green region and Tol2-benz-bodipy or Ph2-benz-bodipy as near infrared absorbers. The broader spectral response allows an efficiency increase from a pure DCV5T-Me triple cell to a triple junction containing a Ph2-benz-bodipy subcell, reaching 10.4%. As often observed for organic photovoltaics, the efficiency is further increased at low light intensities to 11%, which allows improved energy harvesting under real outdoor conditions and better performance indoor.

A four-way junction with triple-helical arms: design, characterization, and stability.

PubMed

Makube, N; Klump, H H

2000-05-01

The formation of the four-way junction containing four triple-helical arms has been demonstrated using chemical methods (polyacrylamide gel electrophoresis and chemical footprinting using OsO(4) as a probe) and physical methods (UV absorbance melting and DSC). The junction J(T1T3) was assembled from two 20-mer purine strands and two 44-mer pyrimidine strands. To determine the contribution of the different arms to the stability of the complete structure of J(T1T3), the junction was compared to two simplified substructures, J(T1) and J(T3), respectively. Common to these complexes is the underlying double-helical four-way junction Js. Addition of Na(+) had a profound effect on stabilizing and subsequently folding the junctions into the stacked X-structures. The following results support the structure present: (i) The native polyacrylamide electrophoresis exhibits only a single band(s) corresponding to one species present when all four single strands are mixed in equal amounts. (ii) OsO(4) modifications were investigated at pH 5.0 and in the presence of 10 mM Mg(2+) and 100 mM Na(+). There is no cleavage of thymine residues at the branch point and throughout the structure. (iii) The thermal unfolding of J(T1) and J(T3) illustrates that the triple-helical arms are more stable than the double-helical arms which are contained in these junctions and that J(T1T3) with four triple-helical arms is slightly more stable than J(T1) and J(T3). (iv) The calorimetric transition enthalpies determined for the arms of J(T1T3) are comparable to those associated with the unfolding of its corresponding arms in J(T1) and J(T3). The results also illustrate that the formation of the junctions is not restricted by the pH, [Na(+)], sequence composition of the arms, and/or the loop position. Copyright 2000 Academic Press.

Signaling from the Podocyte Intercellular Junction to the Actin Cytoskeleton

PubMed Central

George, Britta; Holzman, Lawrence B.

2012-01-01

Observations of hereditary glomerular disease support the contention that podocyte intercellular junction proteins are essential for junction formation and maintenance. Genetic deletion of most of these podocyte intercellular junction proteins results in foot process effacement and proteinuria. This review focuses on the current understanding of molecular mechanisms by which podocyte intercellular junction proteins such as the Nephrin-Neph1-Podocin receptor complex coordinate cytoskeletal dynamics and thus intercellular junction formation, maintenance and injury-dependent remodeling. PMID:22958485

Chaos and multi-scroll attractors in RCL-shunted junction coupled Jerk circuit connected by memristor

PubMed Central

Zhou, Ping; Ahmad, Bashir; Ren, Guodong; Wang, Chunni

2018-01-01

In this paper, a new four-variable dynamical system is proposed to set chaotic circuit composed of memristor and Josephson junction, and the dependence of chaotic behaviors on nonlinearity is investigated. A magnetic flux-controlled memristor is used to couple with the RCL-shunted junction circuit, and the dynamical behaviors can be modulated by changing the coupling intensity between the memristor and the RCL-shunted junction. Bifurcation diagram and Lyapunov exponent are calculated to confirm the emergence of chaos in the improved dynamical system. The outputs and dynamical behaviors can be controlled by the initial setting and external stimulus as well. As a result, chaos can be suppressed and spiking occurs in the sampled outputs under negative feedback, while applying positive feedback type via memristor can be effective to trigger chaos. Furthermore, it is found that the number of multi-attractors in the Jerk circuit can be modulated when memristor coupling is applied on the circuit. These results indicate that memristor coupling can be effective to control chaotic circuits and it is also useful to reproduce dynamical behaviors for neuronal activities. PMID:29342178

Chaos and multi-scroll attractors in RCL-shunted junction coupled Jerk circuit connected by memristor.

PubMed

Ma, Jun; Zhou, Ping; Ahmad, Bashir; Ren, Guodong; Wang, Chunni

2018-01-01

In this paper, a new four-variable dynamical system is proposed to set chaotic circuit composed of memristor and Josephson junction, and the dependence of chaotic behaviors on nonlinearity is investigated. A magnetic flux-controlled memristor is used to couple with the RCL-shunted junction circuit, and the dynamical behaviors can be modulated by changing the coupling intensity between the memristor and the RCL-shunted junction. Bifurcation diagram and Lyapunov exponent are calculated to confirm the emergence of chaos in the improved dynamical system. The outputs and dynamical behaviors can be controlled by the initial setting and external stimulus as well. As a result, chaos can be suppressed and spiking occurs in the sampled outputs under negative feedback, while applying positive feedback type via memristor can be effective to trigger chaos. Furthermore, it is found that the number of multi-attractors in the Jerk circuit can be modulated when memristor coupling is applied on the circuit. These results indicate that memristor coupling can be effective to control chaotic circuits and it is also useful to reproduce dynamical behaviors for neuronal activities.

Collective Calcium Signaling of Defective Multicellular Networks

NASA Astrophysics Data System (ADS)

Potter, Garrett; Sun, Bo

2015-03-01

A communicating multicellular network processes environmental cues into collective cellular dynamics. We have previously demonstrated that, when excited by extracellular ATP, fibroblast monolayers generate correlated calcium dynamics modulated by both the stimuli and gap junction communication between the cells. However, just as a well-connected neural network may be compromised by abnormal neurons, a tissue monolayer can also be defective with cancer cells, which typically have down regulated gap junctions. To understand the collective cellular dynamics in a defective multicellular network we have studied the calcium signaling of co-cultured breast cancer cells and fibroblast cells in various concentrations of ATP delivered through microfluidic devices. Our results demonstrate that cancer cells respond faster, generate singular spikes, and are more synchronous across all stimuli concentrations. Additionally, fibroblast cells exhibit persistent calcium oscillations that increase in regularity with greater stimuli. To interpret these results we quantitatively analyzed the immunostaining of purigenic receptors and gap junction channels. The results confirm our hypothesis that collective dynamics are mainly determined by the availability of gap junction communications.

Structure-dependent magnetoresistance and spin-transfer torque in antiferromagnetic Fe |MgO |FeMn |Cu tunnel junctions

NASA Astrophysics Data System (ADS)

Jia, Xingtao; Tang, Huimin; Wang, Shizhuo; Qin, Minghui

2017-02-01

We predict large magnetoresistance (MR) and spin transfer torque (STT) in antiferromagnetic Fe |MgO |FeMn |Cu tunnel junctions based on first-principles scattering theory. MR as large as ˜100 % is found in one junction. Magnetic dynamic simulations show that STT acting on the antiferromagnetic order parameter dominates the spin dynamics, and an electronic bias of order 10-1mV and current density of order 105Acm-2 can switches a junction of three-layer MgO, they are about one order smaller than that in Fe |MgO |Fe junction with the same barrier thickness, respectively. The multiple scattering in the antiferromagnetic region is considered to be responsible for the enhanced spin torque and smaller switching current density.

Modulation of Connexin-36 Gap Junction Channels by Intracellular pH and Magnesium Ions.

PubMed

Rimkute, Lina; Kraujalis, Tadas; Snipas, Mindaugas; Palacios-Prado, Nicolas; Jotautis, Vaidas; Skeberdis, Vytenis A; Bukauskas, Feliksas F

2018-01-01

Connexin-36 (Cx36) protein forms gap junction (GJ) channels in pancreatic beta cells and is also the main Cx isoform forming electrical synapses in the adult mammalian brain. Cx36 GJs can be regulated by intracellular pH (pH i ) and cytosolic magnesium ion concentration ([Mg 2+ ] i ), which can vary significantly under various physiological and pathological conditions. However, the combined effect and relationship of these two factors over Cx36-dependent coupling have not been previously studied in detail. Our experimental results in HeLa cells expressing Cx36 show that changes in both pH i and [Mg 2+ ] i affect junctional conductance (g j ) in an interdependent manner; in other words, intracellular acidification cause increase or decay in g j depending on whether [Mg 2+ ] i is high or low, respectively, and intracellular alkalization cause reduction in g j independently of [Mg 2+ ] i . Our experimental and modelling data support the hypothesis that Cx36 GJ channels contain two separate gating mechanisms, and both are differentially sensitive to changes in pH i and [Mg 2+ ] i . Using recombinant Cx36 we found that two glutamate residues in the N-terminus could be partly responsible for the observed interrelated effect of pH i and [Mg 2+ ] i . Mutation of glutamate at position 8 attenuated the stimulatory effect of intracellular acidification at high [Mg 2+ ] i , while mutation at position 12 and double mutation at both positions reversed stimulatory effect to inhibition. Moreover, Cx36 * E8Q lost the initial increase of g j at low [Mg 2+ ] i and double mutation lost the sensitivity to high [Mg 2+ ] i . These results suggest that E8 and E12 are involved in regulation of Cx36 GJ channels by Mg 2+ and H + ions.

Hiatus hernia in healthy volunteers is associated with intrasphincteric reflux and cardiac mucosal lengthening without traditional reflux.

PubMed

Robertson, Elaine V; Derakhshan, Mohammad H; Wirz, Angela A; Mitchell, David R; Going, James J; Kelman, Andrew W; Ballantyne, Stuart A; McColl, Kenneth E L

2017-07-01

Hiatus hernia (HH) is a key mediator of gastro-oesophageal reflux disease but little is known about its significance in the general population. We studied the structure and function of the gastro-oesophageal junction in healthy volunteers with and without HH. We compared 15 volunteers with HH, detected by endoscopy or MRI scan, but without gastro-oesophageal reflux disease with 15 controls matched for age, gender and body weight. Jumbo biopsies were taken across the squamocolumnar junction (SCJ). High-resolution pH metry (12 sensors) and manometry (36 sensors) were performed upright and supine, before and after a meal. The SCJ was marked with an endoscopically placed clip and visualised fluoroscopically. Cardiac mucosa was longer in volunteers with HH (3.5 vs 2.5 mm, p=0.01). There was no excessive acid reflux 5 cm above the upper border of the lower oesophageal sphincter (LOS) in either group but those with HH had short segment reflux 11 mm above the pH transition point after the meal when supine (pH<4 for 5.5% vs 0.3% of time, p=0.01). The SCJ and pH transition point were proximally displaced within the gastro-oesophageal junction in those with HH versus controls (p<0.05). The pH transition point was proximal to the peak LOS pressure point in HH subjects but distal to it in controls after the meal (p<0.05). When supine, the postprandial pH transition point crossed the SCJ in those with HH (p=0.03). Healthy volunteers with HH have increased intrasphincteric reflux and lengthening of cardiac mucosa in the absence of traditional transsphincteric reflux. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Recent advances in enhancing the sensitivity of electrophoresis and electrochromatography in capillaries and microchips (2014-2016).

PubMed

Breadmore, Michael C; Wuethrich, Alain; Li, Feng; Phung, Sui Ching; Kalsoom, Umme; Cabot, Joan M; Tehranirokh, Masoomeh; Shallan, Aliaa I; Abdul Keyon, Aemi S; See, Hong Heng; Dawod, Mohamed; Quirino, Joselito P

2017-01-01

One of the most cited limitations of capillary (and microchip) electrophoresis is the poor sensitivity. This review continues to update this series of biennial reviews, first published in Electrophoresis in 2007, on developments in the field of on-line/in-line concentration methods in capillaries and microchips, covering the period July 2014-June 2016. It includes developments in the field of stacking, covering all methods from field amplified sample stacking and large volume sample stacking, through to isotachophoresis, dynamic pH junction, and sweeping. Attention is also given to on-line or in-line extraction methods that have been used for electrophoresis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Single molecule dynamics at a mechanically controllable break junction in solution at room temperature.

PubMed

Konishi, Tatsuya; Kiguchi, Manabu; Takase, Mai; Nagasawa, Fumika; Nabika, Hideki; Ikeda, Katsuyoshi; Uosaki, Kohei; Ueno, Kosei; Misawa, Hiroaki; Murakoshi, Kei

2013-01-23

The in situ observation of geometrical and electronic structural dynamics of a single molecule junction is critically important in order to further progress in molecular electronics. Observations of single molecular junctions are difficult, however, because of sensitivity limits. Here, we report surface-enhanced Raman scattering (SERS) of a single 4,4'-bipyridine molecule under conditions of in situ current flow in a nanogap, by using nano-fabricated, mechanically controllable break junction (MCBJ) electrodes. When adsorbed at room temperature on metal nanoelectrodes in solution to form a single molecule junction, statistical analysis showed that nontotally symmetric b(1) and b(2) modes of 4,4'-bipyridine were strongly enhanced relative to observations of the same modes in solid or aqueous solutions. Significant changes in SERS intensity, energy (wavenumber), and selectivity of Raman vibrational bands that are coincident with current fluctuations provide information on distinct states of electronic and geometrical structure of the single molecule junction, even under large thermal fluctuations occurring at room temperature. We observed the dynamics of 4,4'-bipyridine motion between vertical and tilting configurations in the Au nanogap via b(1) and b(2) mode switching. A slight increase in the tilting angle of the molecule was also observed by noting the increase in the energies of Raman modes and the decrease in conductance of the molecular junction.

Live-cell imaging of ER-PM contact architecture by a novel TIRFM approach reveals extension of junctions in response to store-operated Ca2+-entry.

PubMed

Poteser, Michael; Leitinger, Gerd; Pritz, Elisabeth; Platzer, Dieter; Frischauf, Irene; Romanin, Christoph; Groschner, Klaus

2016-10-19

Nanometer-spaced appositions between endoplasmic reticulum and plasma membrane (ER-PM junctions) stabilized by membrane-joining protein complexes are critically involved in cellular Ca 2+ -handling and lipid trafficking. ER-PM junctional architecture and plasticity associated with inter-membrane communication are as yet barely understood. Here, we introduce a method to precisely characterize ER-PM junction morphology and dynamics with high temporal resolution and minimal disturbance of junctional intermembrane communication. We show that expression of soluble cytosolic fluorophores in combination with TIRFM enables to delineate ER and PM distance in the range of 10-150 nm. Live-cell imaging of sub-plasmalemmal structures in RBL-2H3 mast cells by this method, designated as fluorescence density mapping (FDM), revealed profound dynamics of ER-PM contact sites in response to store-depletion. We report the existence of a Ca 2+ -dependent process that expands the junctional ER to enlarge its contact surface with the PM, thereby promoting and stabilizing STIM1-Orai1 competent ER-PM junctions.

Supramolecular motifs in dynamic covalent PEG-hemiaminal organogels

PubMed Central

Fox, Courtney H.; ter Hurrne, Gijs M.; Wojtecki, Rudy J.; Jones, Gavin O.; Horn, Hans W.; Meijer, E. W.; Frank, Curtis W.; Hedrick, James L.; García, Jeannette M.

2015-01-01

Dynamic covalent materials are stable materials that possess reversible behaviour triggered by stimuli such as light, redox conditions or temperature; whereas supramolecular crosslinks depend on the equilibrium constant and relative concentrations of crosslinks as a function of temperature. The combination of these two reversible chemistries can allow access to materials with unique properties. Here, we show that this combination of dynamic covalent and supramolecular chemistry can be used to prepare organogels comprising distinct networks. Two materials containing hemiaminal crosslink junctions were synthesized; one material is comprised of dynamic covalent junctions and the other contains hydrogen-bonding bis-hemiaminal moieties. Under specific network synthesis conditions, these materials exhibited self-healing behaviour. This work reports on both the molecular-level detail of hemiaminal crosslink junction formation as well as the macroscopic behaviour of hemiaminal dynamic covalent network (HDCN) elastomeric organogels. These materials have potential applications as elastomeric components in printable materials, cargo carriers and adhesives. PMID:26174864

Nonlinear Gap Junctions Enable Long-Distance Propagation of Pulsating Calcium Waves in Astrocyte Networks

PubMed Central

Goldberg, Mati; De Pittà, Maurizio; Volman, Vladislav; Berry, Hugues; Ben-Jacob, Eshel

2010-01-01

A new paradigm has recently emerged in brain science whereby communications between glial cells and neuron-glia interactions should be considered together with neurons and their networks to understand higher brain functions. In particular, astrocytes, the main type of glial cells in the cortex, have been shown to communicate with neurons and with each other. They are thought to form a gap-junction-coupled syncytium supporting cell-cell communication via propagating Ca2+ waves. An identified mode of propagation is based on cytoplasm-to-cytoplasm transport of inositol trisphosphate (IP3) through gap junctions that locally trigger Ca2+ pulses via IP3-dependent Ca2+-induced Ca2+ release. It is, however, currently unknown whether this intracellular route is able to support the propagation of long-distance regenerative Ca2+ waves or is restricted to short-distance signaling. Furthermore, the influence of the intracellular signaling dynamics on intercellular propagation remains to be understood. In this work, we propose a model of the gap-junctional route for intercellular Ca2+ wave propagation in astrocytes. Our model yields two major predictions. First, we show that long-distance regenerative signaling requires nonlinear coupling in the gap junctions. Second, we show that even with nonlinear gap junctions, long-distance regenerative signaling is favored when the internal Ca2+ dynamics implements frequency modulation-encoding oscillations with pulsating dynamics, while amplitude modulation-encoding dynamics tends to restrict the propagation range. As a result, spatially heterogeneous molecular properties and/or weak couplings are shown to give rise to rich spatiotemporal dynamics that support complex propagation behaviors. These results shed new light on the mechanisms implicated in the propagation of Ca2+ waves across astrocytes and the precise conditions under which glial cells may participate in information processing in the brain. PMID:20865153

Experimental Testing and Modeling Analysis of Solute Mixing at Water Distribution Pipe Junctions

EPA Science Inventory

Flow dynamics at a pipe junction controls particle trajectories, solute mixing and concentrations in downstream pipes. Here we have categorized pipe junctions into five hydraulic types, for which flow distribution factors and analytical equations for describing the solute mixing ...

Statistical characterization of voltage-biased SQUIDs with weakly damped junctions

NASA Astrophysics Data System (ADS)

Liu, Chao; Zhang, Yi; Mück, Michael; Zhang, Shulin; Krause, Hans-Joachim; Braginski, Alex I.; Zhang, Guofeng; Wang, Yongliang; Kong, Xiangyan; Xie, Xiaoming; Offenhäusser, Andreas; Jiang, Mianheng

2013-06-01

Recently, it has been shown that voltage-biased readout of SQUIDs with weakly damped junctions (large Stewart-McCumber parameter βc, due to high shunt resistance) is useful for suppression of preamplifier noise. We experimentally studied the characteristics of 53 planar niobium-SQUID magnetometers with junction shunt resistors RJ nominally of 30 Ω fabricated on 5 × 5 mm2 chips. The field-to-flux transfer coefficient ∂B/∂Φ of the magnetometers was 1.5 nT/Φ0, with a SQUID loop inductance Ls of about 350 pH. The distributions of important SQUID parameters, such as the current swing Iswing, the dynamic resistance Rd, and the flux-to-voltage transfer coefficient ∂V/∂Φ, are given. Nearly all the SQUIDs could be stably operated in the voltage bias mode and their ∂V/∂Φ reached a large mean value of 380 μV/Φ0. In this case, the SQUIDs can be read out directly by a commercial operational amplifier without any additional means to suppress preamplifier noise. The mean flux noise of the SQUIDs was found to be 4.5 μΦ0 Hz-1/2, corresponding to a field resolution of 7 fT Hz-1/2. To demonstrate the applicability of these SQUIDs in the direct readout scheme, a simple four-channel SQUID gradiometer system was set up to perform magnetocardiography and magnetoencephalography measurements in a magnetically shielded room.

Calcium dynamics in cardiac excitatory and non-excitatory cells and the role of gap junction.

PubMed

Das, Phonindra Nath; Mehrotra, Parul; Mishra, Aseem; Bairagi, Nandadulal; Chatterjee, Samrat

2017-07-01

Calcium ions aid in the generation of action potential in myocytes and are responsible for the excitation-contraction coupling of heart. The heart muscle has specialized patches of cells, called excitatory cells (EC) such as the Sino-atrial node cells capable of auto-generation of action potential and cells which receive signals from the excitatory cells, called non-excitatory cells (NEC) such as cells of the ventricular and auricular walls. In order to understand cardiac calcium homeostasis, it is, therefore, important to study the calcium dynamics taking into account both types of cardiac cells. Here we have developed a model to capture the calcium dynamics in excitatory and non-excitatory cells taking into consideration the gap junction mediated calcium ion transfer from excitatory cell to non-excitatory cell. Our study revealed that the gap junctional coupling between excitatory and non-excitatory cells plays important role in the calcium dynamics. It is observed that any reduction in the functioning of gap junction may result in abnormal calcium oscillations in NEC, even when the calcium dynamics is normal in EC cell. Sensitivity of gap junction is observed to be independent of the pacing rate and hence a careful monitoring is required to maintain normal cardiomyocyte condition. It also highlights that sarcoplasmic reticulum may not be always able to control the amount of cytoplasmic calcium under the condition of calcium overload. Copyright © 2017 Elsevier Inc. All rights reserved.

Josephson junction in the quantum mesoscopic electric circuits with charge discreteness

NASA Astrophysics Data System (ADS)

Pahlavani, H.

2018-04-01

A quantum mesoscopic electrical LC-circuit with charge discreteness including a Josephson junction is considered and a nonlinear Hamiltonian that describing the dynamic of such circuit is introduced. The quantum dynamical behavior (persistent current probability) is studied in the charge and phase regimes by numerical solution approaches. The time evolution of charge and current, number-difference and the bosonic phase and also the energy spectrum of a quantum mesoscopic electric LC-circuit with charge discreteness that coupled with a Josephson junction device are investigated. We show the role of the coupling energy and the electrostatic Coulomb energy of the Josephson junction in description of the quantum behavior and the spectral properties of a quantum mesoscopic electrical LC-circuits with charge discreteness.

Conditions for synchronization in Josephson-junction arrays

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

Chernikov, A.A.; Schmidt, G.

An effective perturbation theoretical method has been developed to study the dynamics of Josephson Junction series arrays. It is shown that the inclusion of Junction capacitances, often ignored, has a significant impact on synchronization. Comparison of analytic with computational results over a wide range of parameters shows excellent agreement.

Alkaline pH sensor molecules.

PubMed

Murayama, Takashi; Maruyama, Ichiro N

2015-11-01

Animals can survive only within a narrow pH range. This requires continual monitoring of environmental and body-fluid pH. Although a variety of acidic pH sensor molecules have been reported, alkaline pH sensor function is not well understood. This Review describes neuronal alkaline pH sensors, grouped according to whether they monitor extracellular or intracellular alkaline pH. Extracellular sensors include the receptor-type guanylyl cyclase, the insulin receptor-related receptor, ligand-gated Cl- channels, connexin hemichannels, two-pore-domain K+ channels, and transient receptor potential (TRP) channels. Intracellular sensors include TRP channels and gap junction channels. Identification of molecular mechanisms underlying alkaline pH sensing is crucial for understanding how animals respond to environmental alkaline pH and how body-fluid pH is maintained within a narrow range. © 2015 Wiley Periodicals, Inc.

Regional postprandial differences in pH within the stomach and gastroesophageal junction.

PubMed

Simonian, Hrair P; Vo, Lien; Doma, Siva; Fisher, Robert S; Parkman, Henry P

2005-12-01

Our objective was to determine regional differences in intragastric pH after different types of meals. Ten normal subjects underwent 27-hr esophagogastric pH monitoring using a four-probe pH catheter. Meals were a spicy lunch, a high-fat dinner, and a typical bland breakfast. The fatty dinner had the highest postprandial buffering effect, elevating proximal and mid/distal gastric pH to 4.9 +/- 0.4 and 4.0 +/- 0.4, respectively, significantly (P < 0.05) higher compared to 4.2 +/- 0.3 and 3.0 +/- 0.4 for the spicy lunch and 3.0 +/- 0.3 and 2.5 +/- 0.8 for the breakfast. The buffering effect of the high-volume fatty meal to pH > 4 was also longer (150 min) compared to that of the spicy lunch (45 min) and the bland breakfast, which did not increase gastric pH to > 4 at any time. Proximal gastric acid pockets were seen between 15 and 90 min postprandially. These were located 3.4 +/- 0.8 cm below the proximal LES border, extending for a length of 2.3 +/- 0.8 cm, with a drop in mean pH from 4.7 +/- 0.4 to 1.5 +/- 0.9. Acid pockets were seen equally after the spicy lunch and fatty dinner but less frequently after the bland breakfast. We conclude that a high-volume fatty meal has the highest buffering effect on gastric pH compared to a spicy lunch or a bland breakfast. Buffering effects of meals are significantly higher in the proximal than in the mid/distal stomach. Despite the intragastric buffering effect of meals, focal areas of acidity were observed in the region of the cardia-gastroesophageal junction during the postprandial period.

Dynamics between actin and the VE-cadherin/catenin complex

PubMed Central

Abu Taha, Abdallah; Schnittler, Hans-J

2014-01-01

Endothelial adherens junctions are critical for physiological and pathological processes such as differentiation, maintenance of entire monolayer integrity, and the remodeling. The endothelial-specific VE-cadherin/catenin complex provides the backbone of adherens junctions and acts in close interaction with actin filaments and actin/myosin-mediated contractility to fulfill the junction demands. The functional connection between the cadherin/catenin complex and actin filaments might be either directly through α-catenins, or indirectly e.g., via linker proteins such as vinculin, p120ctn, α-actinin, or EPLIN. However, both junction integrity and dynamic remodeling have to be contemporarily coordinated. The actin-related protein complex ARP2/3 and its activating molecules, such as N-WASP and WAVE, have been shown to regulate the lammellipodia-mediated formation of cell junctions in both epithelium and endothelium. Recent reports now demonstrate a novel aspect of the ARP2/3 complex and the nucleating-promoting factors in the maintenance of endothelial barrier function and junction remodeling of established endothelial cell junctions. Those mechanisms open novel possibilities; not only in fulfilling physiological demands but obtained information may be of critical importance in pathologies such as wound healing, angiogenesis, inflammation, and cell diapedesis. PMID:24621569

Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA.

PubMed

Cubero, Elena; Luque, F Javier; Orozco, Modesto

2006-02-01

A series of d (AT)(n) oligonucleotides containing mixtures of normal B-type Watson-Crick and antiparallel Hoogsteen helices have been studied using molecular dynamics simulation techniques to analyze the structural and thermodynamic impact of the junction between Watson-Crick and antiparallel Hoogsteen structures. Analysis of molecular dynamics simulations strongly suggests that for all oligonucleotides studied the antiparallel Hoogsteen appears as a reasonable conformation, only slightly less stable than the canonical B-type Watson-Crick one. The junctions between the Watson-Crick and Hoogsteen structures introduces a priori a sharp discontinuity in the helix, because the properties of each type of conformation are very well preserved in the corresponding fragments. However, and quite counterintuitively, junctions do not largely distort the duplex in structural, dynamics or energetic terms. Our results strongly support the possibility that small fragments of antiparallel Hoogsteen duplex might be embedded into large fragments of B-type Watson-Crick helices, making possible protein-DNA interactions that are specific of the antiparallel Hoogsteen conformation.

Theoretical Study of the Hoogsteen–Watson-Crick Junctions in DNA

PubMed Central

Cubero, Elena; Luque, F. Javier; Orozco, Modesto

2006-01-01

A series of d (AT)n oligonucleotides containing mixtures of normal B-type Watson-Crick and antiparallel Hoogsteen helices have been studied using molecular dynamics simulation techniques to analyze the structural and thermodynamic impact of the junction between Watson-Crick and antiparallel Hoogsteen structures. Analysis of molecular dynamics simulations strongly suggests that for all oligonucleotides studied the antiparallel Hoogsteen appears as a reasonable conformation, only slightly less stable than the canonical B-type Watson-Crick one. The junctions between the Watson-Crick and Hoogsteen structures introduces a priori a sharp discontinuity in the helix, because the properties of each type of conformation are very well preserved in the corresponding fragments. However, and quite counterintuitively, junctions do not largely distort the duplex in structural, dynamics or energetic terms. Our results strongly support the possibility that small fragments of antiparallel Hoogsteen duplex might be embedded into large fragments of B-type Watson-Crick helices, making possible protein-DNA interactions that are specific of the antiparallel Hoogsteen conformation. PMID:16287814

ACF7 regulates inflammatory colitis and intestinal wound response by orchestrating tight junction dynamics

PubMed Central

Ma, Yanlei; Yue, Jiping; Zhang, Yao; Shi, Chenzhang; Odenwald, Matt; Liang, Wenguang G.; Wei, Qing; Goel, Ajay; Gou, Xuewen; Zhang, Jamie; Chen, Shao-Yu; Tang, Wei-Jen; Turner, Jerrold R.; Yang, Feng; Liang, Hong; Qin, Huanlong; Wu, Xiaoyang

2017-01-01

In the intestinal epithelium, the aberrant regulation of cell/cell junctions leads to intestinal barrier defects, which may promote the onset and enhance the severity of inflammatory bowel disease (IBD). However, it remains unclear how the coordinated behaviour of cytoskeletal network may contribute to cell junctional dynamics. In this report, we identified ACF7, a crosslinker of microtubules and F-actin, as an essential player in this process. Loss of ACF7 leads to aberrant microtubule organization, tight junction stabilization and impaired wound closure in vitro. With the mouse genetics approach, we show that ablation of ACF7 inhibits intestinal wound healing and greatly increases susceptibility to experimental colitis in mice. ACF7 level is also correlated with development and progression of ulcerative colitis (UC) in human patients. Together, our results reveal an important molecular mechanism whereby coordinated cytoskeletal dynamics contributes to cell adhesion regulation during intestinal wound repair and the development of IBD. PMID:28541346

Multiscale modeling of current-induced switching in magnetic tunnel junctions using ab initio spin-transfer torques

NASA Astrophysics Data System (ADS)

Ellis, Matthew O. A.; Stamenova, Maria; Sanvito, Stefano

2017-12-01

There exists a significant challenge in developing efficient magnetic tunnel junctions with low write currents for nonvolatile memory devices. With the aim of analyzing potential materials for efficient current-operated magnetic junctions, we have developed a multi-scale methodology combining ab initio calculations of spin-transfer torque with large-scale time-dependent simulations using atomistic spin dynamics. In this work we introduce our multiscale approach, including a discussion on a number of possible schemes for mapping the ab initio spin torques into the spin dynamics. We demonstrate this methodology on a prototype Co/MgO/Co/Cu tunnel junction showing that the spin torques are primarily acting at the interface between the Co free layer and MgO. Using spin dynamics we then calculate the reversal switching times for the free layer and the critical voltages and currents required for such switching. Our work provides an efficient, accurate, and versatile framework for designing novel current-operated magnetic devices, where all the materials details are taken into account.

Low temperature properties of spin filter NbN/GdN/NbN Josephson junctions

NASA Astrophysics Data System (ADS)

Massarotti, D.; Caruso, R.; Pal, A.; Rotoli, G.; Longobardi, L.; Pepe, G. P.; Blamire, M. G.; Tafuri, F.

2017-02-01

A ferromagnetic Josephson junction (JJ) represents a special class of hybrid system where different ordered phases meet and generate novel physics. In this work we report on the transport measurements of underdamped ferromagnetic NbN/GdN/NbN JJs at low temperatures. In these junctions the ferromagnetic insulator gadolinium nitride barrier generates spin-filtering properties and a dominant second harmonic component in the current-phase relation. These features make spin filter junctions quite interesting also in terms of fundamental studies on phase dynamics and dissipation. We discuss the fingerprints of spin filter JJs, through complementary transport measurements, and their implications on the phase dynamics, through standard measurements of switching current distributions. NbN/GdN/NbN JJs, where spin filter properties can be controllably tuned along with the critical current density (Jc), turn to be a very relevant term of reference to understand phase dynamics and dissipation in an enlarged class of JJs, not necessarily falling in the standard tunnel limit characterized by low Jc values.

Evolutionary dynamics and sites of illegitimate recombination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species.

PubMed

Kuhn, G C S; Teo, C H; Schwarzacher, T; Heslop-Harrison, J S

2009-05-01

Satellite DNA (satDNA) is a major component of genomes but relatively little is known about the fine-scale organization of unrelated satDNAs residing at the same chromosome location, and the sequence structure and dynamics of satDNA junctions. We studied the organization and sequence junctions of two nonhomologous satDNAs, pBuM and DBC-150, in three species from the neotropical Drosophila buzzatii cluster (repleta group). In situ hybridization to microchromosomes, interphase nuclei and extended DNA fibers showed frequent interspersion of the two satellites in D. gouveai, D. antonietae and, to a lesser extent, D. seriema. We isolated by PCR six pBuM x DBC-150 junctions: four are exclusive to D. gouveai and two are exclusive to D. antonietae. The six junction breakpoints occur at different positions within monomers, suggesting independent origin. Four junctions showed abrupt transitions between the two satellites, whereas two junctions showed a distinct 10 bp tandem duplication before the junction. Unlike pBuM, DBC-150 junction repeats are more variable than randomly cloned monomers and showed diagnostic features in common to a 3-monomer higher-order repeat seen in the sister species D. serido. The high levels of interspersion between pBuM and DBC-150 repeats suggest extensive rearrangements between the two satellites, maybe favored by specific features of the microchromosomes. Our interpretation is that the junctions evolved by multiples events of illegitimate recombination between nonhomologous satDNA repeats, with subsequent rounds of unequal crossing-over expanding the copy number of some of the junctions.

Pump-Probe Noise Spectroscopy of Molecular Junctions.

PubMed

Ochoa, Maicol A; Selzer, Yoram; Peskin, Uri; Galperin, Michael

2015-02-05

The slow response of electronic components in junctions limits the direct applicability of pump-probe type spectroscopy in assessing the intramolecular dynamics. Recently the possibility of getting information on a sub-picosecond time scale from dc current measurements was proposed. We revisit the idea of picosecond resolution by pump-probe spectroscopy from dc measurements and show that any intramolecular dynamics not directly related to charge transfer in the current direction is missed by current measurements. We propose a pump-probe dc shot noise spectroscopy as a suitable alternative. Numerical examples of time-dependent and average responses of junctions are presented for generic models.

Detachable strong cation exchange monolith, integrated with capillary zone electrophoresis and coupled with pH gradient elution, produces improved sensitivity and numbers of peptide identifications during bottom-up analysis of complex proteomes.

PubMed

Zhang, Zhenbin; Yan, Xiaojing; Sun, Liangliang; Zhu, Guijie; Dovichi, Norman J

2015-04-21

A detachable sulfonate-silica hybrid strong cation-exchange monolith was synthesized in a fused silica capillary, and used for solid phase extraction with online pH gradient elution during capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) proteomic analysis. Tryptic digests were prepared in 50 mM formic acid and loaded onto the strong cation-exchange monolith. Fractions were eluted using a series of buffers with lower concentration but higher pH values than the 50 mM formic acid background electrolyte. This combination of elution and background electrolytes results in both sample stacking and formation of a dynamic pH junction and allows use of relatively large elution buffer volumes while maintaining reasonable peak efficiency and resolution. A series of five pH bumps were applied to elute E. coli tryptic peptides from the monolith, followed by analysis using CZE coupled to an LTQ-Orbitrap Velos mass spectrometer; 799 protein groups and 3381 peptides were identified from 50 ng of the digest in a 2.5 h analysis, which approaches the identification rate for this organism that was obtained with an Orbitrap Fusion. We attribute the improved numbers of peptide and protein identifications to the efficient fractionation by the online pH gradient elution, which decreased the complexity of the sample in each elution step and improved the signal intensity of low abundance peptides. We also performed a comparative analysis using a nanoACQUITY UltraPerformance LCH system. Similar numbers of protein and peptide identifications were produced by the two methods. Protein identifications showed significant overlap between the two methods, whereas peptide identifications were complementary.

Probing effects of pH change on dynamic response of Claudin-2 mediated adhesion using single molecule force spectroscopy.

PubMed

Lim, Tong Seng; Vedula, Sri Ram Krishna; Hui, Shi; Kausalya, P Jaya; Hunziker, Walter; Lim, Chwee Teck

2008-08-15

Claudins belong to a large family of transmembrane proteins that localize at tight junctions (TJs) where they play a central role in regulating paracellular transport of solutes and nutrients across epithelial monolayers. Their ability to regulate the paracellular pathway is highly influenced by changes in extracellular pH. However, the effect of changes in pH on the strength and kinetics of claudin mediated adhesion is poorly understood. Using atomic force microscopy, we characterized the kinetic properties of homophilic trans-interactions between full length recombinant GST tagged Claudin-2 (Cldn2) under different pH conditions. In measurements covering three orders of magnitude change in force loading rate of 10(2)-10(4) pN/s, the Cldn2/Cldn2 force spectrum (i.e., unbinding force versus loading rate) revealed a fast and a slow loading regime that characterized a steep inner activation barrier and a wide outer activation barrier throughout pH range of 4.5-8. Comparing to the neutral condition (pH 6.9), differences in the inner energy barriers for the dissociation of Cldn2/Cldn2 mediated interactions at acidic and alkaline environments were found to be <0.65 k(B)T, which is much lower than the outer dissociation energy barrier (>1.37 k(B)T). The relatively stable interaction of Cldn2/Cldn2 in neutral environment suggests that electrostatic interactions may contribute to the overall adhesion strength of Cldn2 interactions. Our results provide an insight into the changes in the inter-molecular forces and adhesion kinetics of Cldn2 mediated interactions in acidic, neutral and alkaline environments.

The persistent current and energy spectrum on a driven mesoscopic LC-circuit with Josephson junction

NASA Astrophysics Data System (ADS)

Pahlavanias, Hassan

2018-03-01

The quantum theory for a mesoscopic electric circuit including a Josephson junction with charge discreteness is studied. By considering coupling energy of the mesoscopic capacitor in Josephson junction device, a Hamiltonian describing the dynamics of a quantum mesoscopic electric LC-circuit with charge discreteness is introduced. We first calculate the persistent current on a quantum driven ring including Josephson junction. Then we obtain the persistent current and energy spectrum of a quantum mesoscopic electrical circuit which includes capacitor, inductor, time-dependent external source and Josephson junction.

Supramolecular Systems and Chemical Reactions in Single-Molecule Break Junctions.

PubMed

Li, Xiaohui; Hu, Duan; Tan, Zhibing; Bai, Jie; Xiao, Zongyuan; Yang, Yang; Shi, Jia; Hong, Wenjing

2017-04-01

The major challenges of molecular electronics are the understanding and manipulation of the electron transport through the single-molecule junction. With the single-molecule break junction techniques, including scanning tunneling microscope break junction technique and mechanically controllable break junction technique, the charge transport through various single-molecule and supramolecular junctions has been studied during the dynamic fabrication and continuous characterization of molecular junctions. This review starts from the charge transport characterization of supramolecular junctions through a variety of noncovalent interactions, such as hydrogen bond, π-π interaction, and electrostatic force. We further review the recent progress in constructing highly conductive molecular junctions via chemical reactions, the response of molecular junctions to external stimuli, as well as the application of break junction techniques in controlling and monitoring chemical reactions in situ. We suggest that beyond the measurement of single molecular conductance, the single-molecule break junction techniques provide a promising access to study molecular assembly and chemical reactions at the single-molecule scale.

Effect of individual SCFA on the epithelial barrier of sheep rumen under physiological and acidotic luminal pH conditions.

PubMed

Greco, Gabriele; Hagen, Franziska; Meißner, Svenja; Shen, Zanming; Lu, Zhongyan; Amasheh, Salah; Aschenbach, Jörg R

2018-02-15

The objective of this study was to investigate whether individual short-chain fatty acids (SCFA) have a different potential to either regulate the formation of the ruminal epithelial barrier (REB) at physiological pH or to damage the REB at acidotic ruminal pH. Ruminal epithelia of sheep were incubated in Ussing chambers on their mucosal side in buffered solutions (pH 6.1 or 5.1) containing no SCFA (control), 30 mM of either acetate, propionate or butyrate, or 100 mM acetate. Epithelial conductance (Gt), short-circuit current (Isc), and fluorescein flux rates were measured over 7 h. Thereafter, mRNA and protein abundance, as well as localization of the tight junction proteins claudin (Cldn)-1, -4, -7, and occludin were analyzed. At pH 6.1, butyrate increased Gt and decreased Isc, with additional decreases in claudin-7 mRNA and protein abundance (each P < 0.05) and disappearance of Cldn-7 immunosignals from the stratum corneum. By contrast, the mRNA abundance of Cldn-1 and/or Cldn-4 were upregulated by 30 mM propionate, 30 mM butyrate, or 100 mM acetate (P < 0.05), however, without coordinated changes in protein abundance. At luminal pH 5.1, neither Gt, Isc, nor TJ protein abundance was altered in the absence of SCFA; only fluorescein flux rates were slightly increased (P < 0.05) and fluorescein signals were no longer restricted to the stratum corneum. The presence of acetate, propionate, or butyrate at pH 5.1 increased fluorescein flux rates and Gt, and decreased Isc (each P < 0.05). Protein abundance of Cldn-1 was decreased in all SCFA treatments but 30 mM butyrate; abundance of Cldn -4 and -7 was decreased in all SCFA treatments but 30 mM acetate; and abundance of occludin was decreased in all SCFA treatments but 30 mM propionate (each P < 0.05). Immunofluorescence staining of SCFA-treated tissues at pH 5.1 showed disappearance of Cldn-7, discontinuous pattern for Cldn-4 and blurring of occludin and Cldn-1 signals in tight junction complexes. The fluorescein dye appeared to freely diffuse into deeper cell layers. The strongest increase in Gt and consistent decreases in the abundance and immunosignals of tight junction proteins were observed with 100 mM acetate at pH 5.1. We conclude that SCFA may contribute differently to the REB formation at luminal pH 6.1 with possible detrimental effects of butyrate at 30 mM concentration. At luminal pH 5.1, all SCFA elicited REB damage with concentration appearing more critical than SCFA species.

L10-MnGa based magnetic tunnel junction for high magnetic field sensor

NASA Astrophysics Data System (ADS)

Zhao, X. P.; Lu, J.; Mao, S. W.; Yu, Z. F.; Wang, H. L.; Wang, X. L.; Wei, D. H.; Zhao, J. H.

2017-07-01

We report on the investigation of the magnetic tunnel junction structure designed for high magnetic field sensors with a perpendicularly magnetized L10-MnGa reference layer and an in-plane magnetized Fe sensing layer. A large linear tunneling magnetoresistance ratio up to 27.4% and huge dynamic range up to 5600 Oe have been observed at 300 K, with a low nonlinearity of 0.23% in the optimized magnetic tunnel junction (MTJ). The field response of tunneling magnetoresistance is discussed to explain the field sensing properties in the dynamic range. These results indicate that L10-MnGa based orthogonal MTJ is a promising candidate for a high performance magnetic field sensor with a large dynamic range, high endurance and low power consumption.

Experimental testing and modeling analysis of solute mixing at water distribution pipe junctions.

PubMed

Shao, Yu; Jeffrey Yang, Y; Jiang, Lijie; Yu, Tingchao; Shen, Cheng

2014-06-01

Flow dynamics at a pipe junction controls particle trajectories, solute mixing and concentrations in downstream pipes. The effect can lead to different outcomes of water quality modeling and, hence, drinking water management in a distribution network. Here we have investigated solute mixing behavior in pipe junctions of five hydraulic types, for which flow distribution factors and analytical equations for network modeling are proposed. First, based on experiments, the degree of mixing at a cross is found to be a function of flow momentum ratio that defines a junction flow distribution pattern and the degree of departure from complete mixing. Corresponding analytical solutions are also validated using computational-fluid-dynamics (CFD) simulations. Second, the analytical mixing model is further extended to double-Tee junctions. Correspondingly the flow distribution factor is modified to account for hydraulic departure from a cross configuration. For a double-Tee(A) junction, CFD simulations show that the solute mixing depends on flow momentum ratio and connection pipe length, whereas the mixing at double-Tee(B) is well represented by two independent single-Tee junctions with a potential water stagnation zone in between. Notably, double-Tee junctions differ significantly from a cross in solute mixing and transport. However, it is noted that these pipe connections are widely, but incorrectly, simplified as cross junctions of assumed complete solute mixing in network skeletonization and water quality modeling. For the studied pipe junction types, analytical solutions are proposed to characterize the incomplete mixing and hence may allow better water quality simulation in a distribution network. Published by Elsevier Ltd.

Edge mixing dynamics in graphene p–n junctions in the quantum Hall regime

PubMed Central

Matsuo, Sadashige; Takeshita, Shunpei; Tanaka, Takahiro; Nakaharai, Shu; Tsukagoshi, Kazuhito; Moriyama, Takahiro; Ono, Teruo; Kobayashi, Kensuke

2015-01-01

Massless Dirac electron systems such as graphene exhibit a distinct half-integer quantum Hall effect, and in the bipolar transport regime co-propagating edge states along the p–n junction are realized. Additionally, these edge states are uniformly mixed at the junction, which makes it a unique structure to partition electrons in these edge states. Although many experimental works have addressed this issue, the microscopic dynamics of electron partition in this peculiar structure remains unclear. Here we performed shot-noise measurements on the junction in the quantum Hall regime as well as at zero magnetic field. We found that, in sharp contrast with the zero-field case, the shot noise in the quantum Hall regime is finite in the bipolar regime, but is strongly suppressed in the unipolar regime. Our observation is consistent with the theoretical prediction and gives microscopic evidence that the edge states are uniquely mixed along the p–n junction. PMID:26337445

Intragastric pH and pressure profiles after intake of the high-caloric, high-fat meal as used for food effect studies.

PubMed

Koziolek, M; Schneider, F; Grimm, M; Modeβ, Chr; Seekamp, A; Roustom, T; Siegmund, W; Weitschies, W

2015-12-28

The intraluminal conditions of the fed stomach are critical for drug release from solid oral dosage forms and thus, often associated with the occurrence of food effects on oral bioavailability. In this study, intragastric pH and pressure profiles present after the ingestion of the high-caloric, high-fat (964 kcal) FDA standard breakfast were investigated in 19 healthy human subjects by using the telemetric SmartPill® capsule system (26 × 13 mm). Since the gastric emptying of such large non-digestible objects is typically accomplished by the migrating motor complex phase III activity, the time required for recurrence of fasted state motility determined the gastric emptying time (GET). Following the diet recommendations of the FDA guidance on food effect studies, the mean GET of the telemetric motility capsule was 15.3 ± 4.7 h. Thus, the high caloric value of the standard breakfast impeded gastric emptying before lunch in 18 out of 19 subjects. During its gastric transit, the capsule was exposed to highly dynamic conditions in terms of pH and pressure, which were mainly dependent on further meal and liquid intake, as well as the intragastric capsule deposition behavior. Maximum pH values in the stomach were measured immediately after capsule intake. The median pH value of the 5 min period after capsule ingestion ranged between pH 3.3 and 5.3. Subsequently, the pH decreased relatively constantly and reached minimum values of pH 0-1 after approximately 4 h. The maximum pressure within the stomach amounted to 293 ± 109 mbar and was clearly higher than the maximum pressure measured at the ileocaecal junction (60 ± 35 mbar). The physiological data on the intraluminal conditions within the fed stomach generated in this study will hopefully contribute to a better understanding of food effects on oral drug product performance.

Dispersion mechanisms of a tidal river junction in the Sacramento–San Joaquin Delta, California

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

Gleichauf, Karla T.; Wolfram, Philip J.; Monsen, Nancy E.

In branching channel networks, such as in the Sacramento–San Joaquin River Delta, junction flow dynamics contribute to dispersion of ecologically important entities such as fish, pollutants, nutrients, salt, sediment, and phytoplankton. Flow transport through a junction largely arises from velocity phasing in the form of divergent flow between junction channels for a portion of the tidal cycle. Field observations in the Georgiana Slough junction, which is composed of the North and South Mokelumne rivers, Georgiana Slough, and the Mokelumne River, show that flow phasing differences between these rivers arise from operational, riverine, and tidal forcing. A combination of Acoustic Dopplermore » Current Profile (ADCP) boat transecting and moored ADCPs over a spring–neap tidal cycle (May to June 2012) monitored the variability of spatial and temporal velocity, respectively. Two complementary drifter studies enabled assessment of local transport through the junction to identify small-scale intrajunction dynamics. We supplemented field results with numerical simulations using the SUNTANS model to demonstrate the importance of phasing offsets for junction transport and dispersion. Different phasing of inflows to the junction resulted in scalar patchiness that is characteristic of MacVean and Stacey’s (2011) advective tidal trapping. Furthermore, we observed small-scale junction flow features including a recirculation zone and shear layer, which play an important role in intra-junction mixing over time scales shorter than the tidal cycle (i.e., super-tidal time scales). Thus, the study period spanned open- and closed-gate operations at the Delta Cross Channel. Synthesis of field observations and modeling efforts suggest that management operations related to the Delta Cross Channel can strongly affect transport in the Delta by modifying the relative contributions of tidal and riverine flows, thereby changing the junction flow phasing.« less

Dispersion mechanisms of a tidal river junction in the Sacramento–San Joaquin Delta, California

DOE PAGES

Gleichauf, Karla T.; Wolfram, Philip J.; Monsen, Nancy E.; ...

2014-12-17

In branching channel networks, such as in the Sacramento–San Joaquin River Delta, junction flow dynamics contribute to dispersion of ecologically important entities such as fish, pollutants, nutrients, salt, sediment, and phytoplankton. Flow transport through a junction largely arises from velocity phasing in the form of divergent flow between junction channels for a portion of the tidal cycle. Field observations in the Georgiana Slough junction, which is composed of the North and South Mokelumne rivers, Georgiana Slough, and the Mokelumne River, show that flow phasing differences between these rivers arise from operational, riverine, and tidal forcing. A combination of Acoustic Dopplermore » Current Profile (ADCP) boat transecting and moored ADCPs over a spring–neap tidal cycle (May to June 2012) monitored the variability of spatial and temporal velocity, respectively. Two complementary drifter studies enabled assessment of local transport through the junction to identify small-scale intrajunction dynamics. We supplemented field results with numerical simulations using the SUNTANS model to demonstrate the importance of phasing offsets for junction transport and dispersion. Different phasing of inflows to the junction resulted in scalar patchiness that is characteristic of MacVean and Stacey’s (2011) advective tidal trapping. Furthermore, we observed small-scale junction flow features including a recirculation zone and shear layer, which play an important role in intra-junction mixing over time scales shorter than the tidal cycle (i.e., super-tidal time scales). Thus, the study period spanned open- and closed-gate operations at the Delta Cross Channel. Synthesis of field observations and modeling efforts suggest that management operations related to the Delta Cross Channel can strongly affect transport in the Delta by modifying the relative contributions of tidal and riverine flows, thereby changing the junction flow phasing.« less

pH-triggered conduction of amine-functionalized single ZnO wire integrated on a customized nanogap electronic platform

PubMed Central

2014-01-01

The electrical conductance response of single ZnO microwire functionalized with amine-groups was tested upon an acid pH variation of a solution environment after integration on a customized gold electrode array chip. ZnO microwires were easily synthesized by hydrothermal route and chemically functionalized with aminopropyl groups. Single wires were deposited from the solution and then oriented through dielectrophoresis across eight nanogap gold electrodes on a platform single chip. Therefore, eight functionalized ZnO microwire-gold junctions were formed at the same time, and being integrated on an ad hoc electronic platform, they were ready for testing without any further treatment. Experimental and simulation studies confirmed the high pH-responsive behavior of the amine-modified ZnO-gold junctions, obtaining in a simple and reproducible way a ready-to-use device for pH detection in the acidic range. We also compared this performance to bare ZnO wires on the same electronic platform, showing the superiority in pH response of the amine-functionalized material. PMID:24484615

Three-dimensional Distribution of Azimuthal and Radial Anisotropy in the Japan Subduction

NASA Astrophysics Data System (ADS)

Ishise, M.; Kawakatsu, H.; Shiomi, K.

2014-12-01

Seismic anisotropy has close relationships with past and present tectonic and dynamic processes. Therefore, detailed description of seismic anisotropy of subduction zones provides important information for our understanding of the subduction system. The most common method of detecting anisotropy is the S-wave splitting measurement. However, conventional S-wave splitting analysis is not an appropriate way to investigate anisotropy in the mantle and slab because the technique has no vertical resolution. Thus, we have improved common traveltime tomography to estimate three-dimensional anisotropic structures of P-wave, assuming that the modeling space is composed of weakly anisotropic medium with a hexagonal symmetry about a horizontal axis (Ishise & Oda, 2005, JGR; Ishise & Oda, 2008, PEPI). Recently, we extended the anisotropic tomography for P-wave radial anisotropy with vertical hexagonal symmetry axis (Ishise & Kawakatsu, 2012 JpGU). In this study, we expand the study area of our previous regional analyses of P-wave azimuthal and radial anisotropic tomography (Ishise & Oda, 2005; Ishise & Kawakatsu, 2012, JpGU; Ishise et al., 2012, SSJ) using Hi-net arrival time data and examine the subduction system around the Japan islands, where two trenches with different strike directions and plate junction are included. Here are some of the remarkable results associated with the PAC slab and mantle structure. (1) N-S-trending fast axis of P-wave anisotropy is dominant in the PAC slab. (2) the mantle wedge shows trench-normal anisotropy across the trench-trench junction. (3) horizontal velocity (PH) tends to be faster than vertical velocity (PV) in the slab. (4) PV tends to be faster than PH in the mantle wedge. The characteristics of the obtained azimuthal and radial anisotropy of the PAC slab and the mantle wedge qualitatively consistent with heterogeneous plate models (e.g., Furumura & Kennet, 2005) and numerical simulations of mantle flow (Morishige & Honda, 2011; 2013). In addition, the azimuthal anisotropy in the PAC slab that we obtained is subparallel to that in the PAC plate before subducting (e.g., Shimamura et al., 1983). Therefore, we suggest that the slab anisotropy is "frozen anisotropy", which is attributed to the episode before subduction, and mantle wedge anisotropy reflects present dynamics.

Gap Junctional Coupling in Lenses from α8 Connexin Knockout Mice

PubMed Central

Baldo, George J.; Gong, Xiaohua; Martinez-Wittinghan, Francisco J.; Kumar, Nalin M.; Gilula, Norton B.; Mathias, Richard T.

2001-01-01

Lens fiber cell gap junctions contain α3 (Cx46) and α8 (Cx50) connexins. To examine the roles of the two different connexins in lens physiology, we have genetically engineered mice lacking either α3 or α8 connexin. Intracellular impedance studies of these lenses were used to measure junctional conductance and its sensitivity to intracellular pH. In Gong et al. 1998, we described results from α3 connexin knockout lenses. Here, we present original data from α8 connexin knockout lenses and a comparison with the previous results. The lens has two functionally distinct domains of fiber cell coupling. In wild-type mouse lenses, the outer shell of differentiating fibers (see 1, DF) has an average coupling conductance per area of cell–cell contact of ∼1 S/cm2, which falls to near zero when the cytoplasm is acidified. In the inner core of mature fibers (see 1, MF), the average coupling conductance is ∼0.4 S/cm2, and is insensitive to acidification of the cytoplasm. Both connexin isoforms appear to contribute about equally in the DF since the coupling conductance for either heterozygous knockout (+/−) was ∼70% of normal and 30–40% of the normal for both −/− lenses. However, their contribution to the MF was different. About 50% of the normal coupling conductance was found in the MF of α3 +/− lenses. In contrast, the coupling of MF in the α8 +/− lenses was the same as normal. Moreover, no coupling was detected in the MF of α3 −/− lenses. Together, these results suggest that α3 connexin alone is responsible for coupling MF. The pH- sensitive gating of DF junctions was about the same in wild-type and α3 connexin −/− lenses. However, in α8 −/− lenses, the pure α3 connexin junctions did not gate closed in the response to acidification. Since α3 connexin contributes about half the coupling conductance in DF of wild-type lenses, and that conductance goes to zero when the cytoplasmic pH drops, it appears α8 connexin regulates the gating of α3 connexin. Both connexins are clearly important to lens physiology as lenses null for either connexin lose transparency. Gap junctions in the MF survive for the lifetime of the organism without protein turnover. It appears that α3 connexin provides the long-term communication in MF. Gap junctions in DF may be physiologically regulated since they are capable of gating when the cytoplasm is acidified. It appears α8 connexin is required for gating in DF. PMID:11696604

Growth strategies to control tapering in Ge nanowires

NASA Astrophysics Data System (ADS)

Periwal, P.; Baron, T.; Gentile, P.; Salem, B.; Bassani, F.

2014-04-01

We report the effect of PH3 on the morphology of Au catalyzed Ge nanowires (NWs). Ge NWs were grown on Si (111) substrate at 400 °C in the presence of PH3, using vapor-liquid-solid method by chemical vapor deposition. We show that high PH3/GeH4 ratio causes passivation at NW surface. At high PH3 concentration phosphorous atoms attach itself on NW surface and form a self-protection coating that prevents conformal growth and leads to taper free nanostructures. However, in case of low PH3 flux the combination of axial and radial growth mechanism occurs resulting in conical structure. We have also investigated axial PH3-intrinsic junctions in Ge NWs. The unusual NW shape is attributed to a combination of catalyzed, uncatalyzed and diffusion induced growth.

Epithelial junction formation requires confinement of Cdc42 activity by a novel SH3BP1 complex

PubMed Central

Elbediwy, Ahmed; Zihni, Ceniz; Terry, Stephen J.; Clark, Peter

2012-01-01

Epithelial cell–cell adhesion and morphogenesis require dynamic control of actin-driven membrane remodeling. The Rho guanosine triphosphatase (GTPase) Cdc42 regulates sequential molecular processes during cell–cell junction formation; hence, mechanisms must exist that inactivate Cdc42 in a temporally and spatially controlled manner. In this paper, we identify SH3BP1, a GTPase-activating protein for Cdc42 and Rac, as a regulator of junction assembly and epithelial morphogenesis using a functional small interfering ribonucleic acid screen. Depletion of SH3BP1 resulted in loss of spatial control of Cdc42 activity, stalled membrane remodeling, and enhanced growth of filopodia. SH3BP1 formed a complex with JACOP/paracingulin, a junctional adaptor, and CD2AP, a scaffolding protein; both were required for normal Cdc42 signaling and junction formation. The filamentous actin–capping protein CapZ also associated with the SH3BP1 complex and was required for control of actin remodeling. Epithelial junction formation and morphogenesis thus require a dual activity complex, containing SH3BP1 and CapZ, that is recruited to sites of active membrane remodeling to guide Cdc42 signaling and cytoskeletal dynamics. PMID:22891260

76 FR 34207 - Application(s) for Duty-Free Entry of Scientific Instruments

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-13

.... Intended Use: The system will be incorporated into a superconducting quantum bit device, and will be used to deposit and grow Josephson junctions as part of students' research requirements in the physics Ph...

Dissipation in microwave quantum circuits with hybrid nanowire Josephson elements

NASA Astrophysics Data System (ADS)

Mugnai, D.; Ranfagni, A.; Agresti, A.

2017-04-01

Recent experiments on hybrid Josephson junctions have made the argument a topical subject. However, a quantity which remains still unknown is the tunneling (or response) time, which is strictly connected to the role that dissipation plays in the dynamics of the complete system. A simple way for evaluating dissipation in microwave circuits, previously developed for describing the dynamics of conventional Josephson junctions, is now presented as suitable for application even to non-conventional junctions. The method is based on a stochastic model, as derived from the telegrapher's equation, and is particularly devoted to the case of junctions loaded by real transmission lines. When the load is constituted by lumped-constant circuits, a connection with the stochastic model is also maintained. The theoretical model demonstrated its ability to analyze both classically-allowed and forbidden processes, and has found a wide field of applicability, namely in all cases in which dissipative effects cannot be ignored.

Time-Resolved Chemical Mapping in Light-Emitting Electrochemical Cells.

PubMed

Jafari, Mohammad Javad; Liu, Jiang; Engquist, Isak; Ederth, Thomas

2017-01-25

An understanding of the doping and ion distributions in light-emitting electrochemical cells (LECs) is required to approach a realistic conduction model which can precisely explain the electrochemical reactions, p-n junction formation, and ion dynamics in the active layer and to provide relevant information about LECs for systematic improvement of function and manufacture. Here, Fourier-transform infrared (FTIR) microscopy is used to monitor anion density profile and polymer structure in situ and for time-resolved mapping of electrochemical doping in an LEC under bias. The results are in very good agreement with the electrochemical doping model with respect to ion redistribution and formation of a dynamic p-n junction in the active layer. We also physically slow ions by decreasing the working temperature and study frozen-junction formation and immobilization of ions in a fixed-junction LEC device by FTIR imaging. The obtained results show irreversibility of the ion redistribution and polymer doping in a fixed-junction device. In addition, we demonstrate that infrared microscopy is a useful tool for in situ characterization of electroactive organic materials.

Cell junction dynamics in the testis: Sertoli-germ cell interactions and male contraceptive development.

PubMed

Cheng, C Yan; Mruk, Dolores D

2002-10-01

Spermatogenesis is an intriguing but complicated biological process. However, many studies since the 1960s have focused either on the hormonal events of the hypothalamus-pituitary-testicular axis or morphological events that take place in the seminiferous epithelium. Recent advances in biochemistry, cell biology, and molecular biology have shifted attention to understanding some of the key events that regulate spermatogenesis, such as germ cell apoptosis, cell cycle regulation, Sertoli-germ cell communication, and junction dynamics. In this review, we discuss the physiology and biology of junction dynamics in the testis, in particular how these events affect interactions of Sertoli and germ cells in the seminiferous epithelium behind the blood-testis barrier. We also discuss how these events regulate the opening and closing of the blood-testis barrier to permit the timely passage of preleptotene and leptotene spermatocytes across the blood-testis barrier. This is physiologically important since developing germ cells must translocate across the blood-testis barrier as well as traverse the seminiferous epithelium during their development. We also discuss several available in vitro and in vivo models that can be used to study Sertoli-germ cell anchoring junctions and Sertoli-Sertoli tight junctions. An in-depth survey in this subject has also identified several potential targets to be tackled to perturb spermatogenesis, which will likely lead to the development of novel male contraceptives.

Intrinsic islet heterogeneity and gap junction coupling determine spatiotemporal Ca²⁺ wave dynamics.

PubMed

Benninger, Richard K P; Hutchens, Troy; Head, W Steven; McCaughey, Michael J; Zhang, Min; Le Marchand, Sylvain J; Satin, Leslie S; Piston, David W

2014-12-02

Insulin is released from the islets of Langerhans in discrete pulses that are linked to synchronized oscillations of intracellular free calcium ([Ca(2+)]i). Associated with each synchronized oscillation is a propagating calcium wave mediated by Connexin36 (Cx36) gap junctions. A computational islet model predicted that waves emerge due to heterogeneity in β-cell function throughout the islet. To test this, we applied defined patterns of glucose stimulation across the islet using a microfluidic device and measured how these perturbations affect calcium wave propagation. We further investigated how gap junction coupling regulates spatiotemporal [Ca(2+)]i dynamics in the face of heterogeneous glucose stimulation. Calcium waves were found to originate in regions of the islet having elevated excitability, and this heterogeneity is an intrinsic property of islet β-cells. The extent of [Ca(2+)]i elevation across the islet in the presence of heterogeneity is gap-junction dependent, which reveals a glucose dependence of gap junction coupling. To better describe these observations, we had to modify the computational islet model to consider the electrochemical gradient between neighboring β-cells. These results reveal how the spatiotemporal [Ca(2+)]i dynamics of the islet depend on β-cell heterogeneity and cell-cell coupling, and are important for understanding the regulation of coordinated insulin release across the islet. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Connexin-36 gap junctions regulate in vivo first- and second-phase insulin secretion dynamics and glucose tolerance in the conscious mouse.

PubMed

Head, W Steven; Orseth, Meredith L; Nunemaker, Craig S; Satin, Leslie S; Piston, David W; Benninger, Richard K P

2012-07-01

Insulin is secreted from the islets of Langerhans in coordinated pulses. These pulses are thought to lead to plasma insulin oscillations, which are putatively more effective in lowering blood glucose than continuous levels of insulin. Gap-junction coupling of β-cells by connexin-36 coordinates intracellular free calcium oscillations and pulsatile insulin release in isolated islets, however a role in vivo has not been shown. We test whether loss of gap-junction coupling disrupts plasma insulin oscillations and whether this impacts glucose tolerance. We characterized the connexin-36 knockout (Cx36(-/-)) mouse phenotype and performed hyperglycemic clamps with rapid sampling of insulin in Cx36(-/-) and control mice. Our results show that Cx36(-/-) mice are glucose intolerant, despite normal plasma insulin levels and insulin sensitivity. However, Cx36(-/-) mice exhibit reduced insulin pulse amplitudes and a reduction in first-phase insulin secretion. These changes are similarly found in isolated Cx36(-/-) islets. We conclude that Cx36 gap junctions regulate the in vivo dynamics of insulin secretion, which in turn is important for glucose homeostasis. Coordinated pulsatility of individual islets enhances the first-phase elevation and second-phase pulses of insulin. Because these dynamics are disrupted in the early stages of type 2 diabetes, dysregulation of gap-junction coupling could be an important factor in the development of this disease.

Decomposition of the Thermal Boundary Resistance across Carbon Nanotube-Graphene Junctions to Different Mechanisms.

PubMed

Shi, Jingjing; Zhong, Yang; Fisher, Timothy S; Ruan, Xiulin

2018-05-02

Three different mechanisms are identified to contribute to thermal resistances across a carbon nanotube-graphene junction: material mismatch, nonplanar junction, and defects. To isolate the contributions of each mechanism, we have designed five types of junctions and performed nonequilibrium molecular dynamics simulations. The results show that the contributions from the three mechanisms are similar, each at around 2.5 × 10 -11 m 2 K/W. The relations between thermal boundary resistance and both defect number and turning angle at the interface are also studied.

Specific Cx43 phosphorylation events regulate gap junction turnover in vivo

PubMed Central

Solan, Joell L.; Lampe, Paul D.

2014-01-01

Gap junctions, composed of proteins from the connexin gene family, are highly dynamic structures that are regulated by kinase-mediated signaling pathways and interactions with other proteins. Phosphorylation of Connexin43 (Cx43) at different sites controls gap junction assembly, gap junction size and gap junction turnover. Here we present a model describing how Akt, mitogen activated protein kinase (MAPK) and src kinase coordinate to regulate rapid turnover of gap junctions. Specifically, Akt phosphorylates Cx43 at S373 eliminating interaction with zona occludens-1 (ZO-1) allowing gap junctions to enlarge. Then MAPK and src phosphorylate Cx43 to initiate turnover. We integrate published data with new data to test and refine this model. Finally, we propose that differential coordination of kinase activation and Cx43 phosphorylation controls the specific routes of disassembly, e.g., annular junction formation or gap junctions can potentially “unzip” and be internalized/endocytosed into the cell that produced each connexin. PMID:24508467

An EMMPRIN-γ-catenin-Nm23 complex drives ATP production and actomyosin contractility at endothelial junctions.

PubMed

Moreno, Vanessa; Gonzalo, Pilar; Gómez-Escudero, Jesús; Pollán, Ángela; Acín-Pérez, Rebeca; Breckenridge, Mark; Yáñez-Mó, María; Barreiro, Olga; Orsenigo, Fabrizio; Kadomatsu, Kenji; Chen, Christopher S; Enríquez, José A; Dejana, Elisabetta; Sánchez-Madrid, Francisco; Arroyo, Alicia G

2014-09-01

Cell-cell adhesions are important sites through which cells experience and resist forces. In endothelial cells, these forces regulate junction dynamics and determine endothelial barrier strength. We identify the Ig superfamily member EMMPRIN (also known as basigin) as a coordinator of forces at endothelial junctions. EMMPRIN localization at junctions correlates with endothelial junction strength in different mouse vascular beds. Accordingly, EMMPRIN-deficient mice show altered junctions and increased junction permeability. Lack of EMMPRIN alters the localization and function of VE-cadherin (also known as cadherin-5) by decreasing both actomyosin contractility and tugging forces at endothelial cell junctions. EMMPRIN ensures proper actomyosin-driven maturation of competent endothelial junctions by forming a molecular complex with γ-catenin (also known as junction plakoglobin) and Nm23 (also known as NME1), a nucleoside diphosphate kinase, thereby locally providing ATP to fuel the actomyosin machinery. These results provide a novel mechanism for the regulation of actomyosin contractility at endothelial junctions and might have broader implications in biological contexts such as angiogenesis, collective migration and tissue morphogenesis by coupling compartmentalized energy production to junction assembly. © 2014. Published by The Company of Biologists Ltd.

An EMMPRIN–γ-catenin–Nm23 complex drives ATP production and actomyosin contractility at endothelial junctions

PubMed Central

Moreno, Vanessa; Gonzalo, Pilar; Gómez-Escudero, Jesús; Pollán, Ángela; Acín-Pérez, Rebeca; Breckenridge, Mark; Yáñez-Mó, María; Barreiro, Olga; Orsenigo, Fabrizio; Kadomatsu, Kenji; Chen, Christopher S.; Enríquez, José A.; Dejana, Elisabetta; Sánchez-Madrid, Francisco; Arroyo, Alicia G.

2014-01-01

ABSTRACT Cell–cell adhesions are important sites through which cells experience and resist forces. In endothelial cells, these forces regulate junction dynamics and determine endothelial barrier strength. We identify the Ig superfamily member EMMPRIN (also known as basigin) as a coordinator of forces at endothelial junctions. EMMPRIN localization at junctions correlates with endothelial junction strength in different mouse vascular beds. Accordingly, EMMPRIN-deficient mice show altered junctions and increased junction permeability. Lack of EMMPRIN alters the localization and function of VE-cadherin (also known as cadherin-5) by decreasing both actomyosin contractility and tugging forces at endothelial cell junctions. EMMPRIN ensures proper actomyosin-driven maturation of competent endothelial junctions by forming a molecular complex with γ-catenin (also known as junction plakoglobin) and Nm23 (also known as NME1), a nucleoside diphosphate kinase, thereby locally providing ATP to fuel the actomyosin machinery. These results provide a novel mechanism for the regulation of actomyosin contractility at endothelial junctions and might have broader implications in biological contexts such as angiogenesis, collective migration and tissue morphogenesis by coupling compartmentalized energy production to junction assembly. PMID:24994937

Redox-mediated regulation of connexin proteins; focus on nitric oxide.

PubMed

García, Isaac E; Sánchez, Helmuth A; Martínez, Agustín D; Retamal, Mauricio A

2018-01-01

Connexins are membrane proteins that form hemichannels and gap junction channels at the plasma membrane. Through these channels connexins participate in autocrine and paracrine intercellular communication. Connexin-based channels are tightly regulated by membrane potential, phosphorylation, pH, redox potential, and divalent cations, among others, and the imbalance of this regulation have been linked to many acquired and genetic diseases. Concerning the redox potential regulation, the nitric oxide (NO) has been described as a modulator of the hemichannels and gap junction channels properties. However, how NO regulates these channels is not well understood. In this mini-review, we summarize the current knowledge about the effects of redox potential focused in NO on the trafficking, formation and functional properties of hemichannels and gap junction channels. Copyright © 2017 Elsevier B.V. All rights reserved.

Vortex dynamics in two-dimensional Josephson junction arrays

NASA Astrophysics Data System (ADS)

Ashrafuzzaman, Md.; Capezzali, Massimiliano; Beck, Hans

2003-08-01

The dynamic response of two-dimensional Josephson junction arrays close to, but above the Berezinskii-Kosterlitz-Thouless (BKT) transition temperature is described in terms of the vortex dielectric function ɛ(ω) and the flux noise spectrum Sφ(ω). They are calculated by considering both the contributions of free vortices interacting through a screened Coulomb potential and the pair motion of vortices that are closer to each other than the BKT correlation length. This procedure allows us to understand various anomalous features in ɛ(ω) and in Sφ(ω) that have been observed both experimentally and in dynamic simulations.

Dynamic magnetoelectric effect in ferromagnet/superconductor tunnel junctions.

PubMed

Trif, Mircea; Tserkovnyak, Yaroslav

2013-08-23

We study the magnetization dynamics in a ferromagnet/insulator/superconductor tunnel junction and the associated buildup of the electrical polarization. We show that for an open circuit, the induced voltage varies strongly and nonmonotonically with the precessional frequency, and can be enhanced significantly by the superconducting correlations. For frequencies much smaller or much larger than the superconducting gap, the voltage drops to zero, while when these two energy scales are comparable, the voltage is peaked at a value determined by the driving frequency. We comment on the potential utilization of the effect for the low-temperature spatially resolved spectroscopy of magnetic dynamics.

Theory and practice in the electrometric determination of pH in precipitation

NASA Astrophysics Data System (ADS)

Brennan, Carla Jo; Peden, Mark E.

Basic theory and laboratory investigations have been applied to the electrometric determination of pH in precipitation samples in an effort to improve the reliability of the results obtained from these low ionic strength samples. The theoretical problems inherent in the measurement of pH in rain have been examined using natural precipitation samples with varying ionic strengths and pH values. The importance of electrode design and construction has been stressed. The proper choice of electrode can minimize or eliminate problems arising from residual liquid junction potentials, streaming potentials and temperature differences. Reliable pH measurements can be made in precipitation samples using commercially available calibration buffers providing low ionic strength quality control solutions are routinely used to verify electrode and meter performance.

Junction Propagation in Organometal Halide Perovskite-Polymer Composite Thin Films.

PubMed

Shan, Xin; Li, Junqiang; Chen, Mingming; Geske, Thomas; Bade, Sri Ganesh R; Yu, Zhibin

2017-06-01

With the emergence of organometal halide perovskite semiconductors, it has been discovered that a p-i-n junction can be formed in situ due to the migration of ionic species in the perovskite when a bias is applied. In this work, we investigated the junction formation dynamics in methylammonium lead tribromide (MAPbBr 3 )/polymer composite thin films. It was concluded that the p- and n- doped regions propagated into the intrinsic region with an increasing bias, leading to a reduced intrinsic perovskite layer thickness and the formation of an effective light-emitting junction regardless of perovskite layer thicknesses (300 nm to 30 μm). The junction propagation also played a major role in deteriorating the LED operation lifetime. Stable perovskite LEDs can be achieved by restricting the junction propagation after its formation.

Realization of radial p-n junction silicon nanowire solar cell based on low-temperature and shallow phosphorus doping

NASA Astrophysics Data System (ADS)

Dong, Gangqiang; Liu, Fengzhen; Liu, Jing; Zhang, Hailong; Zhu, Meifang

2013-12-01

A radial p-n junction solar cell based on vertically free-standing silicon nanowire (SiNW) array is realized using a novel low-temperature and shallow phosphorus doping technique. The SiNW arrays with excellent light trapping property were fabricated by metal-assisted chemical etching technique. The shallow phosphorus doping process was carried out in a hot wire chemical vapor disposition chamber with a low substrate temperature of 250°C and H2-diluted PH3 as the doping gas. Auger electron spectroscopy and Hall effect measurements prove the formation of a shallow p-n junction with P atom surface concentration of above 1020 cm-3 and a junction depth of less than 10 nm. A short circuit current density of 37.13 mA/cm2 is achieved for the radial p-n junction SiNW solar cell, which is enhanced by 7.75% compared with the axial p-n junction SiNW solar cell. The quantum efficiency spectra show that radial transport based on the shallow phosphorus doping of SiNW array improves the carrier collection property and then enhances the blue wavelength region response. The novel shallow doping technique provides great potential in the fabrication of high-efficiency SiNW solar cells.

Dynamical photo-induced electronic properties of molecular junctions

NASA Astrophysics Data System (ADS)

Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.

2018-03-01

Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.

Advance of Mechanically Controllable Break Junction for Molecular Electronics.

PubMed

Wang, Lu; Wang, Ling; Zhang, Lei; Xiang, Dong

2017-06-01

Molecular electronics stands for the ultimate size of functional elements, keeping up with an unstoppable trend over the past few decades. As a vital component of molecular electronics, single molecular junctions have attracted significant attention from research groups all over the world. Due to its pronounced superiority, the mechanically controllable break junctions (MCBJ) technique has been widely applied to characterize the dynamic performance of single molecular junctions. This review presents a system analysis for single-molecule junctions and offers an overview of four test-beds for single-molecule junctions, thus offering more insight into the mechanisms of electron transport. We mainly focus on the development of state-of-the-art mechanically controlled break junctions. The three-terminal gated MCBJ approaches are introduced to manipulate the electron transport of molecules, and MCBJs are combined with characterization techniques. Additionally, applications of MCBJs and remarkable properties of single molecules are addressed. Finally, the challenges and perspective for the mechanically controllable break junctions technique are provided.

Maximizing entanglement in bosonic Josephson junctions using shortcuts to adiabaticity and optimal control

NASA Astrophysics Data System (ADS)

Stefanatos, Dionisis; Paspalakis, Emmanuel

2018-05-01

In this article we consider a bosonic Josephson junction, a model system composed by two coupled nonlinear quantum oscillators which can be implemented in various physical contexts, initially prepared in a product of weakly populated coherent states. We quantify the maximum achievable entanglement between the modes of the junction and then use shortcuts to adiabaticity, a method developed to speed up adiabatic quantum dynamics, as well as numerical optimization, to find time-dependent controls (the nonlinearity and the coupling of the junction) which bring the system to a maximally entangled state.

RuO2 pH Sensor with Super-Glue-Inspired Reference Electrode

PubMed Central

Wajrak, Magdalena; Alameh, Kamal

2017-01-01

A pH-sensitive RuO2 electrode coated in a commercial cyanoacrylate adhesive typically exhibits very low pH sensitivity, and could be paired with a RuO2 working electrode as a differential type pH sensor. However, such sensors display poor performance in real sample matrices. A pH sensor employing a RuO2 pH-sensitive working electrode and a SiO2-PVB junction-modified RuO2 reference electrode is developed as an alternative high-performance solution. This sensor exhibits a performance similar to that of a commercial glass pH sensor in some common sample matrices, particularly, an excellent pH sensitivity of 55.7 mV/pH, a hysteresis as low as 2.7 mV, and a drift below 2.2 mV/h. The developed sensor structure opens the way towards the development of a simple, cost effective, and robust pH sensor for pH analysis in various sample matrices. PMID:28878182

RuO₂ pH Sensor with Super-Glue-Inspired Reference Electrode.

PubMed

Lonsdale, Wade; Wajrak, Magdalena; Alameh, Kamal

2017-09-06

A pH-sensitive RuO₂ electrode coated in a commercial cyanoacrylate adhesive typically exhibits very low pH sensitivity, and could be paired with a RuO₂ working electrode as a differential type pH sensor. However, such sensors display poor performance in real sample matrices. A pH sensor employing a RuO₂ pH-sensitive working electrode and a SiO₂-PVB junction-modified RuO₂ reference electrode is developed as an alternative high-performance solution. This sensor exhibits a performance similar to that of a commercial glass pH sensor in some common sample matrices, particularly, an excellent pH sensitivity of 55.7 mV/pH, a hysteresis as low as 2.7 mV, and a drift below 2.2 mV/h. The developed sensor structure opens the way towards the development of a simple, cost effective, and robust pH sensor for pH analysis in various sample matrices.

Relating proton pumps with gap junctions: colocalization of ductin, the channel-forming subunit c of V-ATPase, with subunit a and with innexins 2 and 3 during Drosophila oogenesis.

PubMed

Lautemann, Julia; Bohrmann, Johannes

2016-07-13

Ion-transport mechanisms and gap junctions are known to cooperate in creating bioelectric phenomena, like pH gradients, voltage gradients and ion fluxes within single cells, tissues, organs, and whole organisms. Such phenomena have been shown to play regulatory roles in a variety of developmental and regenerative processes. Using Drosophila oogenesis as a model system, we aim at characterizing in detail the mechanisms underlying bioelectric phenomena in order to reveal their regulatory functions. We, therefore, investigated the stage-specific distribution patterns of V-ATPase components in relation to gap-junction proteins. We analysed the localization of the V-ATPase components ductin (subunit c) and subunit a, and the gap-junction components innexins 2 and 3, especially in polar cells, border cells, stalk cells and centripetally migrating cells. These types of follicle cells had previously been shown to exhibit characteristic patterns of membrane channels as well as membrane potential and intracellular pH. Stage-specifically, ductin and subunit a were found either colocalized or separately enriched in different regions of soma and germ-line cells. While ductin was often more prominent in plasma membranes, subunit a was more prominent in cytoplasmic and nuclear vesicles. Particularly, ductin was enriched in polar cells, stalk cells, and nurse-cell membranes, whereas subunit a was enriched in the cytoplasm of border cells, columnar follicle cells and germ-line cells. Comparably, ductin and both innexins 2 and 3 were either colocalized or separately enriched in different cellular regions. While ductin often showed a continuous membrane distribution, the distribution of both innexins was mostly punctate. Particularly, ductin was enriched in polar cells and stalk cells, whereas innexin 2 was enriched in the oolemma, and innexin 3 in centripetally migrating follicle cells. In lateral follicle-cell membranes, the three proteins were found colocalized as well as separately concentrated in presumed gap-junction plaques. Our results support the notion of a large variety of gap junctions existing in the Drosophila ovary. Moreover, since ductin is the channel-forming part of a proton pump and, like the innexins, is able to form junctional as well as non-junctional membrane channels, a plethora of cellular functions could be realized by using these proteins. The distribution and activity patterns of such membrane channels are expected to contribute to developmentally important bioelectric signals.

The role of the baryon junction in relativistic heavy-ion collisions

NASA Astrophysics Data System (ADS)

Vance, Stephen Earl

The non-perturbative nature of the conserved baryon number of nuclei is investigated by studying the role of the baryon junction in relativistic heavy-ion collisions. The junction, J, of a baryon originates in the Standard Model of Strong Interactions (QCD) and is the vertex which connects the color flux (Wilson) lines flowing from the three valence quarks. In high energy interactions, the baryon junction can play a dynamical role through the Regge exchange of junction states. We show that the junction exchange provides a natural mechanism for the transport of baryon number into the central rapidity region and has the remarkable ability to produce valence hyperons, including W- baryons. This mechanism is used to describe the observed baryon stopping and associated hyperon production in nucleus-nucleus collisions at the CERN SPS. We also show that junction - antijunction excitations or JJ loops provide a new mechanism for baryon pair production and lead to enhanced hyperon and antihyperon production. The combination of these two mechanisms is able to explain part of the anomalous hyperon production observed in Pb + Pb collisions at the SPS. Using the junction initial state dynamics, final state strangeness exchange interactions are shown to further enhance hyperon production and are proposed as an explanation of the remaining anomalous hyperon production. With larger phase space (higher energy) accessible at the newly constructed BNL RHIC facility, we propose that the observation of valence W- baryons in pp collisions will be a decisive observable to confirm the junction exchange picture of baryon number transport. In addition, we note that novel rapidity correlations between baryons and antibaryons of completely different quark flavors, like D++(uuu) and W+( ss s) , are predicted by the JJ loop mechanism. For numerical calculations of multiparticle observables associated with these junction mechanisms, we developed the HIJING/BB¯ nuclear event generator. HIJING/BB¯ was then coupled to the General Cascade Program (GCP) to study the role of the final state flavor changing interactions.

Classical analogs for Rabi-oscillations, Ramsey-fringes, and spin-echo in Josephson junctions

NASA Astrophysics Data System (ADS)

Marchese, J. E.; Cirillo, M.; Grønbech-Jensen, N.

2007-08-01

We investigate the results of recently published experiments on the quantum behavior of Josephson circuits in terms of the classical modeling based on the resistively and capacitively-shunted (RCSJ) junction model. Our analysis shows evidence for a close analogy between the nonlinear behavior of a pulsed microwave-driven Josephson junction at low temperature and low dissipation and the experimental observations reported for the Josephson circuits. Specifically, we demonstrate that Rabi-oscillations, Ramsey-fringes, and spin-echo observations are not phenomena with a unique quantum interpretation. In fact, they are natural consequences of transients to phase-locking in classical nonlinear dynamics and can be observed in a purely classical model of a Josephson junction when the experimental recipe for the application of microwaves is followed and the experimental detection scheme followed. We therefore conclude that classical nonlinear dynamics can contribute to the understanding of relevant experimental observations of Josephson response to various microwave perturbations at very low temperature and low dissipation.

RAPID COMMUNICATION: DC superconducting quantum interference devices fabricated using bicrystal grain boundary junctions in Co-doped BaFe2As2 epitaxial films

NASA Astrophysics Data System (ADS)

Katase, Takayoshi; Ishimaru, Yoshihiro; Tsukamoto, Akira; Hiramatsu, Hidenori; Kamiya, Toshio; Tanabe, Keiichi; Hosono, Hideo

2010-08-01

DC superconducting quantum interference devices (dc-SQUIDs) were fabricated in Co-doped BaFe2As2 epitaxial films on (La, Sr)(Al, Ta)O3 bicrystal substrates with 30° misorientation angles. The 18 × 8 µm2 SQUID loop with an estimated inductance of 13 pH contained two 3 µm wide grain boundary junctions. The voltage-flux characteristics clearly exhibited periodic modulations with ΔV = 1.4 µV at 14 K, while the intrinsic flux noise of dc-SQUIDs was 7.8 × 10 - 5 Φ0 Hz - 1/2 above 20 Hz. The rather high flux noise is mainly attributed to the small voltage modulation depth which results from the superconductor-normal-metal-superconductor junction nature of the bicrystal grain boundary.

Ultracompact 1×4 TM-polarized beam splitter based on photonic crystal surface mode.

PubMed

Jiang, Bin; Zhang, Yejin; Wang, Yufei; Liu, Anjin; Zheng, Wanhua

2012-05-01

We provide an improved surface-mode photonic crystal (PhC) T-junction waveguide, combine it with an improved PhC bandgap T-junction waveguide, and then provide an ultracompact 1×4 TM-polarized beam splitter. The energy is split equally into the four output waveguides. The maximal transmission ratio of each output waveguide branch equals 24.7%, and the corresponding total transmission ratio of the ultracompact 1×4 beam splitter equals 98.8%. The normalized frequency of maximal transmission ratio is 0.397(2πc/a), and the bandwidth of the ultracompact 1×4 TM-polarized beam splitter is 0.0106(2πc/a). To the best of our knowledge, this is the first time such a high-efficiency 1×4 beam splitter exploiting the nonradiative surface mode as a guided mode has been proposed. Although we only employed a 1×4 beam splitter, our design can easily be extended to other 1×n beam splitters.

Transition between B-DNA and Z-DNA: free energy landscape for the B-Z junction propagation.

PubMed

Lee, Juyong; Kim, Yang-Gyun; Kim, Kyeong Kyu; Seok, Chaok

2010-08-05

Canonical, right-handed B-DNA can be transformed into noncanonical, left-handed Z-DNA in vitro at high salt concentrations or in vivo under physiological conditions. The molecular mechanism of this drastic conformational transition is still unknown despite numerous studies. Inspired by the crystal structure of a B-Z junction and the previous zipper model, we show here, with the aid of molecular dynamics simulations, that a stepwise propagation of a B-Z junction is a highly probable pathway for the B-Z transition. In this paper, the movement of a B-Z junction by a two-base-pair step in a double-strand nonamer, [d(GpCpGpCpGpCpGpCpG)](2), is considered. Targeted molecular dynamics simulations and umbrella sampling for this transition resulted in a transition pathway with a free energy barrier of 13 kcal/mol. This barrier is much more favorable than those obtained from previous atomistic simulations that lead to concerted transitions of the whole strands. The free energy difference between B-DNA and Z-DNA evaluated from our simulation is 0.9 kcal/mol per dinucleotide unit, which is consistent with previous experiments. The current computation thus strongly supports the proposal that the B-Z transition involves a relatively fast extension of B-DNA or Z-DNA by sequential propagation of B-Z junctions once nucleation of junctions is established.

CLASP2 interacts with p120-catenin and governs microtubule dynamics at adherens junctions

PubMed Central

Shahbazi, Marta N.; Megias, Diego; Epifano, Carolina; Akhmanova, Anna; Gundersen, Gregg G.; Fuchs, Elaine

2013-01-01

Classical cadherins and their connections with microtubules (MTs) are emerging as important determinants of cell adhesion. However, the functional relevance of such interactions and the molecular players that contribute to tissue architecture are still emerging. In this paper, we report that the MT plus end–binding protein CLASP2 localizes to adherens junctions (AJs) via direct interaction with p120-catenin (p120) in primary basal mouse keratinocytes. Reductions in the levels of p120 or CLASP2 decreased the localization of the other protein to cell–cell contacts and altered AJ dynamics and stability. These features were accompanied by decreased MT density and altered MT dynamics at intercellular junction sites. Interestingly, CLASP2 was enriched at the cortex of basal progenitor keratinocytes, in close localization to p120. Our findings suggest the existence of a new mechanism of MT targeting to AJs with potential functional implications in the maintenance of proper cell–cell adhesion in epidermal stem cells. PMID:24368809

Study of Bulk and Elementary Screw Dislocation Assisted Reverse Breakdown in Low-Voltage (< 250 V) 4H-SiC p(sup +)n Junction Diodes--Part II: Dynamic Breakdown Properties. Part 2; Dynamic Breakdown Properties

NASA Technical Reports Server (NTRS)

Neudeck, Philip G.; Fazi, Christian

1999-01-01

This paper outlines the dynamic reverse-breakdown characteristics of low-voltage (<250 V) small-area <5 x 10(exp -4) sq cm 4H-SiC p(sup +)n diodes subjected to nonadiabatic breakdown-bias pulsewidths ranging from 0.1 to 20 microseconds. 4H-SiC diodes with and without elementary screw dislocations exhibited positive temperature coefficient of breakdown voltage and high junction failure power densities approximately five times larger than the average failure power density of reliable silicon pn rectifiers. This result indicates that highly reliable low-voltage SiC rectifiers may be attainable despite the presence of elementary screw dislocations. However, the impact of elementary screw dislocations on other more useful 4H-SiC power device structures, such as high-voltage (>1 kV) pn junction and Schottky rectifiers, and bipolar gain devices (thyristors, IGBT's, etc.) remains to be investigated.

A structural and functional comparison of gap junction channels composed of connexins and innexins

PubMed Central

Williams, Jamal B.

2016-01-01

ABSTRACT Methods such as electron microscopy and electrophysiology led to the understanding that gap junctions were dense arrays of channels connecting the intracellular environments within almost all animal tissues. The characteristics of gap junctions were remarkably similar in preparations from phylogenetically diverse animals such as cnidarians and chordates. Although few studies directly compared them, minor differences were noted between gap junctions of vertebrates and invertebrates. For instance, a slightly wider gap was noted between cells of invertebrates and the spacing between invertebrate channels was generally greater. Connexins were identified as the structural component of vertebrate junctions in the 1980s and innexins as the structural component of pre‐chordate junctions in the 1990s. Despite a lack of similarity in gene sequence, connexins and innexins are remarkably similar. Innexins and connexins have the same membrane topology and form intercellular channels that play a variety of tissue‐ and temporally specific roles. Both protein types oligomerize to form large aqueous channels that allow the passage of ions and small metabolites and are regulated by factors such as pH, calcium, and voltage. Much more is currently known about the structure, function, and structure–function relationships of connexins. However, the innexin field is expanding. Greater knowledge of innexin channels will permit more detailed comparisons with their connexin‐based counterparts, and provide insight into the ubiquitous yet specific roles of gap junctions. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 522–547, 2017 PMID:27582044

A structural and functional comparison of gap junction channels composed of connexins and innexins.

PubMed

Skerrett, I Martha; Williams, Jamal B

2017-05-01

Methods such as electron microscopy and electrophysiology led to the understanding that gap junctions were dense arrays of channels connecting the intracellular environments within almost all animal tissues. The characteristics of gap junctions were remarkably similar in preparations from phylogenetically diverse animals such as cnidarians and chordates. Although few studies directly compared them, minor differences were noted between gap junctions of vertebrates and invertebrates. For instance, a slightly wider gap was noted between cells of invertebrates and the spacing between invertebrate channels was generally greater. Connexins were identified as the structural component of vertebrate junctions in the 1980s and innexins as the structural component of pre-chordate junctions in the 1990s. Despite a lack of similarity in gene sequence, connexins and innexins are remarkably similar. Innexins and connexins have the same membrane topology and form intercellular channels that play a variety of tissue- and temporally specific roles. Both protein types oligomerize to form large aqueous channels that allow the passage of ions and small metabolites and are regulated by factors such as pH, calcium, and voltage. Much more is currently known about the structure, function, and structure-function relationships of connexins. However, the innexin field is expanding. Greater knowledge of innexin channels will permit more detailed comparisons with their connexin-based counterparts, and provide insight into the ubiquitous yet specific roles of gap junctions. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 522-547, 2017. © 2016 The Authors Developmental Neurobiology Published by Wiley Periodicals, Inc.

Dynamics of Defects and Dopants in Complex Systems: Si and Oxide Surfaces and Interfaces

NASA Astrophysics Data System (ADS)

Kirichenko, Taras; Yu, Decai; Banarjee, Sanjay; Hwang, Gyeong

2004-10-01

Fabrication of forthcoming nanometer scale electronic devices faces many difficulties including formation of extremely shallow and highly doped junctions. At present, ultra-low-energy ion implantation followed by high-temperature thermal annealing is most widely used to fabricate such ultra-shallow junctions. In the process, a great challenge lies in achieving precise control of redistribution and electrical activation of dopant impurities. Native defects (such as vacancies and interstitials) generated during implantation are known to be mainly responsible for the TED and also influence significantly the electrical activation/deactivation. Defect-dopant dynamics is rather well understood in crystalline Si and SiO2. However, little is known about their diffusion and annihilation (or precipitation) at the surfaces and interfaces, despite its growing importance in determining junction profiles as device dimensions get smaller. In this talk, we will present our density functional theory calculation results on the atomic and electronic structure and dynamical behavior of native defects and dopant-defect complexes in disordered/strained Si and oxide systems, such as i) clean and absorbent-modified Si(100) surface and subsurface layers, ii) amorphous-crystalline Si interfaces and iii) amorphous SiO2/Si interfaces. The fundamental understanding and data is essential in developing a comprehensive kinetic model for junction formation, which would contribute greatly in improving current process technologies.

Single-molecule FRET studies of the cooperative and non-cooperative binding kinetics of the bacteriophage T4 single-stranded DNA binding protein (gp32) to ssDNA lattices at replication fork junctions

PubMed Central

Lee, Wonbae; Gillies, John P.; Jose, Davis; Israels, Brett A.; von Hippel, Peter H.; Marcus, Andrew H.

2016-01-01

Gene 32 protein (gp32) is the single-stranded (ss) DNA binding protein of the bacteriophage T4. It binds transiently and cooperatively to ssDNA sequences exposed during the DNA replication process and regulates the interactions of the other sub-assemblies of the replication complex during the replication cycle. We here use single-molecule FRET techniques to build on previous thermodynamic studies of gp32 binding to initiate studies of the dynamics of the isolated and cooperative binding of gp32 molecules within the replication complex. DNA primer/template (p/t) constructs are used as models to determine the effects of ssDNA lattice length, gp32 concentration, salt concentration, binding cooperativity and binding polarity at p/t junctions. Hidden Markov models (HMMs) and transition density plots (TDPs) are used to characterize the dynamics of the multi-step assembly pathway of gp32 at p/t junctions of differing polarity, and show that isolated gp32 molecules bind to their ssDNA targets weakly and dissociate quickly, while cooperatively bound dimeric or trimeric clusters of gp32 bind much more tightly, can ‘slide’ on ssDNA sequences, and exhibit binding dynamics that depend on p/t junction polarities. The potential relationships of these binding dynamics to interactions with other components of the T4 DNA replication complex are discussed. PMID:27694621

Non-invasive microfluidic gap junction assay.

PubMed

Chen, Sisi; Lee, Luke P

2010-03-01

Gap junctions are protein channels between cells that allow direct electrical and metabolic coupling via the exchange of biomolecules and ions. Their expression, though ubiquitous in most mammalian cell types, is especially important for the proper functioning of cardiac and neuronal systems. Many existing methods for studying gap junction communication suffer from either unquantifiable data or difficulty of use. Here, we measure the extent of dye spread and effective diffusivities through gap junction connected cells using a quantitative microfluidic cell biology platform. After loading dye by hydrodynamic focusing of calcein/AM, dye transfer dynamics into neighboring, unexposed cells can be monitored via timelapse fluorescent microscopy. By using a selective microfluidic dye loading over a confluent layer of cells, we found that high expression of gap junctions in C6 cells transmits calcein across the monolayer with an effective diffusivity of 3.4 x 10(-13) m(2)/s, which are highly coupled by Cx43. We also found that the gap junction blocker 18alpha-GA works poorly in the presence of serum even at high concentrations (50 microM); however, it is highly effective down to 2.5 microM in the absence of serum. Furthermore, when the drug is washed out, dye spread resumes rapidly within 1 min for all doses, indicating the drug does not affect transcriptional regulation of connexins in these Cx43+ cells, in contrast to previous studies. This integrated microfluidic platform enables the in situ monitoring of gap junction communication, yielding dynamic information about intercellular molecular transfer and pharmacological inhibition and recovery.

Synchronization of a Josephson junction array in terms of global variables

NASA Astrophysics Data System (ADS)

Vlasov, Vladimir; Pikovsky, Arkady

2013-08-01

We consider an array of Josephson junctions with a common LCR load. Application of the Watanabe-Strogatz approach [Physica DPDNPDT0167-278910.1016/0167-2789(94)90196-1 74, 197 (1994)] allows us to formulate the dynamics of the array via the global variables only. For identical junctions this is a finite set of equations, analysis of which reveals the regions of bistability of the synchronous and asynchronous states. For disordered arrays with distributed parameters of the junctions, the problem is formulated as an integro-differential equation for the global variables; here stability of the asynchronous states and the properties of the transition synchrony-asynchrony are established numerically.

Complexity in neuronal noise depends on network interconnectivity.

PubMed

Serletis, Demitre; Zalay, Osbert C; Valiante, Taufik A; Bardakjian, Berj L; Carlen, Peter L

2011-06-01

"Noise," or noise-like activity (NLA), defines background electrical membrane potential fluctuations at the cellular level of the nervous system, comprising an important aspect of brain dynamics. Using whole-cell voltage recordings from fast-spiking stratum oriens interneurons and stratum pyramidale neurons located in the CA3 region of the intact mouse hippocampus, we applied complexity measures from dynamical systems theory (i.e., 1/f(γ) noise and correlation dimension) and found evidence for complexity in neuronal NLA, ranging from high- to low-complexity dynamics. Importantly, these high- and low-complexity signal features were largely dependent on gap junction and chemical synaptic transmission. Progressive neuronal isolation from the surrounding local network via gap junction blockade (abolishing gap junction-dependent spikelets) and then chemical synaptic blockade (abolishing excitatory and inhibitory post-synaptic potentials), or the reverse order of these treatments, resulted in emergence of high-complexity NLA dynamics. Restoring local network interconnectivity via blockade washout resulted in resolution to low-complexity behavior. These results suggest that the observed increase in background NLA complexity is the result of reduced network interconnectivity, thereby highlighting the potential importance of the NLA signal to the study of network state transitions arising in normal and abnormal brain dynamics (such as in epilepsy, for example).

A novel dynamic field-matching technique for treatment of patients with para-aortic node-positive cervical cancer: Clinical experience

PubMed Central

Baden, Craig; Whitley, Alexander; López-Araujo, Javier; Popple, Richard; Duan, Jun; Kim, Robert

2016-01-01

Aim To report outcomes for patients with para-aortic lymph node positive cervical cancer treated with a dynamic field-matching technique. Background PET staging of cervical cancer has increased identification of patients with para-aortic lymph node metastasis. IMRT enables dose escalation in this area, but matching IMRT fields with traditional whole pelvis fields presents a challenge. Materials and methods From 2003 to 2012, 20 patients with cervical cancer and para-aortic lymph node metastasis were treated utilizing the dynamic field-matching technique. As opposed to single-isocenter half-beam junction techniques, this technique employs wedge-shaped dose junctions for the abutment of fields. We reviewed the records of all patients who completed treatment with the technique and abstracted treatment, toxicity, and disease-related outcome data for analysis. Results Median prescribed dose to the whole pelvis field was 45 Gy and para-aortic IMRT field 50.4 Gy. All but 3 patients underwent HDR (13 pts) or LDR (4 pts) brachytherapy. All patients developed lower GI toxicity; 10 grade 1, 9 grade 2, and 1 grade 4 (enterovaginal fistula). Median DFS was 12.4 months with 1 and 2-year DFS 60.0% and 38.1%. One-year OS was 83.7% and 2-year OS, 64.4%. A total of 10 patients developed recurrence; none occurred at the matched junction. Conclusions The dynamic field-matching technique provides a means for joining conventional whole pelvis fields and para-aortic IMRT fields that substantially reduces dose deviations at the junction due to field mismatch. Treatment with the dynamic matching technique is simple, effective, and tolerated with no apparent increase in toxicity. PMID:26900356

Nearly 1000 Protein Identifications from 50 ng of Xenopus laevis Zygote Homogenate Using Online Sample Preparation on a Strong Cation Exchange Monolith Based Microreactor Coupled with Capillary Zone Electrophoresis.

PubMed

Zhang, Zhenbin; Sun, Liangliang; Zhu, Guijie; Cox, Olivia F; Huber, Paul W; Dovichi, Norman J

2016-01-05

A sulfonate-silica hybrid strong cation exchange monolith microreactor was synthesized and coupled to a linear polyacrylamide coated capillary for online sample preparation and capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) bottom-up proteomic analysis. The protein sample was loaded onto the microreactor in an acidic buffer. After online reduction, alkylation, and digestion with trypsin, the digests were eluted with 200 mM ammonium bicarbonate at pH 8.2 for CZE-MS/MS analysis using 1 M acetic acid as the background electrolyte. This combination of basic elution and acidic background electrolytes results in both sample stacking and formation of a dynamic pH junction. 369 protein groups and 1274 peptides were identified from 50 ng of Xenopus laevis zygote homogenate, which is comparable with an offline sample preparation method, but the time required for sample preparation was decreased from over 24 h to less than 40 min. Dramatically improved performance was produced by coupling the reactor to a longer separation capillary (∼100 cm) and a Q Exactive HF mass spectrometer. 975 protein groups and 3749 peptides were identified from 50 ng of Xenopus protein using the online sample preparation method.

A micropatterning approach for imaging Cx43 dynamic trafficking to cell-cell borders

PubMed Central

Zhang, Shan-Shan; Hong, SoonGweon; Kléber, André G.; Lee, Luke P.; Shaw, Robin M.

2014-01-01

The precise expression and timely delivery of connexin 43 (Cx43) proteins to form gap junctions are essential for electrical coupling of cardiomyocytes. Growing evidence supports a cytoskeletal-based trafficking paradigm for Cx43 delivery directly to adherens junctions at the intercalated disc. A limitation of Cx43 localization assays in cultured cells, in which cell-cell contacts are essential, is the inability to control for cell geometry or reproducibly generate contact points. Here we present a micropatterned cell pairing system well suited for live microscopy to examine how the microtubule and actin cytoskeleton confer specificity to Cx43 trafficking to precisely defined cell-cell junctions. This system can also be adapted for other cell types and used to study dynamic intracellular movements of other proteins important for cell-cell communication‥ PMID:24444605

Conformational trapping of mismatch recognition complex MSH2/MSH3 on repair-resistant DNA loops.

PubMed

Lang, Walter H; Coats, Julie E; Majka, Jerzy; Hura, Greg L; Lin, Yuyen; Rasnik, Ivan; McMurray, Cynthia T

2011-10-18

Insertion and deletion of small heteroduplex loops are common mutations in DNA, but why some loops are prone to mutation and others are efficiently repaired is unknown. Here we report that the mismatch recognition complex, MSH2/MSH3, discriminates between a repair-competent and a repair-resistant loop by sensing the conformational dynamics of their junctions. MSH2/MSH3 binds, bends, and dissociates from repair-competent loops to signal downstream repair. Repair-resistant Cytosine-Adenine-Guanine (CAG) loops adopt a unique DNA junction that traps nucleotide-bound MSH2/MSH3, and inhibits its dissociation from the DNA. We envision that junction dynamics is an active participant and a conformational regulator of repair signaling, and governs whether a loop is removed by MSH2/MSH3 or escapes to become a precursor for mutation.

Charge creation and nucleation of the longitudinal plasma wave in coupled Josephson junctions

NASA Astrophysics Data System (ADS)

Shukrinov, Yu. M.; Hamdipour, M.

2010-11-01

We study the phase dynamics in coupled Josephson junctions described by a system of nonlinear differential equations. Results of detailed numerical simulations of charge creation in the superconducting layers and the longitudinal plasma wave (LPW) nucleation are presented. We demonstrate the different time stages in the development of the LPW and present the results of FFT analysis at different values of bias current. The correspondence between the breakpoint position on the outermost branch of current voltage characteristics (CVC) and the growing region in time dependence of the electric charge in the superconducting layer is established. The effects of noise in the bias current and the external microwave radiation on the charge dynamics of the coupled Josephson junctions are found. These effects introduce a way to regulate the process of LPW nucleation in the stack of IJJ.

Invariant submanifold for series arrays of Josephson junctions.

PubMed

Marvel, Seth A; Strogatz, Steven H

2009-03-01

We study the nonlinear dynamics of series arrays of Josephson junctions in the large-N limit, where N is the number of junctions in the array. The junctions are assumed to be identical, overdamped, driven by a constant bias current, and globally coupled through a common load. Previous simulations of such arrays revealed that their dynamics are remarkably simple, hinting at the presence of some hidden symmetry or other structure. These observations were later explained by the discovery of N-3 constants of motion, the choice of which confines the resulting flow in phase space to a low-dimensional invariant manifold. Here we show that the dimensionality can be reduced further by restricting attention to a special family of states recently identified by Ott and Antonsen. In geometric terms, the Ott-Antonsen ansatz corresponds to an invariant submanifold of dimension one less than that found earlier. We derive and analyze the flow on this submanifold for two special cases: an array with purely resistive loading and another with resistive-inductive-capacitive loading. Our results recover (and in some instances improve) earlier findings based on linearization arguments.

Inter-dependent apical microtubule and actin dynamics orchestrate centrosome retention and neuronal delamination

PubMed Central

Kasioulis, Ioannis

2017-01-01

Detachment of newborn neurons from the neuroepithelium is required for correct neuronal architecture and functional circuitry. This process, also known as delamination, involves adherens-junction disassembly and acto-myosin-mediated abscission, during which the centrosome is retained while apical/ciliary membranes are shed. Cell-biological mechanisms mediating delamination are, however, poorly understood. Using live-tissue and super-resolution imaging, we uncover a centrosome-nucleated wheel-like microtubule configuration, aligned with the apical actin cable and adherens-junctions within chick and mouse neuroepithelial cells. These microtubules maintain adherens-junctions while actin maintains microtubules, adherens-junctions and apical end-foot dimensions. During neuronal delamination, acto-myosin constriction generates a tunnel-like actin-microtubule configuration through which the centrosome translocates. This movement requires inter-dependent actin and microtubule activity, and we identify drebrin as a potential coordinator of these cytoskeletal dynamics. Furthermore, centrosome compromise revealed that this organelle is required for delamination. These findings identify new cytoskeletal configurations and regulatory relationships that orchestrate neuronal delamination and may inform mechanisms underlying pathological epithelial cell detachment. PMID:29058679

MLC-based penumbra softener of EDW borders to reduce junction inhomogeneities.

PubMed

Szpala, Stanislaw; Kohli, Kirpal

2017-05-01

Junctions of fields are known to be susceptible to developing cold or hot spots in the presence of even small geometrical misalignments. Reduction of these dose inhomogeneities can be accomplished through decreasing the dose gradients in the penumbra, but currently it cannot be done for enhanced dynamic wedges (EDW). An MLC-based penumbra softener was developed in the developer mode of TrueBeam linacs to reduce dose gradients across the side border of EDWs. The movement of each leaf was individually synchronized with the movement of the dynamic Y jaw to soften the penumbra in the same manner along the entire field border, in spite of the presence of the dose gradient of the EDW. Junction homogeneity upon field misalignment for side-matched EDWs was examined with the MV imager. The fluence inhomogeneities were reduced from about 30% per mm of shift of the field borders for the conventional EDW to about 2% per mm for the softened-penumbra plan. The junction in a four-field monoisocentric breast plan delivered to the Rando phantom was assessed with film. The dose inhomogeneities across the junction in the superior-inferior direction were reduced from about 20% to 25% per mm for the conventional fields to about 5% per mm. The dose near the softened junction of the breast plan with no shifts did not deviate from the conventional plan by more than about 4%. The newly-developed softened-penumbra junction of EDW (and/or open) fields was shown to reduce sensitivity to misalignments without increasing complexity of the planning or delivery. This methodology needs to be adopted by the manufacturers for clinical use. © 2017 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Fast and High Dynamic Range Imaging with Superconducting Tunnel Junction Detectors

NASA Astrophysics Data System (ADS)

Matsuo, Hiroshi

2014-08-01

We have demonstrated a combined test of the submillimeter-wave SIS photon detectors and GaAs-JFET cryogenic integrated circuits. A relatively large background photo-current can be read out by fast-reset integrating amplifiers. An integration time of 1 ms enables fast frame rate readout and large dynamic range imaging, with an expected dynamic range of 8,000 in 1 ms. Ultimate fast and high dynamic range performance of superconducting tunnel junction detectors (STJ) will be obtained when photon counting capabilities are employed. In the terahertz frequencies, when input photon rate of 100 MHz is measured, the photon bunching gives us enough timing resolution to be used as phase information of intensity fluctuation. Application of photon statistics will be a new tool in the terahertz frequency region. The design parameters of STJ terahertz photon counting detectors are discussed.

Molecular dynamics simulation of self-diffusion processes in titanium in bulk material, on grain junctions and on surface.

PubMed

Sushko, Gennady B; Verkhovtsev, Alexey V; Yakubovich, Alexander V; Schramm, Stefan; Solov'yov, Andrey V

2014-08-21

The process of self-diffusion of titanium atoms in a bulk material, on grain junctions and on surface is explored numerically in a broad temperature range by means of classical molecular dynamics simulation. The analysis is carried out for a nanoscale cylindrical sample consisting of three adjacent sectors and various junctions between nanocrystals. The calculated diffusion coefficient varies by several orders of magnitude for different regions of the sample. The calculated values of the bulk diffusion coefficient correspond reasonably well to the experimental data obtained for solid and molten states of titanium. Investigation of diffusion in the nanocrystalline titanium is of a significant importance because of its numerous technological applications. This paper aims to reduce the lack of data on diffusion in titanium and describe the processes occurring in bulk, at different interfaces and on surface of the crystalline titanium.

Broadband spectrally dynamic solid state illumination source

NASA Astrophysics Data System (ADS)

Nicol, David B.; Asghar, Ali; Gupta, Shalini; Kang, Hun; Pan, Ming; Strassburg, Martin; Summers, Chris; Ferguson, Ian T.

2006-06-01

Solid state lighting has done well recently in niche markets such as signage and displays, however, no available SSL technologies incorporate all the necessary attributes for general illumination. Development of a novel solid state general illumination source is discussed here. Two LEDs emitting at two distinct wavelengths can be monolithically grown and used to excite two or more phosphors with varied excitation spectra. The combined phosphorescence spectrum can then be controlled by adjusting the relative intensities of the two LED emissions. Preliminary phosphor analysis shows such a scheme to be viable for use in a spectrally dynamic broadband general illumination source. A tunnel junction is envisioned as a means of current spreading in a buried layer for three terminal operation. However, tunnel junction properties in GaN based materials are not well understood, and require further optimization to be practical devices. Preliminary results on GaN tunnel junctions are presented here as well.

Landauer’s formula with finite-time relaxation: Kramers’ crossover in electronic transport

DOE PAGES

Gruss, Daniel; Velizhanin, Kirill A.; Zwolak, Michael

2016-04-20

Landauer’s formula is the standard theoretical tool to examine ballistic transport in nano- and meso-scale junctions, but it necessitates that any variation of the junction with time must be slow compared to characteristic times of the system, e.g., the relaxation time of local excitations. Transport through structurally dynamic junctions is, however, increasingly of interest for sensing, harnessing fluctuations, and real-time control. Here, we calculate the steady-state current when relaxation of electrons in the reservoirs is present and demonstrate that it gives rise to three regimes of behavior: weak relaxation gives a contact-limited current; strong relaxation localizes electrons, distorting their naturalmore » dynamics and reducing the current; and in an intermediate regime the Landauer view of the system only is recovered. Lastly, we also demonstrate that a simple equation of motion emerges, which is suitable for efficiently simulating time-dependent transport.« less

p - n Junction Dynamics Induced in a Graphene Channel by Ferroelectric-Domain Motion in the Substrate

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

Kurchak, Anatolii I.; Eliseev, Eugene A.; Kalinin, Sergei V.

The p - n junction dynamics induced in a graphene channel by stripe-domain nucleation, motion, and reversal in a ferroelectric substrate is explored using a self-consistent approach based on Landau-Ginzburg-Devonshire phenomenology combined with classical electrostatics. Relatively low gate voltages are required to induce the hysteresis of ferroelectric polarization and graphene charge in response to the periodic gate voltage. Pronounced nonlinear hysteresis of graphene conductance with a wide memory window corresponds to high amplitudes of gate voltage. Also, we reveal the extrinsic size effect in the dependence of the graphene-channel conductivity on its length. We predict that the top-gate–dielectric-layer–graphene-channel–ferroelectric-substrate nanostructure consideredmore » here can be a promising candidate for the fabrication of the next generation of modulators and rectifiers based on the graphene p - n junctions.« less

Structure and function of gap junction proteins: role of gap junction proteins in embryonic heart development.

PubMed

Ahir, Bhavesh K; Pratten, Margaret K

2014-01-01

Intercellular (cell-to-cell) communication is a crucial and complex mechanism during embryonic heart development. In the cardiovascular system, the beating of the heart is a dynamic and key regulatory process, which is functionally regulated by the coordinated spread of electrical activity through heart muscle cells. Heart tissues are composed of individual cells, each bearing specialized cell surface membrane structures called gap junctions that permit the intercellular exchange of ions and low molecular weight molecules. Gap junction channels are essential in normal heart function and they assist in the mediated spread of electrical impulses that stimulate synchronized contraction (via an electrical syncytium) of cardiac tissues. This present review describes the current knowledge of gap junction biology. In the first part, we summarise some relevant biochemical and physiological properties of gap junction proteins, including their structure and function. In the second part, we review the current evidence demonstrating the role of gap junction proteins in embryonic development with particular reference to those involved in embryonic heart development. Genetics and transgenic animal studies of gap junction protein function in embryonic heart development are considered and the alteration/disruption of gap junction intercellular communication which may lead to abnormal heart development is also discussed.

MarvelD3 couples tight junctions to the MEKK1–JNK pathway to regulate cell behavior and survival

PubMed Central

Steed, Emily; Elbediwy, Ahmed; Vacca, Barbara; Dupasquier, Sébastien; Hemkemeyer, Sandra A.; Suddason, Tesha; Costa, Ana C.; Beaudry, Jean-Bernard; Zihni, Ceniz; Gallagher, Ewen; Pierreux, Christophe E.

2014-01-01

MarvelD3 is a transmembrane component of tight junctions, but there is little evidence for a direct involvement in the junctional permeability barrier. Tight junctions also regulate signaling mechanisms that guide cell proliferation; however, the transmembrane components that link the junction to such signaling pathways are not well understood. In this paper, we show that MarvelD3 is a dynamic junctional regulator of the MEKK1–c-Jun NH2-terminal kinase (JNK) pathway. Loss of MarvelD3 expression in differentiating Caco-2 cells resulted in increased cell migration and proliferation, whereas reexpression in a metastatic tumor cell line inhibited migration, proliferation, and in vivo tumor formation. Expression levels of MarvelD3 inversely correlated with JNK activity, as MarvelD3 recruited MEKK1 to junctions, leading to down-regulation of JNK phosphorylation and inhibition of JNK-regulated transcriptional mechanisms. Interplay between MarvelD3 internalization and JNK activation tuned activation of MEKK1 during osmotic stress, leading to junction dissociation and cell death in MarvelD3-depleted cells. MarvelD3 thus couples tight junctions to the MEKK1–JNK pathway to regulate cell behavior and survival. PMID:24567356

Thermodynamic characterization of a triple-helical three-way junction containing a Hoogsteen branch point.

PubMed

Hüsler, P L; Klump, H H

1995-09-10

We have designed a Hoogsteen (HG) triple-helical three-way junction (ternary complex) constructed from three 33-mer oligonucleotides based on the same subset of sequences used for the Watson-Crick (WC) triple-helical three-way junction, characterized previously (P. L. Hüsler and H. H. Klump (1994) Arch. Biochem. Biophys., 313, 29-38). The junction differs primarily in the assembly of the branch point and the ends of the arms. The three oligonucleotides can each fold into a WC hairpin, linked by a four-member cytosine loop, each containing a homo-pyrimidine 10-mer single-strand extension. On lowering the pH (between 6 and 4), the extensions mutually associate to one of the other hairpins via Hoogsteen (HG) hydrogen bonding. Collectively, this process results in the formation of the branch point and the triple-helical arms. The HG triple-helical three-way junction is characterized by gel electrophoresis, circular dichroism, uv melting, and differential scanning calorimetry. The junction undergoes thermal unfolding in two distinct temperature regions. In the temperature range 15 to 50 degrees C loss of HG base pairing results in the dissociation of the three-way junction. Between 55 and 95 degrees C the resulting hairpins undergo further successive unfolding. The overall calorimetric unfolding enthalpy and entropy changes associated with the loss of HG base pairing are approximately equal to the sum of the enthalpy and entropy changes associated with the dissociation of the HG base pairing in the isolated arms (170.6 kcal.mol-1; 540.1 cal.mol-1.K-1). It is apparent from these results that in the proximity of the branch point the structure is not perturb or strain. This result is contrary to the results obtained for the WC triple-helical three-way and for three-way junctions constructed from canonical double-helical DNA. Complete folding of the junction requires either high Na+ (600 mM) ion concentrations or 40-60 mM Mg2+.

Development of Fast NbN RSFQ Logic Gates in Sigma-Delta Converters for Space Telecommunications

DTIC Science & Technology

2005-07-13

spatiales des circuits logiques supraconducteurs ” Internal Technical Reports, Alcatel Space & CEA, 2003. [3] P. Bunyk, K. Likharev and D. Zinoviev...films minces et de junctions Josephson en nitrures supraconducteurs (TiN et NbN), application à la logique RSFQ, PhD Thesis, Université J. Fourier

Effect of single-strand break on branch migration and folding dynamics of Holliday junctions.

PubMed

Palets, Dmytro; Lushnikov, Alexander Y; Karymov, Mikhail A; Lyubchenko, Yuri L

2010-09-22

The Holliday junction (HJ), or four-way junction, is a central intermediate state of DNA for homologous genetic recombination and other genetic processes such as replication and repair. Branch migration is the process by which the exchange of homologous DNA regions occurs, and it can be spontaneous or driven by proteins. Unfolding of the HJ is required for branch migration. Our previous single-molecule fluorescence studies led to a model according to which branch migration is a stepwise process consisting of consecutive migration and folding steps. Folding of the HJ in one of the folded conformations terminates the branch migration phase. At the same time, in the unfolded state HJ rapidly migrates over entire homology region of the HJ in one hop. This process can be affected by irregularities in the DNA double helical structure, so mismatches almost terminate a spontaneous branch migration. Single-stranded breaks or nicks are the most ubiquitous defects in the DNA helix; however, to date, their effect on the HJ branch migration has not been studied. In addition, although nicked HJs are specific substrates for a number of enzymes involved in DNA recombination and repair, the role of this substrate specificity remains unclear. Our main goal in this work was to study the effect of nicks on the efficiency of HJ branch migration and the dynamics of the HJ. To accomplish this goal, we applied two single-molecule methods: atomic force microscopy and fluorescence resonance energy transfer. The atomic force microscopy data show that the nick does not prevent branch migration, but it does decrease the probability that the HJ will pass the DNA lesion. The single-molecule fluorescence resonance energy transfer approaches were instrumental in detailing the effects of nicks. These studies reveal a dramatic change of the HJ dynamics. The nick changes the structure and conformational dynamics of the junctions, leading to conformations with geometries that are different from those for the intact HJ. On the basis of these data, we propose a model of branch migration in which the propensity of the junction to unfold decreases the lifetimes of folded states, thereby increasing the frequency of junction fluctuations between the folded states. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Phase retrapping in a pointlike φ Josephson junction: the butterfly effect.

PubMed

Goldobin, E; Kleiner, R; Koelle, D; Mints, R G

2013-08-02

We consider a φ Josephson junction, which has a bistable zero-voltage state with the stationary phases ψ = ±φ. In the nonzero voltage state the phase "moves" viscously along a tilted periodic double-well potential. When the tilting is reduced quasistatically, the phase is retrapped in one of the potential wells. We study the viscous phase dynamics to determine in which well (-φ or +φ) the phase is retrapped for a given damping, when the junction returns from the finite-voltage state back to the zero-voltage state. In the limit of low damping, the φ Josephson junction exhibits a butterfly effect-extreme sensitivity of the destination well on damping. This leads to an impossibility to predict the destination well.

Tight Coupling of Astrocyte pH Dynamics to Epileptiform Activity Revealed by Genetically Encoded pH Sensors.

PubMed

Raimondo, Joseph V; Tomes, Hayley; Irkle, Agnese; Kay, Louise; Kellaway, Lauriston; Markram, Henry; Millar, Robert P; Akerman, Colin J

2016-06-29

Astrocytes can both sense and shape the evolution of neuronal network activity and are known to possess unique ion regulatory mechanisms. Here we explore the relationship between astrocytic intracellular pH dynamics and the synchronous network activity that occurs during seizure-like activity. By combining confocal and two-photon imaging of genetically encoded pH reporters with simultaneous electrophysiological recordings, we perform pH measurements in defined cell populations and relate these to ongoing network activity. This approach reveals marked differences in the intracellular pH dynamics between hippocampal astrocytes and neighboring pyramidal neurons in rodent in vitro models of epilepsy. With three different genetically encoded pH reporters, astrocytes are observed to alkalinize during epileptiform activity, whereas neurons are observed to acidify. In addition to the direction of pH change, the kinetics of epileptiform-associated intracellular pH transients are found to differ between the two cell types, with astrocytes displaying significantly more rapid changes in pH. The astrocytic alkalinization is shown to be highly correlated with astrocytic membrane potential changes during seizure-like events and mediated by an electrogenic Na(+)/HCO3 (-) cotransporter. Finally, comparisons across different cell-pair combinations reveal that astrocytic pH dynamics are more closely related to network activity than are neuronal pH dynamics. This work demonstrates that astrocytes exhibit distinct pH dynamics during periods of epileptiform activity, which has relevance to multiple processes including neurometabolic coupling and the control of network excitability. Dynamic changes in intracellular ion concentrations are central to the initiation and progression of epileptic seizures. However, it is not known how changes in intracellular H(+) concentration (ie, pH) differ between different cell types during seizures. Using recently developed pH-sensitive proteins, we demonstrate that astrocytes undergo rapid alkalinization during periods of seizure-like activity, which is in stark contrast to the acidification that occurs in neighboring neurons. Rapid astrocytic pH changes are highly temporally correlated with seizure activity, are mediated by an electrogenic Na(+)/HCO3- cotransporter, and are more tightly coupled to network activity than are neuronal pH changes. As pH has profound effects on signaling in the nervous system, this work has implications for our understanding of seizure dynamics. Copyright © 2016 the authors 0270-6474/16/367002-12$15.00/0.

Exploring Instructive Physiological Signaling with the Bioelectric Tissue Simulation Engine

PubMed Central

Pietak, Alexis; Levin, Michael

2016-01-01

Bioelectric cell properties have been revealed as powerful targets for modulating stem cell function, regenerative response, developmental patterning, and tumor reprograming. Spatio-temporal distributions of endogenous resting potential, ion flows, and electric fields are influenced not only by the genome and external signals but also by their own intrinsic dynamics. Ion channels and electrical synapses (gap junctions) both determine, and are themselves gated by, cellular resting potential. Thus, the origin and progression of bioelectric patterns in multicellular tissues is complex, which hampers the rational control of voltage distributions for biomedical interventions. To improve understanding of these dynamics and facilitate the development of bioelectric pattern control strategies, we developed the BioElectric Tissue Simulation Engine (BETSE), a finite volume method multiphysics simulator, which predicts bioelectric patterns and their spatio-temporal dynamics by modeling ion channel and gap junction activity and tracking changes to the fundamental property of ion concentration. We validate performance of the simulator by matching experimentally obtained data on membrane permeability, ion concentration and resting potential to simulated values, and by demonstrating the expected outcomes for a range of well-known cases, such as predicting the correct transmembrane voltage changes for perturbation of single cell membrane states and environmental ion concentrations, in addition to the development of realistic transepithelial potentials and bioelectric wounding signals. In silico experiments reveal factors influencing transmembrane potential are significantly different in gap junction-networked cell clusters with tight junctions, and identify non-linear feedback mechanisms capable of generating strong, emergent, cluster-wide resting potential gradients. The BETSE platform will enable a deep understanding of local and long-range bioelectrical dynamics in tissues, and assist the development of specific interventions to achieve greater control of pattern during morphogenesis and remodeling. PMID:27458581

Cell Geometry Guides the Dynamic Targeting of Apoplastic GPI-Linked Lipid Transfer Protein to Cell Wall Elements and Cell Borders in Arabidopsis thaliana

PubMed Central

Wasteneys, Geoffrey

2013-01-01

During cellular morphogenesis, changes in cell shape and cell junction topology are fundamental to normal tissue and organ development. Here we show that apoplastic Glycophosphatidylinositol (GPI)-anchored Lipid Transfer Protein (LTPG) is excluded from cell junctions and flat wall regions, and passively accumulates around their borders in the epidermal cells of Arabidopsis thaliana. Beginning with intense accumulation beneath highly curved cell junction borders, this enrichment is gradually lost as cells become more bulbous during their differentiation. In fully mature epidermal cells, YFP-LTPG often shows a fibrous cellulose microfibril-like pattern within the bulging outer faces. Physical contact between a flat glass surface and bulbous cell surface induces rapid and reversible evacuation from contact sites and accumulation to the curved wall regions surrounding the contact borders. Thus, LTPG distribution is dynamic, responding to changes in cell shape and wall curvature during cell growth and differentiation. We hypothesize that this geometry-based mechanism guides wax-carrying LTPG to functional sites, where it may act to “seal” the vulnerable border surrounding cell-cell junctions and assist in cell wall fortification and cuticular wax deposition. PMID:24260561

Experiments with BECs in a Painted Potential: Atom SQUID, Matter Wave Bessel Beams, and Matter Wave Circuits

NASA Astrophysics Data System (ADS)

Boshier, Malcolm; Ryu, Changhyun; Blackburn, Paul; Blinova, Alina; Henderson, Kevin

2014-05-01

The painted potential is a time-averaged optical dipole potential which is able to create arbitrary and dynamic two dimensional potentials for Bose Einstein condensates (BECs). This poster reports three recent experiments using this technique. First, we have realized the dc atom SQUID geometry of a BEC in a toroidal trap with two Josephson junctions. We observe Josephson effects, measure the critical current of the junctions, and find dynamic behavior that is in good agreement with the simple Josephson equations for a tunnel junction with the ideal sinusoidal current-phase relation expected for the parameters of the experiment. Second, we have used free expansion of a rotating toroidal BEC to create matter wave Bessel beams, which are of interest because perfect Bessel beams (plane waves with amplitude profiles described by Bessel functions) propagate without diffraction. Third, we have realized the basic circuit elements necessary to create complex matter wave circuits. We launch BECs at arbitrary velocity along straight waveguides, propagate them around curved waveguides and stadium-shaped waveguide traps, and split them coherently at y-junctions that can also act as switches. Supported by LANL/LDRD.

Endoplasmic reticulum-plasma membrane junctions: structure, function and dynamics.

PubMed

Okeke, Emmanuel; Dingsdale, Hayley; Parker, Tony; Voronina, Svetlana; Tepikin, Alexei V

2016-06-01

Endoplasmic reticulum (ER)-plasma membrane (PM) junctions are contact sites between the ER and the PM; the distance between the two organelles in the junctions is below 40 nm and the membranes are connected by protein tethers. A number of molecular tools and technical approaches have been recently developed to visualise, modify and characterise properties of ER-PM junctions. The junctions serve as the platforms for lipid exchange between the organelles and for cell signalling, notably Ca(2+) and cAMP signalling. Vice versa, signalling events regulate the development and properties of the junctions. Two Ca(2+) -dependent mechanisms of de novo formation of ER-PM junctions have been recently described and characterised. The junction-forming proteins and lipids are currently the focus of vigorous investigation. Junctions can be relatively short-lived and simple structures, forming and dissolving on the time scale of a few minutes. However, complex, sophisticated and multifunctional ER-PM junctions, capable of attracting numerous protein residents and other cellular organelles, have been described in some cell types. The road from simplicity to complexity, i.e. the transformation from simple 'nascent' ER-PM junctions to advanced stable multiorganellar complexes, is likely to become an attractive research avenue for current and future junctologists. Another area of considerable research interest is the downstream cellular processes that can be activated by specific local signalling events in the ER-PM junctions. Studies of the cell physiology and indeed pathophysiology of ER-PM junctions have already produced some surprising discoveries, likely to expand with advances in our understanding of these remarkable organellar contact sites. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

The pathophysiology of pulmonary hypertension in left heart disease.

PubMed

Breitling, Siegfried; Ravindran, Krishnan; Goldenberg, Neil M; Kuebler, Wolfgang M

2015-11-01

Pulmonary hypertension (PH) is characterized by elevated pulmonary arterial pressure leading to right-sided heart failure and can arise from a wide range of etiologies. The most common cause of PH, termed Group 2 PH, is left-sided heart failure and is commonly known as pulmonary hypertension with left heart disease (PH-LHD). Importantly, while sharing many clinical features with pulmonary arterial hypertension (PAH), PH-LHD differs significantly at the cellular and physiological levels. These fundamental pathophysiological differences largely account for the poor response to PAH therapies experienced by PH-LHD patients. The relatively high prevalence of this disease, coupled with its unique features compared with PAH, signal the importance of an in-depth understanding of the mechanistic details of PH-LHD. The present review will focus on the current state of knowledge regarding the pathomechanisms of PH-LHD, highlighting work carried out both in human trials and in preclinical animal models. Adaptive processes at the alveolocapillary barrier and in the pulmonary circulation, including alterations in alveolar fluid transport, endothelial junctional integrity, and vasoactive mediator secretion will be discussed in detail, highlighting the aspects that impact the response to, and development of, novel therapeutics. Copyright © 2015 the American Physiological Society.

Low frequency critical current noise and two level system defects in Josephson junctions

NASA Astrophysics Data System (ADS)

Nugroho, Christopher Daniel

The critical current in a Josephson junction is known to exhibit a 1/falpha low frequency noise. Implemented as a superconducting qubit, this low frequency noise can lead to decoherence. While the 1/f noise has been known to arise from an ensemble of two level systems connected to the tunnel barrier, the precise microscopic nature of these TLSs remain a mystery. In this thesis we will present measurements of the 1/f alpha low frequency noise in the critical current and tunneling resistance of Al-AlOx-Al Josephson junctions. Measurements in a wide range of resistively shunted and unshunted junctions confirm the equality of critical current and tunneling resistance noise. That is the critical current fluctuation corresponds to fluctuations of the tunneling resistance. In not too small Al-AlOx-Al junctions we have found that the fractional power spectral density scales linearly with temperature. We confirmed that the 1/falpha power spectrum is the result of a large number of two level systems modulating the tunneling resistance. At small junction areas and low temperatures, the number of thermally active TLSs is insufficient to integrate out a featureless 1/ f spectral shape. By analyzing the spectral variance in small junction areas, we have been able to deduce the TLS defect density, n ≈ 2.53 per micrometer squared per Kelvin spread in the TLS energy per factor e in the TLS lifetimes. This density is consistent with the density of tunneling TLSs found in glassy insulators, as well as the density deduced from coherent TLSs interacting at qubit frequencies. The deduced TLS density combined with the magnitude of the 1/f power spectral density in large area junctions, gives an average TLS effective area, A ˜ 0.3 nanometer squared. In ultra small tunnel junctions, we have studied the time-domain dynamics of isolated TLSs. We have found a TLS whose dynamics is described by the quantum tunneling between the two localized wells, and a one-phonon absorption/emission switching rate. From the quantum limiting rate and the WKB approximation, we estimated that the TLS has a mass and tunneling distance product consistent with an atomic mass tunneling through crystal lattice distances. At higher temperatures TLSs have been found that obey a simple thermal activation dynamics. By analyzing the TLS response to an external electric field, we have deduced that the TLS electric dipole is in the order of, P ˜ 1 electron-Angstrom, consistent with the TLS having the charge of one electron tunneling through a disorder potential of distances, d ˜ 1 Angstrom.

Smad ubiquitination regulatory factor-2 controls gap junction intercellular communication by modulating endocytosis and degradation of connexin43.

PubMed

Fykerud, Tone Aase; Kjenseth, Ane; Schink, Kay Oliver; Sirnes, Solveig; Bruun, Jarle; Omori, Yasufumi; Brech, Andreas; Rivedal, Edgar; Leithe, Edward

2012-09-01

Gap junctions consist of arrays of intercellular channels that enable adjacent cells to communicate both electrically and metabolically. Gap junction channels are made of a family of integral membrane proteins called connexins, of which the best-studied member is connexin43. Gap junctions are dynamic plasma membrane domains, and connexin43 has a high turnover rate in most tissue types. However, the mechanisms involved in the regulation of connexin43 endocytosis and transport to lysosomes are still poorly understood. Here, we demonstrate by live-cell imaging analysis that treatment of cells with 12-O-tetradecanoylphorbol 13-acetate (TPA) induces endocytosis of subdomains of connexin43 gap junctions. The internalized, connexin43-enriched vesicles were found to fuse with early endosomes, which was followed by transport of connexin43 to the lumen of early endosomes. The HECT E3 ubiquitin ligase smad ubiquitination regulatory factor-2 (Smurf2) was found to be recruited to connexin43 gap junctions in response to TPA treatment. Depletion of Smurf2 by small interfering RNA resulted in enhanced levels of connexin43 gap junctions between adjacent cells and increased gap junction intercellular communication. Smurf2 depletion also counteracted the TPA-induced endocytosis and degradation of connexin43. Collectively, these data identify Smurf2 as a novel regulator of connexin43 gap junctions.

Spatio-temporal regulation of connexin43 phosphorylation and gap junction dynamics.

PubMed

Solan, Joell L; Lampe, Paul D

2018-01-01

Gap junctions are specialized membrane domains containing tens to thousands of intercellular channels. These channels permit exchange of small molecules (<1000Da) including ions, amino acids, nucleotides, metabolites and secondary messengers (e.g., calcium, glucose, cAMP, cGMP, IP 3 ) between cells. The common reductionist view of these structures is that they are composed entirely of integral membrane proteins encoded by the 21 member connexin human gene family. However, it is clear that the normal physiological function of this structure requires interaction and regulation by a variety of proteins, especially kinases. Phosphorylation is capable of directly modulating connexin channel function but the most dramatic effects on gap junction activity occur via the organization of the gap junction structures themselves. This is a direct result of the short half-life of the primary gap junction protein, connexin, which requires them to be constantly assembled, remodeled and turned over. The biological consequences of this remodeling are well illustrated during cardiac ischemia, a process wherein gap junctions are disassembled and remodeled resulting in arrhythmia and ultimately heart failure. This article is part of a Special Issue entitled: Gap Junction Proteins edited by Jean Claude Herve. Copyright © 2017 Elsevier B.V. All rights reserved.

Noninvasive Ph-telemetric Measurement of Gastrointestinal Function

NASA Technical Reports Server (NTRS)

Tietze, Karen J.

1991-01-01

The purpose of this study was to gain experience with and validate the Heidelberg pH-telemetric methodology in order to determine if the pH-telemetric methodology would be a useful noninvasive measure of gastrointestinal transit time for future ground-based and in-flight drug evaluation studies. The Heidelberg pH metering system is a noninvasive, nonradioactive telemetric system that, following oral ingestion, continuously measures intraluminal pH of the stomach, duodenum, small bowel, ileocecal junction, and large bowel. Gastrointestinal motility profiles were obtained in normal volunteers using the lactulose breath-hydrogen and Heidelberg pH metering techniques. All profiles were obtained in the morning after an overnight fast. Heidelberg pH profiles were obtained in the fasting and fed states; lactulose breath-hydrogen profiles were obtained after a standard breakfast. Mouth-to-cecum transit time was measured as the interval from administration of lactulose (30 ml; 20 g) to a sustained increase in breath-hydrogen of 10 ppm or more. Gastric emptying time was measured as the interval from the administration of the Heidelberg capsule to a sustained increase in pH of three units or more.

Ferromagnetic resonance with long Josephson junction

NASA Astrophysics Data System (ADS)

Golovchanskiy, I. A.; Abramov, N. N.; Stolyarov, V. S.; Emelyanova, O. V.; Golubov, A. A.; Ustinov, A. V.; Ryazanov, V. V.

2017-05-01

In this work we propose a hybrid device based on a long Josephson junction (JJ) coupled inductively to an external ferromagnetic (FM) layer. The long JJ in a zero-field operation mode induces a localized AC magnetic field in the FM layer and enables a synchronized magnetostatic standing wave. The magnetostatic wave induces additional dissipation for soliton propagation in the junction and also enables a phase locking (resonant soliton synchronization) at a frequency of natural ferromagnetic resonance. The later manifests itself as an additional constant voltage step on the current-voltage characteristics at the corresponding voltage. The proposed device allows to study magnetization dynamics of individual micro-scaled FM samples using just DC technique, and also it provides additional phase locking frequency in the junction, determined exclusively by characteristics of the ferromagnet.

Quantum Dynamics of a d-wave Josephson Junction

NASA Astrophysics Data System (ADS)

Bauch, Thilo

2007-03-01

Thilo Bauch ^1, Floriana Lombardi ^1, Tobias Lindstr"om ^2, Francesco Tafuri ^3, Giacomo Rotoli ^4, Per Delsing ^1, Tord Claeson ^1 1 Quantum Device Physics Laboratory, Department of Microtechnology and Nanoscience, MC2, Chalmers University of Technology, S-412 96 G"oteborg, Sweden. 2 National Physical Laboratory, Queens Road, Teddington, Middlesex TW11 0LW, UK. 3 Istituto Nazionale per la Fisica della Materia-Dipartimento Ingegneria dell'Informazione, Seconda Universita di Napoli, Aversa (CE), Italy. 4 Dipartimento di Ingegneria Meccanica, Energetica e Gestionale, Universita of L'Aquila, Localita Monteluco, L'Aquila, Italy. We present direct observation of macroscopic quantum properties in an all high critical temperature superconductor d-wave Josephson junction. Although dissipation caused by low energy excitations is expected to strongly suppress quantum effects we demonstrate macroscopic quantum tunneling [1] and energy level quantization [2] in our d-wave Josephson junction. The results clearly indicate that the role of dissipation mechanisms in high temperature superconductors has to be revised, and may also have consequences for a new class of solid state ``quiet'' quantum bit with superior coherence time. We show that the dynamics of the YBCO grain boundary Josephson junctions fabricated on a STO substrate are strongly affected by their environment. As a first approximation we model the environment by the stray capacitance and stray inductance of the junction electrodes. The total system consisting of the junction and stray elements has two degrees of freedom resulting in two characteristic resonance frequencies. Both frequencies have to be considered to describe the quantum mechanical behavior of the Josephson circuit. [1] T. Bauch et al, Phys. Rev. Lett. 94, 087003 (2005). [2] T. Bauch et al, Science 311, 57 (2006).

Detailed investigation of the bifurcation diagram of capacitively coupled Josephson junctions in high-Tc superconductors and its self similarity

NASA Astrophysics Data System (ADS)

Hamdipour, Mohammad

2018-04-01

We study an array of coupled Josephson junction of superconductor/insulator/superconductor type (SIS junction) as a model for high temperature superconductors with layered structure. In the current-voltage characteristics of this system there is a breakpoint region in which a net electric charge appear on superconducting layers, S-layers, of junctions which motivate us to study the charge dynamics in this region. In this paper first of all we show a current voltage characteristics (CVC) of Intrinsic Josephson Junctions (IJJs) with N=3 Junctions, then we show the breakpoint region in that CVC, then we try to investigate the chaos in this region. We will see that at the end of the breakpoint region, behavior of the system is chaotic and Lyapunov exponent become positive. We also study the route by which the system become chaotic and will see this route is bifurcation. Next goal of this paper is to show the self similarity in the bifurcation diagram of the system and detailed analysis of bifurcation diagram.

Myosin II promotes the anisotropic loss of the apical domain during Drosophila neuroblast ingression

PubMed Central

Simões, Sérgio; Oh, Youjin; Wang, Michael F.Z.; Fernandez-Gonzalez, Rodrigo

2017-01-01

Epithelial–mesenchymal transitions play key roles in development and cancer and entail the loss of epithelial polarity and cell adhesion. In this study, we use quantitative live imaging of ingressing neuroblasts (NBs) in Drosophila melanogaster embryos to assess apical domain loss and junctional disassembly. Ingression is independent of the Snail family of transcriptional repressors and down-regulation of Drosophila E-cadherin (DEcad) transcription. Instead, the posttranscriptionally regulated decrease in DEcad coincides with the reduction of cell contact length and depends on tension anisotropy between NBs and their neighbors. A major driver of apical constriction and junctional disassembly are periodic pulses of junctional and medial myosin II that result in progressively stronger cortical contractions during ingression. Effective contractions require the molecular coupling between myosin and junctions and apical relaxation of neighboring cells. Moreover, planar polarization of myosin leads to the loss of anterior–posterior junctions before the loss of dorsal–ventral junctions. We conclude that planar-polarized dynamic actomyosin networks drive apical constriction and the anisotropic loss of cell contacts during NB ingression. PMID:28363972

Cdc42 regulates junctional actin but not cell polarization in the Caenorhabditis elegans epidermis

PubMed Central

Zilberman, Yuliya; Abrams, Joshua; Anderson, Dorian C.

2017-01-01

During morphogenesis, adherens junctions (AJs) remodel to allow changes in cell shape and position while preserving adhesion. Here, we examine the function of Rho guanosine triphosphatase CDC-42 in AJ formation and regulation during Caenorhabditis elegans embryo elongation, a process driven by asymmetric epidermal cell shape changes. cdc-42 mutant embryos arrest during elongation with epidermal ruptures. Unexpectedly, we find using time-lapse fluorescence imaging that cdc-42 is not required for epidermal cell polarization or junction assembly, but rather is needed for proper junctional actin regulation during elongation. We show that the RhoGAP PAC-1/ARHGAP21 inhibits CDC-42 activity at AJs, and loss of PAC-1 or the interacting linker protein PICC-1/CCDC85A-C blocks elongation in embryos with compromised AJ function. pac-1 embryos exhibit dynamic accumulations of junctional F-actin and an increase in AJ protein levels. Our findings identify a previously unrecognized molecular mechanism for inhibiting junctional CDC-42 to control actin organization and AJ protein levels during epithelial morphogenesis. PMID:28903999

FSGS3/CD2AP is a barbed-end capping protein that stabilizes actin and strengthens adherens junctions

PubMed Central

Brieher, William M.

2013-01-01

By combining in vitro reconstitution biochemistry with a cross-linking approach, we have identified focal segmental glomerulosclerosis 3/CD2-associated protein (FSGS3/CD2AP) as a novel actin barbed-end capping protein responsible for actin stability at the adherens junction. FSGS3/CD2AP colocalizes with E-cadherin and α-actinin-4 at the apical junction in polarized Madin-Darby canine kidney (MDCK) cells. Knockdown of FSGS3/CD2AP compromised actin stability and decreased actin accumulation at the adherens junction. Using a novel apparatus to apply mechanical stress to cell–cell junctions, we showed that knockdown of FSGS3/CD2AP compromised adhesive strength, resulting in tearing between cells and disruption of barrier function. Our results reveal a novel function of FSGS3/CD2AP and a previously unrecognized role of barbed-end capping in junctional actin dynamics. Our study underscores the complexity of actin regulation at cell–cell contacts that involves actin activators, inhibitors, and stabilizers to control adhesive strength, epithelial behavior, and permeability barrier integrity. PMID:24322428

Triptolide disrupts the actin-based Sertoli-germ cells adherens junctions by inhibiting Rho GTPases expression

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

Wang, Xiang; Zhao, Fang

Triptolide (TP), derived from the medicinal plant Triterygium wilfordii Hook. f. (TWHF), is a diterpene triepoxide with variety biological and pharmacological activities. However, TP has been restricted in clinical application due to its narrow therapeutic window especially in reproductive system. During spermatogenesis, Sertoli cell cytoskeleton plays an essential role in facilitating germ cell movement and cell-cell actin-based adherens junctions (AJ). At Sertoli cell-spermatid interface, the anchoring device is a kind of AJ, known as ectoplasmic specializations (ES). In this study, we demonstrate that β-actin, an important component of cytoskeleton, has been significantly down-regulated after TP treatment. TP can inhibit themore » expression of Rho GTPase such as, RhoA, RhoB, Cdc42 and Rac1. Downstream of Rho GTPase, Rho-associated protein kinase (ROCKs) gene expressions were also suppressed by TP. F-actin immunofluorescence proved that TP disrupts Sertoli cells cytoskeleton network. As a result of β-actin down-regulation, TP treatment increased expression of testin, which indicating ES has been disassembled. In summary, this report illustrates that TP induces cytoskeleton dysfunction and disrupts cell-cell adherens junctions via inhibition of Rho GTPases. - Highlights: • Triptolide induced the disruption of Sertoli-germ cell adherens junction. • Rho GTPases expression and actin dynamics have been suppressed by triptolide. • Actin-based adherens junction is a potential antifertility target of triptolide. • Rho-Rock is involved in the regulation of actin dynamics.« less

Coherent and dissipative transport in a Josephson junction between fermionic superfluids of 6Li atoms

NASA Astrophysics Data System (ADS)

Neri, Elettra; Scazza, Francesco; Roati, Giacomo

2018-04-01

Quantum systems out of equilibrium offer the possibility of understanding intriguing and challenging problems in modern physics. Studying transport properties is not only valuable to unveil fundamental properties of quantum matter but it is also an excellent tool for developing new quantum devices which inherently employ quantum-mechanical effects. In this contribution, we present our experimental studies on quantum transport using ultracold Fermi gases of 6Li atoms. We realize the analogous of a Josephson junction by bisecting fermionic superfluids by a thin optical barrier. We observe coherent dynamics in both the population and in the relative phase between the two reservoirs. For critical parameters, the superfluid dynamics exhibits both coherent and resistive flow due to phase-slippage events manifesting as vortices propagating into the bulk. We uncover also a regime of strong dissipation where the junction operation is irreversibly affected by vortex proliferation. Our studies open new directions for investigating dissipation and superfluid transport in strongly correlated fermionic systems.

Fluorescence recovery after photobleaching reveals regulation and distribution of connexin36 gap junction coupling within mouse islets of Langerhans

PubMed Central

Farnsworth, Nikki L; Hemmati, Alireza; Pozzoli, Marina; Benninger, Richard K P

2014-01-01

The pancreatic islets are central to the maintenance of glucose homeostasis through insulin secretion. Glucose-stimulated insulin secretion is tightly linked to electrical activity in β cells within the islet. Gap junctions, composed of connexin36 (Cx36), form intercellular channels between β cells, synchronizing electrical activity and insulin secretion. Loss of gap junction coupling leads to altered insulin secretion dynamics and disrupted glucose homeostasis. Gap junction coupling is known to be disrupted in mouse models of pre-diabetes. Although approaches to measure gap junction coupling have been devised, they either lack cell specificity, suitable quantification of coupling or spatial resolution, or are invasive. The purpose of this study was to develop fluorescence recovery after photobleaching (FRAP) as a technique to accurately and robustly measure gap junction coupling in the islet. The cationic dye Rhodamine 123 was used with FRAP to quantify dye diffusion between islet β cells as a measure of Cx36 gap junction coupling. Measurements in islets with reduced Cx36 verified the accuracy of this technique in distinguishing between distinct levels of gap junction coupling. Analysis of individual cells revealed that the distribution of coupling across the islet is highly heterogeneous. Analysis of several modulators of gap junction coupling revealed glucose- and cAMP-dependent modulation of gap junction coupling in islets. Finally, FRAP was used to determine cell population specific coupling, where no functional gap junction coupling was observed between α cells and β cells in the islet. The results of this study show FRAP to be a robust technique which provides the cellular resolution to quantify the distribution and regulation of Cx36 gap junction coupling in specific cell populations within the islet. Future studies utilizing this technique may elucidate the role of gap junction coupling in the progression of diabetes and identify mechanisms of gap junction regulation for potential therapies. PMID:25172942

Fluorescence recovery after photobleaching reveals regulation and distribution of connexin36 gap junction coupling within mouse islets of Langerhans.

PubMed

Farnsworth, Nikki L; Hemmati, Alireza; Pozzoli, Marina; Benninger, Richard K P

2014-10-15

The pancreatic islets are central to the maintenance of glucose homeostasis through insulin secretion. Glucose‐stimulated insulin secretion is tightly linked to electrical activity in β cells within the islet. Gap junctions, composed of connexin36 (Cx36), form intercellular channels between β cells, synchronizing electrical activity and insulin secretion. Loss of gap junction coupling leads to altered insulin secretion dynamics and disrupted glucose homeostasis. Gap junction coupling is known to be disrupted in mouse models of pre‐diabetes. Although approaches to measure gap junction coupling have been devised, they either lack cell specificity, suitable quantification of coupling or spatial resolution, or are invasive. The purpose of this study was to develop fluorescence recovery after photobleaching (FRAP) as a technique to accurately and robustly measure gap junction coupling in the islet. The cationic dye Rhodamine 123 was used with FRAP to quantify dye diffusion between islet β cells as a measure of Cx36 gap junction coupling. Measurements in islets with reduced Cx36 verified the accuracy of this technique in distinguishing between distinct levels of gap junction coupling. Analysis of individual cells revealed that the distribution of coupling across the islet is highly heterogeneous. Analysis of several modulators of gap junction coupling revealed glucose‐ and cAMP‐dependent modulation of gap junction coupling in islets. Finally, FRAP was used to determine cell population specific coupling, where no functional gap junction coupling was observed between α cells and β cells in the islet. The results of this study show FRAP to be a robust technique which provides the cellular resolution to quantify the distribution and regulation of Cx36 gap junction coupling in specific cell populations within the islet. Future studies utilizing this technique may elucidate the role of gap junction coupling in the progression of diabetes and identify mechanisms of gap junction regulation for potential therapies.

Vertically aligned silicon microwire arrays of various lengths by repeated selective vapor-liquid-solid growth of n-type silicon/n-type silicon

NASA Astrophysics Data System (ADS)

Ikedo, Akihito; Kawashima, Takahiro; Kawano, Takeshi; Ishida, Makoto

2009-07-01

Repeated vapor-liquid-solid (VLS) growth with Au and PH3-Si2H6 mixture gas as the growth catalyst and silicon source, respectively, was used to construct n-type silicon/n-type silicon wire arrays of various lengths. Silicon wires of various lengths within an array could be grown by employing second growth over the first VLS grown wire. Additionally, the junction at the interface between the first and the second wires were examined. Current-voltage measurements of the wires exhibited linear behavior with a resistance of 850 Ω, confirming nonelectrical barriers at the junction, while bending tests indicated that the mechanical properties of the wire did not change.

Carbon Nanotubes: Molecular Electronic Components

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Saini, Subhash; Menon, Madhu

1997-01-01

The carbon Nanotube junctions have recently emerged as excellent candidates for use as the building blocks in the formation of nanoscale molecular electronic networks. While the simple joint of two dissimilar tubes can be generated by the introduction of a pair of heptagon-pentagon defects in an otherwise perfect hexagonal graphene sheet, more complex joints require other mechanisms. In this work we explore structural characteristics of complex 3-point junctions of carbon nanotubes using a generalized tight-binding molecular-dynamics scheme. The study of pi-electron local densities of states (LDOS) of these junctions reveal many interesting features, most prominent among them being the defect-induced states in the gap.

Measure Guideline: Optimizing the Configuration of Flexible Duct Junction Boxes

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

Beach, R.; Burdick, A.

2014-03-01

This measure guideline offers additional recommendations to heating, ventilation, and air conditioning (HVAC) system designers for optimizing flexible duct, constant-volume HVAC systems using junction boxes within Air Conditioning Contractors of America (ACCA) Manual D guidance. IBACOS used computational fluid dynamics software to explore and develop guidance to better control the airflow effects of factors that may impact pressure losses within junction boxes among various design configurations. These recommendations can help to ensure that a system aligns more closely with the design and the occupants' comfort expectations. Specifically, the recommendations described herein show how to configure a rectangular box with fourmore » outlets, a triangular box with three outlets, metal wyes with two outlets, and multiple configurations for more than four outlets. Designers of HVAC systems, contractors who are fabricating junction boxes on site, and anyone using the ACCA Manual D process for sizing duct runs will find this measure guideline invaluable for more accurately minimizing pressure losses when using junction boxes with flexible ducts.« less

Effect of intrinsic curvature and edge tension on the stability of binary mixed-membrane three-junctions

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

Gardner, Jasmine M.; Abrams, Cameron F.; Deserno, Markus

We use a combination of coarse-grained molecular dynamics simulations and theoretical modeling to examine three-junctions in mixed lipid bilayer membranes. These junctions are localized defect lines in which three bilayers merge in such a way that each bilayer shares one monolayer with one of the other two bilayers. The resulting local morphology is non-lamellar, resembling the threefold symmetric defect lines in inverse hexagonal phases, but it regularly occurs during membrane fission and fusion events. We realize a system of junctions by setting up a honeycomb lattice, which in its primitive cell contains two hexagons and four three-line junctions, permitting usmore » to study their stability as well as their line tension. We specifically consider the effects of lipid composition and intrinsic curvature in binary mixtures, which contain a fraction of negatively curved lipids in a curvature-neutral background phase. Three-junction stability results from a competition between the junction and an open edge, which arises if one of the three bilayers detaches from the other two. We show that the stable phase is the one with the lower defect line tension. The strong and opposite monolayer curvatures present in junctions and edges enhance the mole fraction of negatively curved lipids in junctions and deplete it in edges. This lipid sorting affects the two line tensions and in turn the relative stability of the two phases. It also leads to a subtle entropic barrier for the transition between junction and edge that is absent in uniform membranes.« less

Phase-dependent noise in Josephson junctions

NASA Astrophysics Data System (ADS)

Sheldon, Forrest; Peotta, Sebastiano; Di Ventra, Massimiliano

2018-03-01

In addition to the usual superconducting current, Josephson junctions (JJs) support a phase-dependent conductance related to the retardation effect of tunneling quasi-particles. This introduces a dissipative current with a memory-resistive (memristive) character that should also affect the current noise. By means of the microscopic theory of tunnel junctions we compute the complete current autocorrelation function of a Josephson tunnel junction and show that this memristive component gives rise to both a previously noted phase-dependent thermal noise, and an undescribed non-stationary, phase-dependent dynamic noise. As experiments are approaching ranges in which these effects may be observed, we examine the form and magnitude of these processes. Their phase dependence can be realized experimentally as a hysteresis effect and may be used to probe defects present in JJ based qubits and in other superconducting electronics applications.

Voltage noise of current-driven vortices in disordered Josephson junction arrays.

PubMed

He, G L; Zhao, Z G; Liu, S; Yang, Y H; Liu, M; Xing, D Y

2006-08-16

Dynamical phenomena of moving vortices and voltage noise spectra are studied in disordered Josephson junction arrays (JJAs). The plastic motion of vortices, smectic flow, and moving Bragg glass phases are separated by two dynamic melting transitions driven by current. From the voltage noise spectra of moving vortices, it is found that the driving current plays an important role in the melting of pinning vortices glass and ordering of moving vortices. The features of noise spectra obtained in the disordered JJA model have been observed recently in the high-temperature superconductor Bi(2)Sr(2)CaCu(2)O(y) near the first-order melting transition, indicating that both of them are related to each other.

Correlation of doping, structure, and carrier dynamics in a single GaN nanorod

NASA Astrophysics Data System (ADS)

Zhou, Xiang; Lu, Ming-Yen; Lu, Yu-Jung; Gwo, Shangjr; Gradečak, Silvija

2013-06-01

We report the nanoscale optical investigation of a single GaN p-n junction nanorod by cathodoluminescence (CL) in a scanning transmission electron microscope. CL emission characteristic of dopant-related transitions was correlated to doping and structural defect in the nanorod, and used to determine p-n junction position and minority carrier diffusion lengths of 650 nm and 165 nm for electrons and holes, respectively. Temperature-dependent CL study reveals an activation energy of 19 meV for non-radiative recombination in Mg-doped GaN nanorods. These results directly correlate doping, structure, carrier dynamics, and optical properties of GaN nanostructure, and provide insights for device design and fabrication.

Distinct moieties underlie biphasic H+ gating of connexin43 channels, producing a pH optimum for intercellular communication

PubMed Central

Garciarena, Carolina D.; Malik, Akif; Swietach, Pawel; Moreno, Alonso P.; Vaughan-Jones, Richard D.

2018-01-01

Most mammalian cells can intercommunicate via connexin-assembled, gap-junctional channels. To regulate signal transmission, connexin (Cx) channel permeability must respond dynamically to physiological and pathophysiological stimuli. One key stimulus is intracellular pH (pHi), which is modulated by a tissue’s metabolic and perfusion status. Our understanding of the molecular mechanism of H+ gating of Cx43 channels—the major isoform in the heart and brain—is incomplete. To interrogate the effects of acidic and alkaline pHi on Cx43 channels, we combined voltage-clamp electrophysiology with pHi imaging and photolytic H+ uncaging, performed over a range of pHi values. We demonstrate that Cx43 channels expressed in HeLa or N2a cell pairs are gated biphasically by pHi via a process that consists of activation by H+ ions at alkaline pHi and inhibition at more acidic pHi. For Cx43 channel–mediated solute/ion transmission, the ensemble of these effects produces a pHi optimum, near resting pHi. By using Cx43 mutants, we demonstrate that alkaline gating involves cysteine residues of the C terminus and is independent of motifs previously implicated in acidic gating. Thus, we present a molecular mechanism by which cytoplasmic acid–base chemistry fine tunes intercellular communication and establishes conditions for the optimal transmission of solutes and signals in tissues, such as the heart and brain.—Garciarena, C. D., Malik, A., Swietach, P., Moreno, A. P., Vaughan-Jones, R. D. Distinct moieties underlie biphasic H+ gating of connexin43 channels, producing a pH optimum for intercellular communication. PMID:29183963

Dye-sensitized photoelectrochemical water oxidation through a buried junction.

PubMed

Xu, Pengtao; Huang, Tian; Huang, Jianbin; Yan, Yun; Mallouk, Thomas E

2018-06-18

Water oxidation has long been a challenge in artificial photosynthetic devices that convert solar energy into fuels. Water-splitting dye-sensitized photoelectrochemical cells (WS-DSPECs) provide a modular approach for integrating light-harvesting molecules with water-oxidation catalysts on metal-oxide electrodes. Despite recent progress in improving the efficiency of these devices by introducing good molecular water-oxidation catalysts, WS-DSPECs have poor stability, owing to the oxidation of molecular components at very positive electrode potentials. Here we demonstrate that a solid-state dye-sensitized solar cell (ss-DSSC) can be used as a buried junction for stable photoelectrochemical water splitting. A thin protecting layer of TiO 2 grown by atomic layer deposition (ALD) stabilizes the operation of the photoanode in aqueous solution, although as a solar cell there is a performance loss due to increased series resistance after the coating. With an electrodeposited iridium oxide layer, a photocurrent density of 1.43 mA cm -2 was observed in 0.1 M pH 6.7 phosphate solution at 1.23 V versus reversible hydrogen electrode, with good stability over 1 h. We measured an incident photon-to-current efficiency of 22% at 540 nm and a Faradaic efficiency of 43% for oxygen evolution. While the potential profile of the catalyst layer suggested otherwise, we confirmed the formation of a buried junction in the as-prepared photoelectrode. The buried junction design of ss-DSSs adds to our understanding of semiconductor-electrocatalyst junction behaviors in the presence of a poor semiconducting material.

Modeling light-induced charge transfer dynamics across a metal-molecule-metal junction: Bridging classical electrodynamics and quantum dynamics

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

Hu, Zixuan; Ratner, Mark A.; Seideman, Tamar, E-mail: t-seideman@northwestern.edu

2014-12-14

We develop a numerical approach for simulating light-induced charge transport dynamics across a metal-molecule-metal conductance junction. The finite-difference time-domain method is used to simulate the plasmonic response of the metal structures. The Huygens subgridding technique, as adapted to Lorentz media, is used to bridge the vastly disparate length scales of the plasmonic metal electrodes and the molecular system, maintaining accuracy. The charge and current densities calculated with classical electrodynamics are transformed to an electronic wavefunction, which is then propagated through the molecular linker via the Heisenberg equations of motion. We focus mainly on development of the theory and exemplify ourmore » approach by a numerical illustration of a simple system consisting of two silver cylinders bridged by a three-site molecular linker. The electronic subsystem exhibits fascinating light driven dynamics, wherein the charge density oscillates at the driving optical frequency, exhibiting also the natural system timescales, and a resonance phenomenon leads to strong conductance enhancement.« less

A Sarsa(λ)-based control model for real-time traffic light coordination.

PubMed

Zhou, Xiaoke; Zhu, Fei; Liu, Quan; Fu, Yuchen; Huang, Wei

2014-01-01

Traffic problems often occur due to the traffic demands by the outnumbered vehicles on road. Maximizing traffic flow and minimizing the average waiting time are the goals of intelligent traffic control. Each junction wants to get larger traffic flow. During the course, junctions form a policy of coordination as well as constraints for adjacent junctions to maximize their own interests. A good traffic signal timing policy is helpful to solve the problem. However, as there are so many factors that can affect the traffic control model, it is difficult to find the optimal solution. The disability of traffic light controllers to learn from past experiences caused them to be unable to adaptively fit dynamic changes of traffic flow. Considering dynamic characteristics of the actual traffic environment, reinforcement learning algorithm based traffic control approach can be applied to get optimal scheduling policy. The proposed Sarsa(λ)-based real-time traffic control optimization model can maintain the traffic signal timing policy more effectively. The Sarsa(λ)-based model gains traffic cost of the vehicle, which considers delay time, the number of waiting vehicles, and the integrated saturation from its experiences to learn and determine the optimal actions. The experiment results show an inspiring improvement in traffic control, indicating the proposed model is capable of facilitating real-time dynamic traffic control.

Two dimensional thermal and charge mapping of power thyristors

NASA Technical Reports Server (NTRS)

Hu, S. P.; Rabinovici, B. M.

1975-01-01

The two dimensional static and dynamic current density distributions within the junction of semiconductor power switching devices and in particular the thyristors were obtained. A method for mapping the thermal profile of the device junctions with fine resolution using an infrared beam and measuring the attenuation through the device as a function of temperature were developed. The results obtained are useful in the design and quality control of high power semiconductor switching devices.

Traction force dynamics predict gap formation in activated endothelium

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

Valent, Erik T.; Nieuw Amerongen, Geerten P. van; Hinsbergh, Victor W.M. van

In many pathological conditions the endothelium becomes activated and dysfunctional, resulting in hyperpermeability and plasma leakage. No specific therapies are available yet to control endothelial barrier function, which is regulated by inter-endothelial junctions and the generation of acto-myosin-based contractile forces in the context of cell-cell and cell-matrix interactions. However, the spatiotemporal distribution and stimulus-induced reorganization of these integral forces remain largely unknown. Traction force microscopy of human endothelial monolayers was used to visualize contractile forces in resting cells and during thrombin-induced hyperpermeability. Simultaneously, information about endothelial monolayer integrity, adherens junctions and cytoskeletal proteins (F-actin) were captured. This revealed a heterogeneousmore » distribution of traction forces, with nuclear areas showing lower and cell-cell junctions higher traction forces than the whole-monolayer average. Moreover, junctional forces were asymmetrically distributed among neighboring cells. Force vector orientation analysis showed a good correlation with the alignment of F-actin and revealed contractile forces in newly formed filopodia and lamellipodia-like protrusions within the monolayer. Finally, unstable areas, showing high force fluctuations within the monolayer were prone to form inter-endothelial gaps upon stimulation with thrombin. To conclude, contractile traction forces are heterogeneously distributed within endothelial monolayers and force instability, rather than force magnitude, predicts the stimulus-induced formation of intercellular gaps. - Highlights: • Endothelial monolayers exert dynamic- and heterogeneous traction forces. • High traction forces correlate with junctional areas and the F-actin cytoskeleton. • Newly formed inter-endothelial gaps are characterized by opposing traction forces. • Force stability is a key feature controlling endothelial permeability.« less

Binary dislocation junction formation and strength in hexagonal close-packed crystals

DOE PAGES

Wu, Chi -Chin; Aubry, Sylvie; Arsenlis, Athanasios; ...

2015-12-17

This work examines binary dislocation interactions, junction formation and junction strengths in hexagonal close-packed ( hcp ) crystals. Through a line-tension model and dislocation dynamics (DD) simulations, the interaction and dissociation of different sets of binary junctions are investigated involving one dislocation on the (011¯0) prismatic plane and a second dislocation on one of the following planes: (0001) basal, (11¯00) prismatic, (11¯01) primary pyramidal, or (2¯112) secondary pyramidal. Varying pairs of Burgers vectors are chosen from among the common types the basal type < a > 1/3 < 112¯0 >, prismatic type < c > <0001>, and pyramidal type 1/3 < 112¯3¯ >. For binary interaction due to dislocation intersection, both the analytical results and DD-simulations indicate a relationship between symmetry of interaction maps and the relative magnitude of the Burgers vectors that constitute the junction. Using analytical formulae, a simple regressive model is also developed to represent the junction yield surface. The equation is treated as a degenerated super elliptical equation to quantify the aspect ratio and tilting angle. Lastly, the results provide analytical insights on binary dislocation interactions that may occur in general hcp metals.« less

Tight junction-associated MARVEL proteins marveld3, tricellulin, and occludin have distinct but overlapping functions.

PubMed

Raleigh, David R; Marchiando, Amanda M; Zhang, Yong; Shen, Le; Sasaki, Hiroyuki; Wang, Yingmin; Long, Manyuan; Turner, Jerrold R

2010-04-01

In vitro studies have demonstrated that occludin and tricellulin are important for tight junction barrier function, but in vivo data suggest that loss of these proteins can be overcome. The presence of a heretofore unknown, yet related, protein could explain these observations. Here, we report marvelD3, a novel tight junction protein that, like occludin and tricellulin, contains a conserved four-transmembrane MARVEL (MAL and related proteins for vesicle trafficking and membrane link) domain. Phylogenetic tree reconstruction; analysis of RNA and protein tissue distribution; immunofluorescent and electron microscopic examination of subcellular localization; characterization of intracellular trafficking, protein interactions, dynamic behavior, and siRNA knockdown effects; and description of remodeling after in vivo immune activation show that marvelD3, occludin, and tricellulin have distinct but overlapping functions at the tight junction. Although marvelD3 is able to partially compensate for occludin or tricellulin loss, it cannot fully restore function. We conclude that marvelD3, occludin, and tricellulin define the tight junction-associated MARVEL protein family. The data further suggest that these proteins are best considered as a group with both redundant and unique contributions to epithelial function and tight junction regulation.

Respiratory signaling of locus coeruleus neurons during hypercapnic acidosis in the bullfrog, Lithobates catesbeianus.

PubMed

Santin, J M; Hartzler, L K

2013-02-01

The locus coeruleus (LC) in the brainstem senses alterations in CO(2)/pH and influences ventilatory adjustments that restore blood gas values to starting levels in bullfrogs (Lithobates catesbeianus). We hypothesized that neurons of the bullfrog LC are sensitive to changes in CO(2)/pH and that chemosensitive responses are intrinsic to individual neurons. In addition, we hypothesized putative respiratory control neurons of the bullfrog LC would be stimulated by hypercapnic acidosis within physiological ranges of P(CO(2))/pH. 84% of LC neurons depolarized and increased firing rates during exposure to hypercapnic acidosis (HA). A pH dose response curve shows LC neurons from bullfrogs increase firing rates during physiologically relevant CO(2)/pH changes. With chemical synapses blocked, half of chemosensitive neurons lost sensitivity to HA; however, gap junction blockade did not alter chemosensitive responses. Intrinsically chemosensitive neurons increased input resistance during HA. These data demonstrate that majority of neurons within the bullfrog LC elicit robust firing responses during physiological ΔCO(2)/pH, likely enabling adjustment of acid-base balance through breathing. Copyright © 2012 Elsevier B.V. All rights reserved.

External noise-induced transitions in a current-biased Josephson junction

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

Huang, Qiongwei; Xue, Changfeng, E-mail: cfxue@163.com; Tang, Jiashi

We investigate noise-induced transitions in a current-biased and weakly damped Josephson junction in the presence of multiplicative noise. By using the stochastic averaging procedure, the averaged amplitude equation describing dynamic evolution near a constant phase difference is derived. Numerical results show that a stochastic Hopf bifurcation between an absorbing and an oscillatory state occurs. This means the external controllable noise triggers a transition into the non-zero junction voltage state. With the increase of noise intensity, the stationary probability distribution peak shifts and is characterised by increased width and reduced height. And the different transition rates are shown for large andmore » small bias currents.« less

First-principles spin-transfer torque in CuMnAs |GaP |CuMnAs junctions

NASA Astrophysics Data System (ADS)

Stamenova, Maria; Mohebbi, Razie; Seyed-Yazdi, Jamileh; Rungger, Ivan; Sanvito, Stefano

2017-02-01

We demonstrate that an all-antiferromagnetic tunnel junction with current perpendicular to the plane geometry can be used as an efficient spintronic device with potential high-frequency operation. By using state-of-the-art density functional theory combined with quantum transport, we show that the Néel vector of the electrodes can be manipulated by spin-transfer torque. This is staggered over the two different magnetic sublattices and can generate dynamics and switching. At the same time the different magnetization states of the junction can be read by standard tunneling magnetoresistance. Calculations are performed for CuMnAs |GaP |CuMnAs junctions with different surface terminations between the antiferromagnetic CuMnAs electrodes and the insulating GaP spacer. We find that the torque remains staggered regardless of the termination, while the magnetoresistance depends on the microscopic details of the interface.

Dynamic Tunneling Junctions at the Atomic Intersection of Two Twisted Graphene Edges.

PubMed

Bellunato, Amedeo; Vrbica, Sasha D; Sabater, Carlos; de Vos, Erik W; Fermin, Remko; Kanneworff, Kirsten N; Galli, Federica; van Ruitenbeek, Jan M; Schneider, Grégory F

2018-04-11

The investigation of the transport properties of single molecules by flowing tunneling currents across extremely narrow gaps is relevant for challenges as diverse as the development of molecular electronics and sequencing of DNA. The achievement of well-defined electrode architectures remains a technical challenge, especially due to the necessity of high precision fabrication processes and the chemical instability of most bulk metals. Here, we illustrate a continuously adjustable tunneling junction between the edges of two twisted graphene sheets. The unique property of the graphene electrodes is that the sheets are rigidly supported all the way to the atomic edge. By analyzing the tunneling current characteristics, we also demonstrate that the spacing across the gap junction can be controllably adjusted. Finally, we demonstrate the transition from the tunneling regime to contact and the formation of an atomic-sized junction between the two edges of graphene.

Adherens junction turnover: regulating adhesion through cadherin endocytosis, degradation, and recycling

PubMed Central

Nanes, Benjamin A.; Kowalczyk, Andrew P.

2014-01-01

Adherens junctions are important mediators of intercellular adhesion, but they are not static structures. They are regularly formed, broken, and rearranged in a variety of situations, requiring changes in the amount of cadherins, the main adhesion molecule in adherens junctions, present at the cell surface. Thus, endocytosis, degradation, and recycling of cadherins are crucial for dynamic regulation of adherens junctions and control of intercellular adhesion. In this chapter, we review the involvement of cadherin endocytosis in development and disease. We discuss the various endocytic pathways available to cadherins, the adaptors involved, and the sorting of internalized cadherin for recycling or lysosomal degradation. In addition, we review the regulatory pathways controlling cadherin endocytosis and degradation, including regulation of cadherin endocytosis by catenins, cadherin ubiquitination, and growth factor receptor signaling pathways. Lastly, we discuss the proteolytic cleavage of cadherins at the plasma membrane. PMID:22674073

Dynamic Tunneling Junctions at the Atomic Intersection of Two Twisted Graphene Edges

PubMed Central

2018-01-01

The investigation of the transport properties of single molecules by flowing tunneling currents across extremely narrow gaps is relevant for challenges as diverse as the development of molecular electronics and sequencing of DNA. The achievement of well-defined electrode architectures remains a technical challenge, especially due to the necessity of high precision fabrication processes and the chemical instability of most bulk metals. Here, we illustrate a continuously adjustable tunneling junction between the edges of two twisted graphene sheets. The unique property of the graphene electrodes is that the sheets are rigidly supported all the way to the atomic edge. By analyzing the tunneling current characteristics, we also demonstrate that the spacing across the gap junction can be controllably adjusted. Finally, we demonstrate the transition from the tunneling regime to contact and the formation of an atomic-sized junction between the two edges of graphene. PMID:29513997

[Successful esophageal pH monitoring with Bravo capsule in patients with gastroesophageal reflux disease].

PubMed

Valdovinos Díaz, Miguel A; Remes Troche, José Ma; Ruiz Aguilar, Juan Carlos; Schmulson, Max J; Valdovinos-Andraca, Francisco

2004-01-01

Esophageal 24-h pH monitoring (24-pH) is the most useful test to diagnose and treat patients with gastroesophageal reflux disease (GERD). The traditional system for 24-pH requires transnasal introduction of a catheter with pH sensors. This technique produces discomfort, inconvenience and interference with daily activity. Recently, the Bravo pH system has been proposed as an alternative and promising method for 24-pH. In this study, the initial experience in Mexico with this system is reported. To evaluate safety, tolerability and performance of the pH Bravo capsule in patients with GERD. Patients with GERD symptoms at least twice a week during the last three months, with indication for 24-pH were evaluated. pH Bravo capsule was placed 6 cm above squamocolumnar junction (SCJ). Symptoms, quality and duration of pH tracings, capsule detachment and patient global satisfaction were evaluated. Eleven patients (nine female, two male) mean age 42 years (range 26-62 years), two with erosive and nine with non-erosive GERD were studied. pH capsule was correctly positioned at 6 cm above SCJ in all patients. Nine patients noted a mild foreign body sensation (especially while eating) and four had mild chest pain; two patients had no discomfort. Capsule detachment occurred spontaneously in all patients on day 10. pH record for > 43 h was obtained in the 11 patients. There were no differences in pH parameters between days 1 and 2. Two patients with normal acid exposure on day 1 had abnormal pH parameters on day 2. Esophageal pH monitoring with Bravo capsule is a safe, reliable and tolerable method in patients with GERD. Extended pH recordings increases abnormal esophageal acid exposure detection in patients with this disease.

Regulation by a TGFβ-ROCK-actomyosin axis secures a non-linear lumen expansion that is essential for tubulogenesis.

PubMed

Denker, Elsa; Sehring, Ivonne M; Dong, Bo; Audisso, Julien; Mathiesen, Birthe; Jiang, Di

2015-05-01

Regulation of lumen growth is crucial to ensure the correct morphology, dimensions and function of a tubular structure. How this is controlled is still poorly understood. During Ciona intestinalis notochord tubulogenesis, single extracellular lumen pockets grow between pairs of cells and eventually fuse into a continuous tube. Here, we show that lumen growth exhibits a lag phase, during which the luminal membranes continue to grow but the expansion of the apical/lateral junction pauses for ∼30 min. Inhibition of non-muscle myosin II activity abolishes this lag phase and accelerates expansion of the junction, resulting in the formation of narrower lumen pockets partially fusing into a tube of reduced size. Disruption of actin dynamics, conversely, causes a reversal of apical/lateral junction expansion, leading to a dramatic conversion of extracellular lumen pockets to intracellular vacuoles and a tubulogenesis arrest. The onset of the lag phase is correlated with a de novo accumulation of actin that forms a contractile ring at the apical/lateral junctions. This actin ring actively restricts the opening of the lumen in the transverse plane, allowing sufficient time for lumen growth via an osmotic process along the longitudinal dimension. The dynamics of lumen formation is controlled by the TGFβ pathway and ROCK activity. Our findings reveal a TGFβ-ROCK-actomyosin contractility axis that coordinates lumen growth, which is powered by the dynamics of luminal osmolarity. The regulatory system may function like a sensor/checkpoint that responds to the change of luminal pressure and fine-tunes actomyosin contractility to effect proper tubulogenesis. © 2015. Published by The Company of Biologists Ltd.

Modulation of Connexin-36 Gap Junction Channels by Intracellular pH and Magnesium Ions

PubMed Central

Rimkute, Lina; Kraujalis, Tadas; Snipas, Mindaugas; Palacios-Prado, Nicolas; Jotautis, Vaidas; Skeberdis, Vytenis A.; Bukauskas, Feliksas F.

2018-01-01

Connexin-36 (Cx36) protein forms gap junction (GJ) channels in pancreatic beta cells and is also the main Cx isoform forming electrical synapses in the adult mammalian brain. Cx36 GJs can be regulated by intracellular pH (pHi) and cytosolic magnesium ion concentration ([Mg2+]i), which can vary significantly under various physiological and pathological conditions. However, the combined effect and relationship of these two factors over Cx36-dependent coupling have not been previously studied in detail. Our experimental results in HeLa cells expressing Cx36 show that changes in both pHi and [Mg2+]i affect junctional conductance (gj) in an interdependent manner; in other words, intracellular acidification cause increase or decay in gj depending on whether [Mg2+]i is high or low, respectively, and intracellular alkalization cause reduction in gj independently of [Mg2+]i. Our experimental and modelling data support the hypothesis that Cx36 GJ channels contain two separate gating mechanisms, and both are differentially sensitive to changes in pHi and [Mg2+]i. Using recombinant Cx36 we found that two glutamate residues in the N-terminus could be partly responsible for the observed interrelated effect of pHi and [Mg2+]i. Mutation of glutamate at position 8 attenuated the stimulatory effect of intracellular acidification at high [Mg2+]i, while mutation at position 12 and double mutation at both positions reversed stimulatory effect to inhibition. Moreover, Cx36*E8Q lost the initial increase of gj at low [Mg2+]i and double mutation lost the sensitivity to high [Mg2+]i. These results suggest that E8 and E12 are involved in regulation of Cx36 GJ channels by Mg2+ and H+ ions. PMID:29706896

pH-dependent modulation of connexin-based gap junctional uncouplers

PubMed Central

Skeberdis, Vytenis A; Rimkute, Lina; Skeberdyte, Aiste; Paulauskas, Nerijus; Bukauskas, Feliksas F

2011-01-01

Abstract Gap junction (GJ) channels formed from connexin (Cx) proteins provide a direct pathway for electrical and metabolic cell–cell communication exhibiting high sensitivity to intracellular pH (pHi). We examined pHi-dependent modulation of junctional conductance (gj) of GJs formed of Cx26, mCx30.2, Cx36, Cx40, Cx43, Cx45, Cx46, Cx47 and Cx50 by reagents representing several distinct groups of uncouplers, such as long carbon chain alkanols (LCCAs), arachidonic acid, carbenoxolone, isoflurane, flufenamic acid and mefloquine. We demonstrate that alkalization by NH4Cl to pH ∼8 increased gj in cells expressing mCx30.2 and Cx45, yet did not affect gj of Cx26, Cx40, Cx46, Cx47 and Cx50 and decreased it in Cx43 and Cx36 GJs. Unexpectedly, cells expressing Cx45, but not other Cxs, exhibited full coupling recovery after alkalization with NH4Cl under the continuous presence of LCCAs, isoflurane and mefloquine. There was no coupling recovery by alkalization in the presence of arachidonic acid, carbenoxolone and flufenamic acid. In cells expressing Cx45, IC50 for octanol was 0.1, 0.25 and 2.68 mm at pHi values of 6.9, 7.2 and 8.1, respectively. Histidine modification of Cx45 protein by N-bromosuccinimide reduced the coupling-promoting effect of NH4Cl as well as the uncoupling effect of octanol. This suggests that LCCAs and some other uncouplers may act through the formation of hydrogen bonds with the as-of-yet unidentified histidine/s of the Cx45 GJ channel protein. PMID:21606109

Black Phosphorus-Zinc Oxide Nanomaterial Heterojunction for p-n Diode and Junction Field-Effect Transistor.

PubMed

Jeon, Pyo Jin; Lee, Young Tack; Lim, June Yeong; Kim, Jin Sung; Hwang, Do Kyung; Im, Seongil

2016-02-10

Black phosphorus (BP) nanosheet is two-dimensional (2D) semiconductor with distinct band gap and attracting recent attention from researches because it has some similarity to gapless 2D semiconductor graphene in the following two aspects: single element (P) for its composition and quite high mobilities depending on its fabrication conditions. Apart from several electronic applications reported with BP nanosheet, here we report for the first time BP nanosheet-ZnO nanowire 2D-1D heterojunction applications for p-n diodes and BP-gated junction field effect transistors (JFETs) with n-ZnO channel on glass. For these nanodevices, we take advantages of the mechanical flexibility of p-type conducting of BP and van der Waals junction interface between BP and ZnO. As a result, our BP-ZnO nanodimension p-n diode displays a high ON/OFF ratio of ∼10(4) in static rectification and shows kilohertz dynamic rectification as well while ZnO nanowire channel JFET operations are nicely demonstrated by BP gate switching in both electrostatics and kilohertz dynamics.

Anomalous Photovoltaic Response of Graphene-on-GaN Schottky Photodiodes.

PubMed

Lee, Jae Hyung; Lee, Won Woo; Yang, Dong Won; Chang, Won Jun; Kwon, Sun Sang; Park, Won Il

2018-04-25

Graphene has attracted great attention as an alternative to conventional metallic or transparent conducting electrodes. Despite its similarities with conventional electrodes, recent studies have shown that a single-atom layer of graphene possesses unique characteristics, such as a tunable work function and transparencies for electric potential, reactivity, and wetting. Nevertheless, a systematic analysis of graphene and semiconductor junction characteristics has not yet been carried out. Here, we report the photoresponse characteristics of graphene-on-GaN Schottky junction photodiodes (Gr-GaN SJPDs), showing a typical rectifying behavior and distinct photovoltaic and photoelectric responses. Following the initial abrupt response to UV illumination, the Gr-GaN SJPDs exhibited a distinct difference in photocarrier dynamics depending on the applied bias voltage, which is characterized by either a negative or positive change in photocurrent with time. We propose underlying mechanisms for the anomalous photocarrier dynamics based on the interplay between electrostatic molecular interactions over the one-atom-thick graphene and GaN junction and trapped photocarriers at the defect states in the GaN thin film.

Fullerene Derived Molecular Electronic Devices

NASA Technical Reports Server (NTRS)

Menon, Madhu; Srivastava, Deepak; Saini, Subbash

1998-01-01

The carbon Nanotube junctions have recently emerged as excellent candidates for use as the building blocks in the formation of nanoscale electronic devices. While the simple joint of two dissimilar tubes can be generated by the introduction of a pair of heptagon-pentagon defects in an otherwise perfect hexagonal grapheme sheet, more complex joints require other mechanisms. In this work we explore structural and electronic properties of complex 3-point junctions of carbon nanotubes using a generalized tight-binding molecular-dynamics scheme.

Remodelling of cellular excitation (reaction) and intercellular coupling (diffusion) by chronic atrial fibrillation represented by a reaction-diffusion system

NASA Astrophysics Data System (ADS)

Zhang, Henggui; Garratt, Clifford J.; Kharche, Sanjay; Holden, Arun V.

2009-06-01

Human atrial tissue is an excitable system, in which myocytes are excitable elements, and cell-to-cell electrotonic interactions are via diffusive interactions of cell membrane potentials. We developed a family of excitable system models for human atrium at cellular, tissue and anatomical levels for both normal and chronic atrial fibrillation (AF) conditions. The effects of AF-induced remodelling of cell membrane ionic channels (reaction kinetics) and intercellular gap junctional coupling (diffusion) on atrial excitability, conduction of excitation waves and dynamics of re-entrant excitation waves are quantified. Both ionic channel and gap junctional coupling remodelling have rate dependent effects on atrial propagation. Membrane channel conductance remodelling allows the propagation of activity at higher rates than those sustained in normal tissue or in tissue with gap junctional remodelling alone. Membrane channel conductance remodelling is essential for the propagation of activity at rates higher than 300/min as seen in AF. Spatially heterogeneous gap junction coupling remodelling increased the risk of conduction block, an essential factor for the genesis of re-entry. In 2D and 3D anatomical models, the dynamical behaviours of re-entrant excitation waves are also altered by membrane channel modelling. This study provides insights to understand the pro-arrhythmic effects of AF-induced reaction and diffusion remodelling in atrial tissue.

Dynamic change of pH in acidogenic fermentation of cheese whey towards polyhydroxyalkanoates production: Impact on performance and microbial population.

PubMed

Gouveia, Ana R; Freitas, Elisabete B; Galinha, Cláudia F; Carvalho, Gilda; Duque, Anouk F; Reis, Maria A M

2017-07-25

Polyhydroxyalkanoates (PHA) are a sustainable alternative to conventional plastics that can be obtained from industrial wastes/by-products using mixed microbial cultures (MMC). MMC PHA production is commonly carried out in a 3-stage process of acidogenesis, PHA culture selection and accumulation. This research focused on the possibility of tailoring PHA by controlling the acidogenic reactor operating conditions, namely pH, using cheese whey as model feedstock. The objective was to investigate the impact that dynamically varying the acidogenic pH, when targeting different PHA monomer profiles, had on the performance and microbial community profile of the anaerobic reactor. To accomplish this, an anaerobic reactor was continuously operated under dynamic pH changes, ranging from pH 4 to 7, turning to pH 6 after each change of pH. At pH 6, lactate and acetate were the dominant products (41-48% gCOD basis and 22-44% gCOD basis, respectively). At low pH, lactate production was higher while at high pH acetate production was favoured. Despite the dynamic change of pH, the fermentation product composition at pH 6 was always similar, showing the resilience of the process, i.e. when the same pH value was imposed, the culture produced the same metabolic products independently of the history of changes occurring in the system. The different fermentation product fractions led to PHAs of different compositions. The microbial community, analysed by high throughput sequencing of bacterial 16S rRNA gene fragments, was dominated by Lactobacillus, but varied markedly when subjected to the highest and lowest pH values of the tested range (4 and 7), with increase in the abundance of Lactococcus and a member of the Candidate Division TM7. Different bacterial profiles obtained at pH 6 during this dynamic operation were able to produce a consistent profile of fermentation products (and consequently a constant PHA composition), demonstrating the community's functional redundancy. Copyright © 2016 Elsevier B.V. All rights reserved.

The role of dynamic renal scintigraphy on clinical decision making in hydronephrotic children.

PubMed

Çamlar, Seçil Arslansoyu; Deveci, Nazlı; Soylu, Alper; Türkmen, Mehmet Atilla; Özmen, Derya; Çapakaya, Gamze; Kavukçu, Salih

2017-01-01

Hydronephrosis may be related to an obstructive cause, ureteropelvic/uretero-vesical junction obstruction or nonobstructive [vesicoureteral reflux (VUR)]. When an obstructive pathology is considered, dynamic renal scintigraphy may help to predict whether it is a true obstruction or not. In this study, we aimed to determine the contribution of dynamic renal scintigraphy with [99] mTc-MAG-3 to the clinical decision-making for surgery in hydronephrotic children. Files of the patients evaluated by MAG-3 scintigraphy for antenatal (AH)/postnatal (PH) hydronephrosis between 1992 and 2014 were reviewed. Gender, age, hydronephrosis (HN) grade by ultrasound (US), presence of VUR, MAG-3 result (obstructive vs. nonobstructive), ultimate diagnosis, and need for surgery were assessed. Cases with double collecting system and neurogenic bladder were excluded from the study. All of the patients had normal serum creatinine and eGFR. There were a total of 178 patients with 218 hydronephrotic renal units (mean age 34.7 ± 52.7 months; male/ female = 121/57, AH of 62%). MAG-3 was nonobstructive in 134 and obstructive in 84 hydronephrotic renal units. MAG-3 was obstructive in 47 of 121 (39%) males and 30 of 57 (53%) females (P = 0.058, odds ratio (OR) for obstruction was 1.9 for girls). MAG-3 was obstructive in 47 of 135 (35%) units with AH and 37 of 83 (45%) units with PH (P = 0.137). In 81 units with the society of fetal urology-4 HN by US, MAG-3 was obstructive in 55 (68%), and surgery was required in 52 of 55 (95%). Surgery was required for only two (7%) of the remaining 26 units with nonobstructive dilatation (P <0.001, sensitivity 96%, specificity 89%, OR 208). Antero-posterior diameter >16.5 mm was the best cutoff level for predicting obstruction by MAG-3 (sensitivity 75.2%; specificity 71%; OR 3.8). MAG-3 significantly affects clinical decision for surgery in HN. Hydronephrotic girls have more risk in terms of true obstruction. Combining MAG-3 with US improves the discrimination of true obstruction during follow-up.

Recent developments in water quality monitoring for Space Station reclaimed wastewaters

NASA Technical Reports Server (NTRS)

Small, John W.; Verostko, Charles E.; Linton, Arthur T.; Burchett, Ray

1987-01-01

This paper discusses the recent developments in water quality monitoring for Space Station reclaimed wastewaters. A preprototype unit that contains an ultraviolet absorbance organic carbon monitor integrated with pH and conductivity sensors is presented. The preprototype has provisions for automated operation and is a reagentless flow-through system without any gas/liquid interfaces. The organic carbon monitor detects by utraviolet absorbance the organic impurities in reclaimed wastewater which may be correlated to the organic carbon content of the water. A comparison of the preprototype organic carbon detection values with actual total organic carbon measurements is presented. The electrolyte double junction concept for the pH sensor and fixed electrodes for both the pH and conductivity sensors are discussed. In addition, the development of a reagentless organic carbon analyzer that incorporates ultraviolet oxidation and infrared detection is presented. Detection sensitivities, hardware development, and operation are included.

Evidence that Resorption of Bone by Rat Peritoneal Macrophages Occurs in an Acidic Environment

NASA Technical Reports Server (NTRS)

Blair, H. C.

1985-01-01

Skeletal loss in space, like any form of osteoporosis, reflects a relative imbalance of the activities of cells resorbing (degrading) or forming bone. Consequently, prevention of weightlessness induced bone loss may theoretically be accomplished by (1) stimulating bone formation or (2) inhibiting bone resorption. This approach, however, requires fundamental understanding of the mechanisms by which cells form or degrade bone, information not yet at hand. An issue central to bone resorption is the pH at which resorption takes place. The pH dependent spectral shift of a fluorescent dye (fluorescein isothiocyanate) conjugated to bone matrix was used to determine the pH at the resorptive cell bone matrix interface. Devitalized rat bone was used as the substrate, and rat peritoneal macrophages were used as the bone resorbing cells. The results suggest that bone resorption is the result of generation of an acidic microenvironment at the cell matrix junction.

A New, Directly Computer-Controlled pH Stat.

DTIC Science & Technology

1982-03-08

Currently, potentiometric reaction-rate methods of analysis find a wide range of analytical application and a number of such procedeires and corresponding...oxidase glucose + 0 2 - gluconic acid + H20 2 Glucose concentrations are determined by potentiometrically measuring the rate at which gluconic acid is...of lKIlz. Electrodes and Reaction Vessel. Changes in pl! are measured * potentiometrically with a combination Ag/AgCl ceramic junction electrode (No

The Role of the Acid Pocket in Gastroesophageal Reflux Disease.

PubMed

Mitchell, David R; Derakhshan, Mohammad H; Robertson, Elaine V; McColl, Kenneth E L

2016-02-01

Gastroesophageal reflux disease is one of the commonest chronic conditions in the western world and its prevalence is increasing worldwide. The discovery of the acid pocket explained the paradox of acid reflux occurring more frequently in the postprandial period despite intragastric acidity being low due to the buffering effect of the meal. The acid pocket was first described in 2001 when it was detected as an area of low pH immediately distal to the cardia using dual pH electrode pull-through studies 15 minutes after a meal. It was hypothesized that there was a local pocket of acid close to the gastroesophageal junction that escapes the buffering effect of the meal, and that this is the source of postprandial acidic reflux. The presence of the acid pocket has been confirmed in other studies using different techniques including high-resolution pHmetry, Bravo capsule, magnetic resonance imaging, and scintigraphy. This review aims to describe what we know about the acid pocket including its length, volume, fluid constituents, and its relationship to the lower esophageal sphincter and squamocolumnar junction. We will discuss the possible mechanisms that lead to the formation of the acid pocket and examine what differences exist in patients who suffer from acid reflux. Treatments for reflux disease that affect the acid pocket will also be discussed.

VASP, zyxin and TES are tension-dependent members of Focal Adherens Junctions independent of the α-catenin-vinculin module.

PubMed

Oldenburg, Joppe; van der Krogt, Gerard; Twiss, Floor; Bongaarts, Annika; Habani, Yasmin; Slotman, Johan A; Houtsmuller, Adriaan; Huveneers, Stephan; de Rooij, Johan

2015-11-27

Mechanical forces are integrated at cadherin-based adhesion complexes to regulate morphology and strength of cell-cell junctions and organization of associated F-actin. A central mechanosensor at the cadherin complex is α-catenin, whose stretching recruits vinculin to regulate adhesion strength. The identity of the F-actin regulating signals that are also activated by mechanical forces at cadherin-based junctions has remained elusive. Here we identify the actin-regulators VASP, zyxin and TES as members of punctate, tensile cadherin-based junctions called Focal Adherens Junctions (FAJ) and show that they display mechanosensitive recruitment similar to that of vinculin. However, this recruitment is not altered by destroying or over-activating the α-catenin/vinculin module. Structured Illumination Microscopy (SIM) indicates that these tension sensitive proteins concentrate at locations within FAJs that are distinct from the core cadherin complex proteins. Furthermore, localization studies using mutated versions of VASP and zyxin indicate that these two proteins require binding to each other in order to localize to the FAJs. We conclude that there are multiple force sensitive modules present at the FAJ that are activated at distinct locations along the cadherin-F-actin axis and regulate specific aspects of junction dynamics.

Measure Guideline: Optimizing the Configuration of Flexible Duct Junction Boxes

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

Beach, R.; Burdick, A.

2014-03-01

This measure guideline offers additional recommendations to heating, ventilation, and air conditioning (HVAC) system designers for optimizing flexible duct, constant-volume HVAC systems using junction boxes within Air Conditioning Contractors of America (ACCA) Manual D guidance (Rutkowski, H. Manual D -- Residential Duct Systems, 3rd edition, Version 1.00. Arlington, VA: Air Conditioning Contractors of America, 2009.). IBACOS used computational fluid dynamics software to explore and develop guidance to better control the airflow effects of factors that may impact pressure losses within junction boxes among various design configurations (Beach, R., Prahl, D., and Lange, R. CFD Analysis of Flexible Duct Junction Boxmore » Design. Golden, CO: National Renewable Energy Laboratory, submitted for publication 2013). These recommendations can help to ensure that a system aligns more closely with the design and the occupants' comfort expectations. Specifically, the recommendations described herein show how to configure a rectangular box with four outlets, a triangular box with three outlets, metal wyes with two outlets, and multiple configurations for more than four outlets. Designers of HVAC systems, contractors who are fabricating junction boxes on site, and anyone using the ACCA Manual D process for sizing duct runs will find this measure guideline invaluable for more accurately minimizing pressure losses when using junction boxes with flexible ducts.« less

VASP, zyxin and TES are tension-dependent members of Focal Adherens Junctions independent of the α-catenin-vinculin module

PubMed Central

Oldenburg, Joppe; van der Krogt, Gerard; Twiss, Floor; Bongaarts, Annika; Habani, Yasmin; Slotman, Johan A.; Houtsmuller, Adriaan; Huveneers, Stephan; de Rooij, Johan

2015-01-01

Mechanical forces are integrated at cadherin-based adhesion complexes to regulate morphology and strength of cell-cell junctions and organization of associated F-actin. A central mechanosensor at the cadherin complex is α-catenin, whose stretching recruits vinculin to regulate adhesion strength. The identity of the F-actin regulating signals that are also activated by mechanical forces at cadherin-based junctions has remained elusive. Here we identify the actin-regulators VASP, zyxin and TES as members of punctate, tensile cadherin-based junctions called Focal Adherens Junctions (FAJ) and show that they display mechanosensitive recruitment similar to that of vinculin. However, this recruitment is not altered by destroying or over-activating the α-catenin/vinculin module. Structured Illumination Microscopy (SIM) indicates that these tension sensitive proteins concentrate at locations within FAJs that are distinct from the core cadherin complex proteins. Furthermore, localization studies using mutated versions of VASP and zyxin indicate that these two proteins require binding to each other in order to localize to the FAJs. We conclude that there are multiple force sensitive modules present at the FAJ that are activated at distinct locations along the cadherin-F-actin axis and regulate specific aspects of junction dynamics. PMID:26611125

A Sarsa(λ)-Based Control Model for Real-Time Traffic Light Coordination

PubMed Central

Zhu, Fei; Liu, Quan; Fu, Yuchen; Huang, Wei

2014-01-01

Traffic problems often occur due to the traffic demands by the outnumbered vehicles on road. Maximizing traffic flow and minimizing the average waiting time are the goals of intelligent traffic control. Each junction wants to get larger traffic flow. During the course, junctions form a policy of coordination as well as constraints for adjacent junctions to maximize their own interests. A good traffic signal timing policy is helpful to solve the problem. However, as there are so many factors that can affect the traffic control model, it is difficult to find the optimal solution. The disability of traffic light controllers to learn from past experiences caused them to be unable to adaptively fit dynamic changes of traffic flow. Considering dynamic characteristics of the actual traffic environment, reinforcement learning algorithm based traffic control approach can be applied to get optimal scheduling policy. The proposed Sarsa(λ)-based real-time traffic control optimization model can maintain the traffic signal timing policy more effectively. The Sarsa(λ)-based model gains traffic cost of the vehicle, which considers delay time, the number of waiting vehicles, and the integrated saturation from its experiences to learn and determine the optimal actions. The experiment results show an inspiring improvement in traffic control, indicating the proposed model is capable of facilitating real-time dynamic traffic control. PMID:24592183

Structural and functional diversity of cadherin at the adherens junction

PubMed Central

2011-01-01

Adhesion between cells is essential to the evolution of multicellularity. Indeed, morphogenesis in animals requires firm but flexible intercellular adhesions that are mediated by subcellular structures like the adherens junction (AJ). A key component of AJs is classical cadherins, a group of transmembrane proteins that maintain dynamic cell–cell associations in many animal species. An evolutionary reconstruction of cadherin structure and function provides a comprehensive framework with which to appreciate the diversity of morphogenetic mechanisms in animals. PMID:21708975

Study of charge-phase diagrams for coupled system of Josephson junctions

NASA Astrophysics Data System (ADS)

Hamdipour, M.; Shukrinov, Y. U. M.

2010-11-01

Dynamics of stacked intrinsic Josephson junctions (IJJ) in the high-Tc superconductors is theoretically investigated. We calculate the current-voltage characteristics (CVC) of IJJ and study the breakpoint region on the outermost branch of the CVC for the stacks with 9 IJJ. A method for investigation of the fine structure in CVC of IJJ based on the recording the "phase-charge" diagrams is suggested. It is demonstrated that this method reflects the main features of the breakpoint region.

Dynamic patterns and ecological impacts of declining ocean pH in a high-resolution multi-year dataset.

PubMed

Wootton, J Timothy; Pfister, Catherine A; Forester, James D

2008-12-02

Increasing global concentrations of atmospheric CO(2) are predicted to decrease ocean pH, with potentially severe impacts on marine food webs, but empirical data documenting ocean pH over time are limited. In a high-resolution dataset spanning 8 years, pH at a north-temperate coastal site declined with increasing atmospheric CO(2) levels and varied substantially in response to biological processes and physical conditions that fluctuate over multiple time scales. Applying a method to link environmental change to species dynamics via multispecies Markov chain models reveals strong links between in situ benthic species dynamics and variation in ocean pH, with calcareous species generally performing more poorly than noncalcareous species in years with low pH. The models project the long-term consequences of these dynamic changes, which predict substantial shifts in the species dominating the habitat as a consequence of both direct effects of reduced calcification and indirect effects arising from the web of species interactions. Our results indicate that pH decline is proceeding at a more rapid rate than previously predicted in some areas, and that this decline has ecological consequences for near shore benthic ecosystems.

Broad gap junction blocker carbenoxolone disrupts uterine preparation for embryo implantation in mice.

PubMed

Diao, Honglu; Xiao, Shuo; Howerth, Elizabeth W; Zhao, Fei; Li, Rong; Ard, Mary B; Ye, Xiaoqin

2013-08-01

Gap junctions have an important role in cell-to-cell communication, a process obviously required for embryo implantation. Uterine luminal epithelium (LE) is the first contact for an implanting embryo and is critical for the establishment of uterine receptivity. Microarray analysis of the LE from peri-implantation mouse uterus showed low-level expression of 19 gap junction proteins in preimplantation LE and upregulation of gap junction protein, beta 2 (GJB2, connexin 26, Cx26) in postimplantation LE. Time course study using in situ hybridization and immunofluorescence revealed upregulation of GJB2 in the LE surrounding the implantation site before decidualization. Similar dynamic expression of GJB2 was observed in the LE of artificially decidualized mice but not pseudopregnant mice. To determine the potential function of uterine gap junctions in embryo implantation, carbenoxolone (CBX), a broad gap junction blocker, was injected i.p. (100 mg/kg) or via local uterine fat pad (10 mg/kg) into pregnant mice on Gestation Day 3 at 1800 h, a few hours before embryo attachment to the LE. These CBX treatments disrupted embryo implantation, suggesting local effects of CBX in the uterus. However, i.p. injection of glycyrrhizic acid (100 mg/kg), which shares similar structure and multiple properties with CBX but is ineffective in blocking gap junctions, did not affect embryo implantation. Carbenoxolone also inhibited oil-induced artificial decidualization, concomitant with suppressed molecular changes and ultrastructural transformations associated with uterine preparation for embryo implantation, underscoring the adverse effect of CBX on uterine preparation for embryo implantation. These data demonstrate that uterine gap junctions are important for embryo implantation.

Petri Net-Based Model of Helicobacter pylori Mediated Disruption of Tight Junction Proteins in Stomach Lining during Gastric Carcinoma

PubMed Central

Naz, Anam; Obaid, Ayesha; Awan, Faryal M.; Ikram, Aqsa; Ahmad, Jamil; Ali, Amjad

2017-01-01

Tight junctions help prevent the passage of digestive enzymes and microorganisms through the space between adjacent epithelial cells lining. However, Helicobacter pylori encoded virulence factors negatively regulate these tight junctions and contribute to dysfunction of gastric mucosa. Here, we have predicted the regulation of important tight junction proteins, such as Zonula occludens-1, Claudin-2 and Connexin32 in the presence of pathogenic proteins. Molecular events such as post translational modifications and crosstalk between phosphorylation, O-glycosylation, palmitoylation and methylation are explored which may compromise the integrity of these tight junction proteins. Furthermore, the signaling pathways disrupted by dysregulated kinases, proteins and post-translational modifications are reviewed to design an abstracted computational model showing the situation-dependent dynamic behaviors of these biological processes and entities. A qualitative hybrid Petri Net model is therefore constructed showing the altered host pathways in the presence of virulence factor cytotoxin-associated gene A, leading to the disruption of tight junction proteins. The model is qualitative logic-based, which does not depend on any kinetic parameter and quantitative data and depends on knowledge derived from experiments. The designed model provides insights into the tight junction disruption and disease progression. Model is then verified by the available experimental data, nevertheless formal in vitro experimentation is a promising way to ensure its validation. The major findings propose that H. pylori activated kinases are responsible to trigger specific post translational modifications within tight junction proteins, at specific sites. These modifications may favor alterations in gastric barrier and provide a route to bacterial invasion into host cells. PMID:28932213

The role of ultra-thin SiO2 layers in metal-insulator-semiconductor (MIS) photoelectrochemical devices (Presentation Recording)

NASA Astrophysics Data System (ADS)

Esposito, Daniel V.

2015-08-01

Solid-state junctions based on a metal-insulator-semiconductor (MIS) architecture are of great interest for a number of optoelectronic applications such as photovoltaics, photoelectrochemical cells, and photodetection. One major advantage of the MIS junction compared to the closely related metal-semiconductor junction, or Schottky junction, is that the thin insulating layer (1-3 nm thick) that separates the metal and semiconductor can significantly reduce the density of undesirable interfacial mid-gap states. The reduction in mid-gap states helps "un-pin" the junction, allowing for significantly higher built-in-voltages to be achieved. A second major advantage of the MIS junction is that the thin insulating layer can also protect the underlying semiconductor from corrosion in an electrochemical environment, making the MIS architecture well-suited for application in (photo)electrochemical applications. In this presentation, discontinuous Si-based MIS junctions immersed in electrolyte are explored for use as i.) photoelectrodes for solar-water splitting in photoelectrochemical cells (PECs) and ii.) position-sensitive photodetectors. The development and optimization of MIS photoelectrodes for both of these applications relies heavily on understanding how processing of the thin SiO2 layer impacts the properties of nano- and micro-scale MIS junctions, as well as the interactions of the insulating layer with the electrolyte. In this work, we systematically explore the effects of insulator thickness, synthesis method, and chemical treatment on the photoelectrochemical and electrochemical properties of these MIS devices. It is shown that electrolyte-induced inversion plays a critical role in determining the charge carrier dynamics within the MIS photoelectrodes for both applications.

Petri Net-Based Model of Helicobacter pylori Mediated Disruption of Tight Junction Proteins in Stomach Lining during Gastric Carcinoma.

PubMed

Naz, Anam; Obaid, Ayesha; Awan, Faryal M; Ikram, Aqsa; Ahmad, Jamil; Ali, Amjad

2017-01-01

Tight junctions help prevent the passage of digestive enzymes and microorganisms through the space between adjacent epithelial cells lining. However, Helicobacter pylori encoded virulence factors negatively regulate these tight junctions and contribute to dysfunction of gastric mucosa. Here, we have predicted the regulation of important tight junction proteins, such as Zonula occludens-1, Claudin-2 and Connexin32 in the presence of pathogenic proteins. Molecular events such as post translational modifications and crosstalk between phosphorylation, O-glycosylation, palmitoylation and methylation are explored which may compromise the integrity of these tight junction proteins. Furthermore, the signaling pathways disrupted by dysregulated kinases, proteins and post-translational modifications are reviewed to design an abstracted computational model showing the situation-dependent dynamic behaviors of these biological processes and entities. A qualitative hybrid Petri Net model is therefore constructed showing the altered host pathways in the presence of virulence factor cytotoxin-associated gene A, leading to the disruption of tight junction proteins. The model is qualitative logic-based, which does not depend on any kinetic parameter and quantitative data and depends on knowledge derived from experiments. The designed model provides insights into the tight junction disruption and disease progression. Model is then verified by the available experimental data, nevertheless formal in vitro experimentation is a promising way to ensure its validation. The major findings propose that H. pylori activated kinases are responsible to trigger specific post translational modifications within tight junction proteins, at specific sites. These modifications may favor alterations in gastric barrier and provide a route to bacterial invasion into host cells.

Ratiometric, filter-free optical sensor based on a complementary metal oxide semiconductor buried double junction photodiode.

PubMed

Yung, Ka Yi; Zhan, Zhiyong; Titus, Albert H; Baker, Gary A; Bright, Frank V

2015-07-16

We report a complementary metal oxide semiconductor integrated circuit (CMOS IC) with a buried double junction (BDJ) photodiode that (i) provides a real-time output signal that is related to the intensity ratio at two emission wavelengths and (ii) simultaneously eliminates the need for an optical filter to block Rayleigh scatter. We demonstrate the BDJ platform performance for gaseous NH3 and aqueous pH detection. We also compare the BDJ performance to parallel results obtained by using a slew scanned fluorimeter (SSF). The BDJ results are functionally equivalent to the SSF results without the need for any wavelength filtering or monochromators and the BDJ platform is not prone to errors associated with source intensity fluctuations or sensor signal drift. Copyright © 2015 Elsevier B.V. All rights reserved.

Regulation of K transport in a mathematical model of the cortical collecting tubule.

PubMed

Strieter, J; Weinstein, A M; Giebisch, G; Stephenson, J L

1992-12-01

The effect of luminal flow rate and peritubular pH on Na and K transport is investigated in a mathematical model of the rabbit cortical collecting tubule. The model is used to simulate a 0.4-cm segment of tubule comprised of principal cell, alpha- and beta-intercalated cells, and lateral interspace. Calculations produce luminal profiles of Na, K, Cl, HCO3, and phosphate, as well as of electrical potential and pH. Parameter sets are developed that permit representation of both unstimulated and deoxycorticosterone acetate-stimulated tubules. A series of simulations is performed in which initial luminal flow rate is varied over the range of values between 0.1 and 30 nl/min. A marked flow-dependent enhancement of Na reabsorption and K secretion is seen, especially at lower flows, while Cl and HCO3 transport remain relatively constant. In experimental studies, it has been observed that metabolic alkalosis stimulates and metabolic acidosis inhibits K secretion, while leaving Na transport relatively unaffected [B. A. Stanton and G. Giebisch. Am. J. Physiol. 242 (Renal Fluid Electrolyte Physiol. 11): F544-F551, 1982; K. Tabei, S. Muto, Y. Ando, Y. Sakairi, and Y. Asano. J. Am. Soc. Nephrol. 1: 693, 1990; and K. Tabei, S. Muto, H. Furuya, and Y. Asano. J. Am. Soc. Nephrol. 2: 752, 1991]. Model calculations indicate that, when ion permeabilities are fixed and not dependent on pH, the impact of peritubular HCO3 on K secretion cannot be simulated. When junctional Cl permeability decreases with increasing interspace pH (E. M. Wright and J. M. Diamond. Biochim. Biophys. Acta 163: 57-74, 1968) in the model, there is a marked stimulation of K secretion with alkalosis and inhibition with acidosis. Furthermore, inclusion of a pH-dependent apical Na permeability [L. G. Palmer and G. Frindt. Am. J. Physiol. 253 (Renal Fluid Electrolyte Physiol. 22): F333-F339, 1987] that increases with increasing principal cell pH significantly reduces the change in Na+ reabsorption seen with the pH-dependent junctional Cl permeability alone. In these calculations, a pH-dependent apical K permeability [W. Wang, A. Schwab, and G. Giebisch. Am. J. Physiol. 259 (Renal Fluid Electrolyte Physiol. 28): F494-F502, 1990] that increases with increasing principal cell pH shows relatively little impact on K secretion.

Constant pH Accelerated Molecular Dynamics Investigation of the pH Regulation Mechanism of Dinoflagellate Luciferase.

PubMed

Donnan, Patrick H; Ngo, Phong D; Mansoorabadi, Steven O

2018-01-23

The bioluminescence reaction in dinoflagellates involves the oxidation of an open-chain tetrapyrrole by the enzyme dinoflagellate luciferase (LCF). The activity of LCF is tightly regulated by pH, where the enzyme is essentially inactive at pH ∼8 and optimally active at pH ∼6. Little is known about the mechanism of LCF or the structure of the active form of the enzyme, although it has been proposed that several intramolecularly conserved histidine residues in the N-terminal region are important for the pH regulation mechanism. Here, constant pH accelerated molecular dynamics was employed to gain insight into the conformational activation of LCF induced by acidification.

A supine cranio-spinal irradiation technique using moving field junctions

NASA Astrophysics Data System (ADS)

Mani, Karthick Raj; Sapru, Shantanu; Maria Das, K. J.; Basu, Ayan

2016-12-01

Aim: To demonstrate a simple technique of cranio-spinal irradiation (CSI) in supine position using inter fraction moving field junctions to feather out any potential hot and cold spots. Materials and Methods: Fifteen patients diagnosed with medulloblastoma were treated during the period February 2011 to June 2015 were included in this study. Out of fifteen patients in the study nine were male and 6 were female with a median age of 13.4 years (range 5-27 years). All the patients were positioned supine on CT simulation, immobilized using thermoplastic mask and aligned using room based laser system. Two parallel opposed lateral fields for the whole brain using an asymmetrical jaw with isocenter at C2 vertebral body. A posterior field also placed to cover the cervical and dorsal field using the same isocenter at C2. The second isocenter was placed at lumbar vertebral region to cover the remaining dorsal, lumbar and sacral region using an inter-fraction moving junction. Field-in-field and enhanced dynamic wedge used to homogeneous dose distribution when required. Results and Discussion: In this study, we found that only two patients failed in the primary site, no radiation myelitis or recurrences in the filed junctions were reported in these fifteen patients with a median follow-up of 36.4 months. The automated sequence of treatment plans with moving junctions in the comfortable supine position negating the need for manual junction matching or junction shifts avoiding potential treatment errors and also facilitating delivery of anesthesia where necessary.

Actin-interacting protein 1 controls assembly and permeability of intestinal epithelial apical junctions

PubMed Central

Baranwal, Somesh

2015-01-01

Adherens junctions (AJs) and tight junctions (TJs) are crucial regulators of the integrity and restitution of the intestinal epithelial barrier. The structure and function of epithelial junctions depend on their association with the cortical actin cytoskeleton that, in polarized epithelial cells, is represented by a prominent perijunctional actomyosin belt. The assembly and stability of the perijunctional cytoskeleton is controlled by constant turnover (disassembly and reassembly) of actin filaments. Actin-interacting protein (Aip) 1 is an emerging regulator of the actin cytoskeleton, playing a critical role in filament disassembly. In this study, we examined the roles of Aip1 in regulating the structure and remodeling of AJs and TJs in human intestinal epithelium. Aip1 was enriched at apical junctions in polarized human intestinal epithelial cells and normal mouse colonic mucosa. Knockdown of Aip1 by RNA interference increased the paracellular permeability of epithelial cell monolayers, decreased recruitment of AJ/TJ proteins to steady-state intercellular contacts, and attenuated junctional reassembly in a calcium-switch model. The observed defects of AJ/TJ structure and functions were accompanied by abnormal organization and dynamics of the perijunctional F-actin cytoskeleton. Moreover, loss of Aip1 impaired the apico-basal polarity of intestinal epithelial cell monolayers and inhibited formation of polarized epithelial cysts in 3-D Matrigel. Our findings demonstrate a previously unanticipated role of Aip1 in regulating the structure and remodeling of intestinal epithelial junctions and early steps of epithelial morphogenesis. PMID:25792565

Actin-interacting protein 1 controls assembly and permeability of intestinal epithelial apical junctions.

PubMed

Lechuga, Susana; Baranwal, Somesh; Ivanov, Andrei I

2015-05-01

Adherens junctions (AJs) and tight junctions (TJs) are crucial regulators of the integrity and restitution of the intestinal epithelial barrier. The structure and function of epithelial junctions depend on their association with the cortical actin cytoskeleton that, in polarized epithelial cells, is represented by a prominent perijunctional actomyosin belt. The assembly and stability of the perijunctional cytoskeleton is controlled by constant turnover (disassembly and reassembly) of actin filaments. Actin-interacting protein (Aip) 1 is an emerging regulator of the actin cytoskeleton, playing a critical role in filament disassembly. In this study, we examined the roles of Aip1 in regulating the structure and remodeling of AJs and TJs in human intestinal epithelium. Aip1 was enriched at apical junctions in polarized human intestinal epithelial cells and normal mouse colonic mucosa. Knockdown of Aip1 by RNA interference increased the paracellular permeability of epithelial cell monolayers, decreased recruitment of AJ/TJ proteins to steady-state intercellular contacts, and attenuated junctional reassembly in a calcium-switch model. The observed defects of AJ/TJ structure and functions were accompanied by abnormal organization and dynamics of the perijunctional F-actin cytoskeleton. Moreover, loss of Aip1 impaired the apico-basal polarity of intestinal epithelial cell monolayers and inhibited formation of polarized epithelial cysts in 3-D Matrigel. Our findings demonstrate a previously unanticipated role of Aip1 in regulating the structure and remodeling of intestinal epithelial junctions and early steps of epithelial morphogenesis. Copyright © 2015 the American Physiological Society.

Mapping the dynamics of force transduction at cell–cell junctions of epithelial clusters

PubMed Central

Ng, Mei Rosa; Besser, Achim; Brugge, Joan S; Danuser, Gaudenz

2014-01-01

Force transduction at cell-cell adhesions regulates tissue development, maintenance and adaptation. We developed computational and experimental approaches to quantify, with both sub-cellular and multi-cellular resolution, the dynamics of force transmission in cell clusters. Applying this technology to spontaneously-forming adherent epithelial cell clusters, we found that basal force fluctuations were coupled to E-cadherin localization at the level of individual cell-cell junctions. At the multi-cellular scale, cell-cell force exchange depended on the cell position within a cluster, and was adaptive to reconfigurations due to cell divisions or positional rearrangements. Importantly, force transmission through a cell required coordinated modulation of cell-matrix adhesion and actomyosin contractility in the cell and its neighbors. These data provide insights into mechanisms that could control mechanical stress homeostasis in dynamic epithelial tissues, and highlight our methods as a resource for the study of mechanotransduction in cell-cell adhesions. DOI: http://dx.doi.org/10.7554/eLife.03282.001 PMID:25479385

Effect of temperature variations and thermal noise on the static and dynamic behavior of straintronics devices

NASA Astrophysics Data System (ADS)

Barangi, Mahmood; Mazumder, Pinaki

2015-11-01

A theoretical model quantifying the effect of temperature variations on the magnetic properties and static and dynamic behavior of the straintronics magnetic tunneling junction is presented. Four common magnetostrictive materials (Nickel, Cobalt, Terfenol-D, and Galfenol) are analyzed to determine their temperature sensitivity and to provide a comprehensive database for different applications. The variations of magnetic anisotropies are studied in detail for temperature levels up to the Curie temperature. The energy barrier of the free layer and the critical voltage required for flipping the magnetization vector are inspected as important metrics that dominate the energy requirements and noise immunity when the device is incorporated into large systems. To study the dynamic thermal noise, the effect of the Langevin thermal field on the free layer's magnetization vector is incorporated into the Landau-Lifshitz-Gilbert equation. The switching energy, flipping delay, write, and hold error probabilities are studied, which are important metrics for nonvolatile memories, an important application of the straintronics magnetic tunneling junctions.

Atomically Thin Al2O3 Films for Tunnel Junctions

NASA Astrophysics Data System (ADS)

Wilt, Jamie; Gong, Youpin; Gong, Ming; Su, Feifan; Xu, Huikai; Sakidja, Ridwan; Elliot, Alan; Lu, Rongtao; Zhao, Shiping; Han, Siyuan; Wu, Judy Z.

2017-06-01

Metal-insulator-metal tunnel junctions are common throughout the microelectronics industry. The industry standard AlOx tunnel barrier, formed through oxygen diffusion into an Al wetting layer, is plagued by internal defects and pinholes which prevent the realization of atomically thin barriers demanded for enhanced quantum coherence. In this work, we employ in situ scanning tunneling spectroscopy along with molecular-dynamics simulations to understand and control the growth of atomically thin Al2O3 tunnel barriers using atomic-layer deposition. We find that a carefully tuned initial H2O pulse hydroxylated the Al surface and enabled the creation of an atomically thin Al2O3 tunnel barrier with a high-quality M -I interface and a significantly enhanced barrier height compared to thermal AlOx . These properties, corroborated by fabricated Josephson junctions, show that atomic-layer deposition Al2O3 is a dense, leak-free tunnel barrier with a low defect density which can be a key component for the next generation of metal-insulator-metal tunnel junctions.

Nonadiabatic effect on the quantum heat flux control.

PubMed

Uchiyama, Chikako

2014-05-01

We provide a general formula of quantum transfer that includes the nonadiabatic effect under periodic environmental modulation by using full counting statistics in Hilbert-Schmidt space. Applying the formula to an anharmonic junction model that interacts with two bosonic environments within the Markovian approximation, we find that the quantum transfer is divided into the adiabatic (dynamical and geometrical phases) and nonadiabatic contributions. This extension shows the dependence of quantum transfer on the initial condition of the anharmonic junction just before the modulation, as well as the characteristic environmental parameters such as interaction strength and cut-off frequency of spectral density. We show that the nonadiabatic contribution represents the reminiscent effect of past modulation including the transition from the initial condition of the anharmonic junction to a steady state determined by the very beginning of the modulation. This enables us to tune the frequency range of modulation, whereby we can obtain the quantum flux corresponding to the geometrical phase by setting the initial condition of the anharmonic junction.

YAP and TAZ regulate adherens junction dynamics and endothelial cell distribution during vascular development

PubMed Central

Neto, Filipa; Klaus-Bergmann, Alexandra; Ong, Yu Ting; Alt, Silvanus; Vion, Anne-Clémence; Szymborska, Anna; Carvalho, Joana R; Hollfinger, Irene; Bartels-Klein, Eireen; Franco, Claudio A

2018-01-01

Formation of blood vessel networks by sprouting angiogenesis is critical for tissue growth, homeostasis and regeneration. How endothelial cells arise in adequate numbers and arrange suitably to shape functional vascular networks is poorly understood. Here we show that YAP/TAZ promote stretch-induced proliferation and rearrangements of endothelial cells whilst preventing bleeding in developing vessels. Mechanistically, YAP/TAZ increase the turnover of VE-Cadherin and the formation of junction associated intermediate lamellipodia, promoting both cell migration and barrier function maintenance. This is achieved in part by lowering BMP signalling. Consequently, the loss of YAP/TAZ in the mouse leads to stunted sprouting with local aggregation as well as scarcity of endothelial cells, branching irregularities and junction defects. Forced nuclear activity of TAZ instead drives hypersprouting and vascular hyperplasia. We propose a new model in which YAP/TAZ integrate mechanical signals with BMP signaling to maintain junctional compliance and integrity whilst balancing endothelial cell rearrangements in angiogenic vessels. PMID:29400648

Effects of an acidic environment on coagulation dynamics.

PubMed

Gissel, M; Brummel-Ziedins, K E; Butenas, S; Pusateri, A E; Mann, K G; Orfeo, T

2016-10-01

Essentials Acidosis, an outcome of traumatic injury, has been linked to impaired procoagulant efficiency. In vitro model systems were used to assess coagulation dynamics at pH 7.4 and 7.0. Clot formation dynamics are slightly enhanced at pH 7.0 in blood ex vivo. Acidosis induced decreases in antithrombin efficacy offset impairments in procoagulant activity. Background Disruption of hydrogen ion homeostasis is a consequence of traumatic injury often associated with clinical coagulopathy. Mechanisms by which acidification of the blood leads to aberrant coagulation require further elucidation. Objective To examine the effects of acidified conditions on coagulation dynamics using in vitro models of increasing complexity. Methods Coagulation dynamics were assessed at pH 7.4 and 7.0 as follows: (i) tissue factor (TF)-initiated coagulation proteome mixtures (±factor [F]XI, ±fibrinogen/FXIII), with reaction progress monitored as thrombin generation or fibrin formation; (ii) enzyme/inhibitor reactions; and (iii) TF-dependent or independent clot dynamics in contact pathway-inhibited blood via viscoelastometry. Results Rate constants for antithrombin inhibition of FXa and thrombin were reduced by ~ 25-30% at pH 7.0. At pH 7.0 (+FXI), TF-initiated thrombin generation showed a 20% increase in maximum thrombin levels and diminished thrombin clearance rates. Viscoelastic analyses showed a 25% increase in clot time and a 25% reduction in maximum clot firmness (MCF). A similar MCF reduction was observed at pH 7.0 when fibrinogen/FXIII were reacted with thrombin. In contrast, in contact pathway-inhibited blood (n = 6) at pH 7.0, MCF values were elevated 6% (95% confidence interval [CI]: 1%-11%) in TF-initiated blood and 15% (95% CI: 1%- 29%) in the absence of TF. Clot times at pH 7.0 decreased 32% (95% CI: 15%-49%) in TF-initiated blood and 51% (95% CI: 35%-68%) in the absence of TF. Conclusions Despite reported decreased procoagulant catalysis at pH 7.0, clot formation dynamics are slightly enhanced in blood ex vivo and suppression of thrombin generation is not observed. A decrease in antithrombin reactivity is one potential mechanism contributing to these outcomes. © 2016 International Society on Thrombosis and Haemostasis.

Quantitative cell polarity imaging defines leader-to-follower transitions during collective migration and the key role of microtubule-dependent adherens junction formation.

PubMed

Revenu, Céline; Streichan, Sebastian; Donà, Erika; Lecaudey, Virginie; Hufnagel, Lars; Gilmour, Darren

2014-03-01

The directed migration of cell collectives drives the formation of complex organ systems. A characteristic feature of many migrating collectives is a 'tissue-scale' polarity, whereby 'leader' cells at the edge of the tissue guide trailing 'followers' that become assembled into polarised epithelial tissues en route. Here, we combine quantitative imaging and perturbation approaches to investigate epithelial cell state transitions during collective migration and organogenesis, using the zebrafish lateral line primordium as an in vivo model. A readout of three-dimensional cell polarity, based on centrosomal-nucleus axes, allows the transition from migrating leaders to assembled followers to be quantitatively resolved for the first time in vivo. Using live reporters and a novel fluorescent protein timer approach, we investigate changes in cell-cell adhesion underlying this transition by monitoring cadherin receptor localisation and stability. This reveals that while cadherin 2 is expressed across the entire tissue, functional apical junctions are first assembled in the transition zone and become progressively more stable across the leader-follower axis of the tissue. Perturbation experiments demonstrate that the formation of these apical adherens junctions requires dynamic microtubules. However, once stabilised, adherens junction maintenance is microtubule independent. Combined, these data identify a mechanism for regulating leader-to-follower transitions within migrating collectives, based on the relocation and stabilisation of cadherins, and reveal a key role for dynamic microtubules in this process.

Molecular Basis of Circadian Photoreception

DTIC Science & Technology

2006-06-30

dusk transitions . For example, proper circadian entrainment permits animals to inhabit precise “temporal niches” that minimize exposure to predation...into the spectral sensitivity of any unidentified circadian photoreceptors. Such a study in the golden hamster (Mesocricetus auratus) indicated a...0.05–0.3mM GTP-Tris; (280–300 mOsm, pH 7.3). Liquid junction potentials (-14mV) were corrected. In darkness, most cells had series resistance ᝺MΩ

Alterations in the Local Axonal Environment Influence Target Reinnervation and Neuronal Survival After PostnataI Axotomy

DTIC Science & Technology

2000-06-21

2000 Dissertation directed by: Rosemary C. Borke, Ph.D. Professor Department of Anatomy and Cell Biology Following peripheral nerve injury in adult...augmented at the injury site and the neuromuscular junction (NMJ) following sciatic nerve axotomy. The current work determined that SC apoptosis occurs in...related and location-specific response to peripheral nerve injury . Apoptotic SC were found in two strategic locations for guiding axonal outgrowth during

Measurement of Quantum Phase-Slips in Josephson Junction Chains

NASA Astrophysics Data System (ADS)

Guichard, Wiebke

2011-03-01

Quantum phase-slip dynamics in Josephson junction chains could provide the basis for the realization of a new type of topologically protected qubit or for the implementation of a new current standard. I will present measurements of the effect of quantum phase-slips on the ground state of a Josephson junction chain. We can tune in situ the strength of the phase-slips. These phase-slips are the result of fluctuations induced by the finite charging energy of each junction in the chain. Our measurements demonstrate that a Josephson junction chain under phase bias constraint behaves in a collective way. I will also show evidence of coherent phase-slip interference, the so called Aharonov-Casher effect. This phenomenon is the dual of the well known Aharonov-Bohm interference. In collaboration with I.M. Pop, Institut Neel, C.N.R.S. and Universite Joseph Fourier, BP 166, 38042 Grenoble, France; I. Protopopov, L. D. Landau Institute for Theoretical Physics, Kosygin str. 2, Moscow 119334, Russia and Institut fuer Nanotechnologie, Karlsruher Institut fuer Technologie, 76021 Karlsruhe, Germany; and F. Lecocq, Z. Peng, B. Pannetier, O. Buisson, Institut Neel, C.N.R.S. and Universite Joseph Fourier. European STREP MIDAS, ANR QUANTJO.

Interlocked positive and negative feedback network motifs regulate β-catenin activity in the adherens junction pathway

PubMed Central

Klinke, David J.; Horvath, Nicholas; Cuppett, Vanessa; Wu, Yueting; Deng, Wentao; Kanj, Rania

2015-01-01

The integrity of epithelial tissue architecture is maintained through adherens junctions that are created through extracellular homotypic protein–protein interactions between cadherin molecules. Cadherins also provide an intracellular scaffold for the formation of a multiprotein complex that contains signaling proteins, including β-catenin. Environmental factors and controlled tissue reorganization disrupt adherens junctions by cleaving the extracellular binding domain and initiating a series of transcriptional events that aim to restore tissue homeostasis. However, it remains unclear how alterations in cell adhesion coordinate transcriptional events, including those mediated by β-catenin in this pathway. Here were used quantitative single-cell and population-level in vitro assays to quantify the endogenous pathway dynamics after the proteolytic disruption of the adherens junctions. Using prior knowledge of isolated elements of the overall network, we interpreted these data using in silico model-based inference to identify the topology of the regulatory network. Collectively the data suggest that the regulatory network contains interlocked network motifs consisting of a positive feedback loop, which is used to restore the integrity of adherens junctions, and a negative feedback loop, which is used to limit β-catenin–induced gene expression. PMID:26224311

Quench dynamics of the Josephson current in a topological Josephson junction

NASA Astrophysics Data System (ADS)

Sun, Dihao; Liu, Jie

2018-01-01

The 4 π -periodic Josephson effect is a distinguishing feature of a topological Josephson junction. However, stringent conditions make it hard to observe in experiments. In this work, we study the transient transport properties in a topological Josephson junction numerically. We show that the 4 π Josephson current can be sustained under nonequilibrium conditions. The properties of the Josephson current are analyzed for different conditions and three main regimes are identified. First, when both the superconducting wires of the Josephson junction lie in the topologically nontrivial region, a 4 π Josephson current can appear upon suddenly applying a dc voltage. Second, when one superconducting wire lies in the trivial region, while the other wire lies in the nontrivial region, the Josephson current is 2 π periodic but the component of the higher-order Josephson current increases. Third, when both wires lie in the trivial region, a stable 2 π Josephson current is observed. Most importantly, the fractional Josephson effect is fragile in the presence of disorder. Hence experiments should be designed carefully to eliminate the effect of disorder. These results could be helpful to optimize fine-tuning of the experimental parameters to observe the 4 π -periodic Josephson current in a topological Josephson junction.

Dynamic formation of ER–PM junctions presents a lipid phosphatase to regulate phosphoinositides

PubMed Central

Jensen, Jill B.; Vivas, Oscar; Kruse, Martin; Traynor-Kaplan, Alexis E.; Hille, Bertil

2016-01-01

Endoplasmic reticulum–plasma membrane (ER–PM) contact sites play an integral role in cellular processes such as excitation–contraction coupling and store-operated calcium entry (SOCE). Another ER–PM assembly is one tethered by the extended synaptotagmins (E-Syt). We have discovered that at steady state, E-Syt2 positions the ER and Sac1, an integral ER membrane lipid phosphatase, in discrete ER–PM junctions. Here, Sac1 participates in phosphoinositide homeostasis by limiting PM phosphatidylinositol 4-phosphate (PI(4)P), the precursor of PI(4,5)P2. Activation of G protein–coupled receptors that deplete PM PI(4,5)P2 disrupts E-Syt2–mediated ER–PM junctions, reducing Sac1’s access to the PM and permitting PM PI(4)P and PI(4,5)P2 to recover. Conversely, depletion of ER luminal calcium and subsequent activation of SOCE increases the amount of Sac1 in contact with the PM, depleting PM PI(4)P. Thus, the dynamic presence of Sac1 at ER–PM contact sites allows it to act as a cellular sensor and controller of PM phosphoinositides, thereby influencing many PM processes. PMID:27044890

Phase control synthesis of α, β and α/β Bi2O3 hetero-junction with enhanced and synergistic photocatalytic activity on degradation of toxic dye, Rhodamine-B under natural sunlight.

PubMed

Bera, Kamal Kanti; Majumdar, Rituparna; Chakraborty, Malay; Bhattacharya, Swapan Kumar

2018-06-15

Nano particles of a few α/β Bi 2 O 3 hetero-junctions of various compositions synthesized by one- pot hydrothermal method, exhibit exceptional and synergistic photo-catalytic activity for the degradation of Rhodamine-B in aqueous solution under natural sunlight. Pure α and pure β Bi 2 O 3 are also synthesized by control post heating of synthesized hetero-junction. The nano-materials were characterized by diffraction (XRD), microscopic and spectroscopic techniques. The XRD reveals α-β phase hetero-junctions of Bi 2 O 3 are made of α-Bi 2 O 3 and β-Bi 2 O 3 with average dimensions within 13-113 and 5-71 nm respectively and having band gap range of 2.4- 2.9 eV. The spectrophotometrically determined % degradation of the dye and associated rate constant on the best hetero-junction are increased by 4.5(/2.1) and 3.3(/1.2) times than these on pure α (/β). The effects of operational parameters and trapping agents have been analyzed. The maximum removal of the dye was achieved up to 99.6% in 3 h using 0.5 g/L photo-catalyst at pH 3. The reusability test shows that the photo-catalytic activity is retained excellently due to change in chemical nature of the catalyst from α -Bi 2 O 3 to β-Bi 2 O 3, Bi 2 O 2 CO 3 and BiOCl. A suitable mechanism is proposed. Copyright © 2018 Elsevier B.V. All rights reserved.

Design and characterization of the first peptidomimetic molecule that prevents acidification-induced closure of cardiac gap junctions

PubMed Central

Verma, Vandana; Larsen, Bjarne Due; Coombs, Wanda; Lin, Xianming; Sarrou, Eliana; Taffet, Steven M.; Delmar, Mario

2010-01-01

Background Gap junctions are potential targets for pharmacological intervention. We have previously developed a series of peptide sequences that prevent closure of Cx43 channels, bind to cardiac Cx43 and prevent acidification-induced uncoupling of cardiac gap junctions. Objective We aimed to identify and validate the minimum core active structure in peptides containing an RR-N/Q-Y motif. Based on that information, we sought to generate a peptidomimetic molecule that acts on the chemical regulation of Cx43 channels. Methods Experiments were based on a combination of biochemical, spectroscopic and electrophysiological techniques, as well as molecular modeling of active pharmacophores with Cx43 activity. Results Molecular modeling analysis indicated that the functional elements of the side chains in the motif RRXY form a triangular structure. Experimental data revealed that compounds containing such a structure bind to Cx43 and prevent Cx43 chemical gating. These results provided us with the first platform for drug design targeted to the carboxyl terminal of Cx43. Using that platform, we designed and validated a peptidomimetic compound (ZP2519; molecular weight 619 Da) that prevented octanol-induced uncoupling of Cx43 channels, and pH gating of cardiac gap junctions. Conclusion Structure-based drug design can be applied to the development of pharmacophores that act directly on Cx43. Small molecules containing these pharmacophores can serve as tools to determine the role of gap junction regulation in the control of cardiac rhythm. Future studies will determine whether these compounds can function as pharmacological agents for the treatment of a selected subset of cardiac arrhythmias. PMID:20601149

Bar dynamics and channel junctions in scale-experiments of estuaries

NASA Astrophysics Data System (ADS)

Leuven, J.; Braat, L.; van Dijk, W. M.; Haas, T. D.; Kleinhans, M. G.

2017-12-01

The evolution of channels and bars in estuaries has high socio-economic relevance, with strong implications for navigation, dredging and ecology. However, the spatial and temporal evolution of channels and bars in estuaries is poorly understood. Here, we study feedbacks of bar morphodynamics on widening and narrowing of estuaries. Therefore, we conducted an experiment in a 20 m long and 3 m wide tilting flume (the 'Metronome'), in which we monitored the evolution of a self-formed estuary that developed from an intial straight channel into an irregular planform with multiple channels, braided bars and a meandering ebb channel. At locations where the estuary width is confined, major channel junctions occur, while the zones between the junctions are characterised by high braiding indices, periodically migrating channels and a relatively large estuary width. The junction locations were forced by the in- and outflow locations on the sides of the ebb-tidal delta and at the location where the channel pattern transitions from multiple channels into a single channel. In the middle of the estuary, self-confinement occurred by sedimentation on the sides of the estuary, which caused another major junction. The channel orientation at the junctions steers the morphodynamics of channels and bars immediately landward and seaward, because the orientation of inflow from the ebb-tidal delta and landward river perpetually varies. In natural systems major junction locations are mostly forced by inherited geology or human engineering. However, this study concludes that even without external forcing, the estuary planform will not converge to an ideal shape but will self-confine at major junctions and widens in the adjacent zones, resulting in an irregular planform shape.

Mechanics of flow and sediment transport in delta distributary channels

USGS Publications Warehouse

Nelson, Jonathan M.; Kinzel, Paul J.; Duc Toan, Duong; Shimizu, Yasuyuki; McDonald, Richard R.

2011-01-01

boundary conditions. Over time, the pattern of erosion and deposition in the distributary channels gives rise to variations in the amount of water and sediment routed into them. In the simplest case, this results in channel switching on deltas, but in a more general sense these dynamics produce a rich suite of interesting morphologic change contributing both to the evolution of the channel distributary network and the overall evolution of the delta. As part of a study to develop a better understanding of these processes, we conducted a field study measuring the detailed morphology of the Hong-Luoc junction on the Red River downstream of Hanoi, Vietnam. This junction was selected for such a study because it has a 1,000-year history, modern observations suggest that it is currently switching (changing the proportion of sediment and streamflow provided to each of the distributary channels), and hydrologic configuration of the junction allows for the study of two bifurcations and one confluence in a single junction complex. In this paper, our morphologic observations are used in computational flow models to show how flow and sediment transport changes as a function of total discharge upstream of the junction. This is a key component of understanding how the junction attains stability over a range of flows or how imbalances in the distribution of flow and sediment transport lead to destabilization of the channel bifurcation.

GABA and Gap Junctions in the Development of Synchronized Activity in Human Pluripotent Stem Cell-Derived Neural Networks

PubMed Central

Mäkinen, Meeri Eeva-Liisa; Ylä-Outinen, Laura; Narkilahti, Susanna

2018-01-01

The electrical activity of the brain arises from single neurons communicating with each other. However, how single neurons interact during early development to give rise to neural network activity remains poorly understood. We studied the emergence of synchronous neural activity in human pluripotent stem cell (hPSC)-derived neural networks simultaneously on a single-neuron level and network level. The contribution of gamma-aminobutyric acid (GABA) and gap junctions to the development of synchronous activity in hPSC-derived neural networks was studied with GABA agonist and antagonist and by blocking gap junctional communication, respectively. We characterized the dynamics of the network-wide synchrony in hPSC-derived neural networks with high spatial resolution (calcium imaging) and temporal resolution microelectrode array (MEA). We found that the emergence of synchrony correlates with a decrease in very strong GABA excitation. However, the synchronous network was found to consist of a heterogeneous mixture of synchronously active cells with variable responses to GABA, GABA agonists and gap junction blockers. Furthermore, we show how single-cell distributions give rise to the network effect of GABA, GABA agonists and gap junction blockers. Finally, based on our observations, we suggest that the earliest form of synchronous neuronal activity depends on gap junctions and a decrease in GABA induced depolarization but not on GABAA mediated signaling. PMID:29559893

Voltage-induced ferromagnetic resonance in magnetic tunnel junctions.

PubMed

Zhu, Jian; Katine, J A; Rowlands, Graham E; Chen, Yu-Jin; Duan, Zheng; Alzate, Juan G; Upadhyaya, Pramey; Langer, Juergen; Amiri, Pedram Khalili; Wang, Kang L; Krivorotov, Ilya N

2012-05-11

We demonstrate excitation of ferromagnetic resonance in CoFeB/MgO/CoFeB magnetic tunnel junctions (MTJs) by the combined action of voltage-controlled magnetic anisotropy (VCMA) and spin transfer torque (ST). Our measurements reveal that GHz-frequency VCMA torque and ST in low-resistance MTJs have similar magnitudes, and thus that both torques are equally important for understanding high-frequency voltage-driven magnetization dynamics in MTJs. As an example, we show that VCMA can increase the sensitivity of an MTJ-based microwave signal detector to the sensitivity level of semiconductor Schottky diodes.

Electron transfer dynamics of bistable single-molecule junctions.

PubMed

Danilov, Andrey V; Kubatkin, Sergey E; Kafanov, Sergey G; Flensberg, Karsten; Bjørnholm, Thomas

2006-10-01

We present transport measurements of single-molecule junctions bridged by a molecule with three benzene rings connected by two double bonds and with thiol end-groups that allow chemical binding to gold electrodes. The I-V curves show switching behavior between two distinct states. By statistical analysis of the switching events, we show that a 300 meV mode mediates the transition between the two states. We propose that breaking and reformation of a S-H bond in the contact zone between molecule and electrode explains the observed bistability.

Suppression of the "Quasiclassical" proximity gap in correlated-metal--superconductor structures.

PubMed

Nikolić, Branislav K; Freericks, J K; Miller, P

2002-02-18

We study the energy and spatial dependence of the local density of states in a superconductor--correlated-metal--superconductor Josephson junction, where the correlated metal is a non-Fermi liquid (described by the Falicov-Kimball model). Many-body correlations are treated with dynamical mean-field theory, extended to inhomogeneous systems. While quasiclassical theories predict a minigap in the spectrum of a disordered Fermi liquid which is proximity-coupled within a mesoscopic junction, we find that increasing electron correlations destroy any minigap that might be opened in the absence of many-body correlations.

Chaotic Dynamics of a Josephson Junction with a Ratchet Potential and Current-Modulating Damping

NASA Astrophysics Data System (ADS)

Li, Fei; Li, Wenwu; Xu, Lan

2018-06-01

The chaotic dynamics of a Josephson junction with a ratchet potential and current-modulating damping are studied. Under the first-order approximation, we construct the general solution of the first-order equation whose boundedness condition contains the famous Melnikov chaotic criterion. Based on the general solution, the incomputability and unpredictability of the system's chaotic behavior are discussed. For the case beyond perturbation conditions, the evolution of stroboscopic Poincaré sections shows that the system undergoes a quasi-periodic transition to chaos with an increasing intensity of the rf-current. Through a suitable feedback controlling strategy, the chaos can be effectively suppressed and the intensity of the controller can vary in a large range. It is also found that the current between the two separated superconductors increases monotonously in some specific parameter spaces.

Chaotic Dynamics of a Josephson Junction with a Ratchet Potential and Current-Modulating Damping

NASA Astrophysics Data System (ADS)

Li, Fei; Li, Wenwu; Xu, Lan

2018-04-01

The chaotic dynamics of a Josephson junction with a ratchet potential and current-modulating damping are studied. Under the first-order approximation, we construct the general solution of the first-order equation whose boundedness condition contains the famous Melnikov chaotic criterion. Based on the general solution, the incomputability and unpredictability of the system's chaotic behavior are discussed. For the case beyond perturbation conditions, the evolution of stroboscopic Poincaré sections shows that the system undergoes a quasi-periodic transition to chaos with an increasing intensity of the rf-current. Through a suitable feedback controlling strategy, the chaos can be effectively suppressed and the intensity of the controller can vary in a large range. It is also found that the current between the two separated superconductors increases monotonously in some specific parameter spaces.

A comparison of three electrodes for the measurement of pH in small volumes.

PubMed

Smit, A; Pollard, M; Cleaton-Jones, P; Preston, A

1997-01-01

An ion-sensitive field effect transistor (ISFET, Sentron, Sentron, Inc.) electrode was compared with a glass combination micro-electrode (MI-410, Micro-electrodes, Inc.) and a solid-state metal wire oxide pH sensor (Beetrode, World Precision Instruments, Inc.) with a liquid junction reference electrode (MERE1, World Precision Instruments, Inc.). The electrodes were assessed for linearity, reproducibility, accuracy, drift from the initial calibration between pH 4 and pH 7 and the time taken to record a stable reading. The ISFET was used to determine the pH in dental plaque samples (1 mg suspended in 20 microliters). The pH values correlated with the hydrogen ion concentration for all the electrodes (r = 0.98). The MI-410 fractured before this evaluation was completed. Coefficients of variation were 0.65% (pH 4) and 0.08% (pH 7) for the ISFET and 4.69% (pH 4) and 3.46% (pH 7) for the Beetrode. Both electrodes gave readings that differed significantly from the initial calibration, but the drift was greater for the Beetrode (F = 7.93; p = 0.0005) than the ISFET (F = 1.89; p = 0.1519). However, this drift was smaller than the change in pH as measured in dental plaque samples. The Beetrode gave a stable reading after 3.39 +/- 0.83 s and the ISFET after 2.2 +/- 0.76 s, while the MI-410 required at least 20 s. The ISFET type electrode is suitable for use in small volumes such as plaque suspensions, is easier to operate and yields results closer to the initial calibration than the Beetrode and is more robust than the MI-410 and the Beetrode.

The combination of pH monitoring in the most distal esophagus and symptom association analysis markedly improves the clinical value of esophageal pH tests.

PubMed

Hall, Mats Guerrero Garcia; Wenner, Jörgen; Öberg, Stefan

2016-01-01

The poor sensitivity of esophageal pH monitoring substantially limits the clinical value of the test. The aim of this study was to compare the diagnostic accuracy of esophageal pH monitoring and symptom association analysis performed at the conventional level with that obtained in the most distal esophagus. Eighty-two patients with typical reflux symptoms and 49 asymptomatic subjects underwent dual 48-h pH monitoring with the electrodes positioned immediately above, and 6 cm above the squamo-columnar junction (SCJ). The degree of esophageal acid exposure and the temporal relationship between reflux events and symptoms were evaluated. The sensitivity of pH recording and the diagnostic yield of Symptom Association Probability (SAP) were significantly higher for pH monitoring performed at the distal compared with the conventional level (82% versus 65%, p<0.001 and 74% versus 62%, p<0.001, respectively). The greatest improvement was observed in patients with non-erosive disease. In this group, the sensitivity increased from 46% at the standard level to 66% immediately above the SCJ, and with the combination of a positive SAP as a marker for a positive pH test, the diagnostic yield further increased to 94%. The diagnostic accuracy of esophageal pH monitoring in the most distal esophagus is superior to that performed at the conventional level and it is further improved with the combination of symptom association analysis. PH monitoring with the pH electrode positioned immediately above the SCJ should be introduced in clinical practice and always combined with symptom association analysis.

Universal Readers Based on Hydrogen Bonding or π-π Stacking for Identification of DNA Nucleotides in Electron Tunnel Junctions.

PubMed

Biswas, Sovan; Sen, Suman; Im, JongOne; Biswas, Sudipta; Krstic, Predrag; Ashcroft, Brian; Borges, Chad; Zhao, Yanan; Lindsay, Stuart; Zhang, Peiming

2016-12-27

A reader molecule, which recognizes all the naturally occurring nucleobases in an electron tunnel junction, is required for sequencing DNA by a recognition tunneling (RT) technique, referred to as a universal reader. In the present study, we have designed a series of heterocyclic carboxamides based on hydrogen bonding and a large-sized pyrene ring based on a π-π stacking interaction as universal reader candidates. Each of these compounds was synthesized to bear a thiolated linker for attachment to metal electrodes and examined for their interactions with naturally occurring DNA nucleosides and nucleotides by 1 H NMR, ESI-MS, computational calculations, and surface plasmon resonance. RT measurements were carried out in a scanning tunnel microscope. All of these molecules generated electrical signals with DNA nucleotides in tunneling junctions under physiological conditions (phosphate buffered aqueous solution, pH 7.4). Using a support vector machine as a tool for data analysis, we found that these candidates distinguished among naturally occurring DNA nucleotides with the accuracy of pyrene (by π-π stacking interactions) > azole carboxamides (by hydrogen-bonding interactions). In addition, the pyrene reader operated efficiently in a larger tunnel junction. However, the azole carboxamide could read abasic (AP) monophosphate, a product from spontaneous base hydrolysis or an intermediate of base excision repair. Thus, we envision that sequencing DNA using both π-π stacking and hydrogen-bonding-based universal readers in parallel should generate more comprehensive genome sequences than sequencing based on either reader molecule alone.

Comparative 1D and 3D numerical investigation of open-channel junction flows and energy losses

NASA Astrophysics Data System (ADS)

Luo, Hao; Fytanidis, Dimitrios K.; Schmidt, Arthur R.; García, Marcelo H.

2018-07-01

The complexity of open channel confluences stems from flow mixing, secondary circulation, post-confluence flow separation, contraction and backwater effects. These effects in turn result in a large number of parameters required to adequately quantify the junction induced hydraulic resistance and describe mean flow pattern and turbulent flow structures due to flow merging. The recent development in computing power advances the application of 3D Computational Fluid Dynamics (CFD) codes to visualize and understand the Confluence Hydrodynamic Zone (CHZ). Nevertheless, 1D approaches remain the mainstay in large drainage network or waterway system modeling considering computational efficiency and data availability. This paper presents (i) a modified 1D nonlinear dynamic model; (ii) a fully 3D non-hydrostatic, Reynolds-averaged Navier-Stokes Equations (RANS)-based, Computational Fluid Dynamics (CFD) model; (iii) an analysis of changing confluence hydrodynamics and 3D turbulent flow structure under various controls; (iv) a comparison of flow features (i.e. upstream water depths, energy losses and post-confluence contraction) predicted by 1D and 3D models; and (v) parameterization of 3D flow characteristics in 1D modeling through the computation of correction coefficients associated with contraction, energy and momentum. The present comprehensive 3D numerical investigation highlights the driving mechanisms for junction induced energy losses. Moreover, the comparative 1D and 3D study quantifies the deviation of 1D approximations and associated underlying assumptions from the 'true' resultant flow field. The study may also shed light on improving the accuracy of the 1D large network modeling through the parameterization of the complex 3D feature of the flow field and correction of interior boundary conditions at junctions of larger angles and/or with substantial lateral inflows. Moreover, the enclosed numerical investigations may enhance the understanding of the primary mechanisms contributing to hydraulic structure induced turbulent flow behavior and increased hydraulic resistance.

Current conduction in junction gate field effect transistors. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Kim, C.

1970-01-01

The internal physical mechanism that governs the current conduction in junction-gate field effect transistors is studied. A numerical method of analyzing the devices with different length-to-width ratios and doping profiles is developed. This method takes into account the two dimensional character of the electric field and the field dependent mobility. Application of the method to various device models shows that the channel width and the carrier concentration in the conductive channel decrease with increasing drain-to-source voltage for conventional devices. It also shows larger differential drain conductances for shorter devices when the drift velocity is not saturated. The interaction of the source and the drain gives the carrier accumulation in the channel which leads to the space-charge-limited current flow. The important parameters for the space-charge-limited current flow are found to be the L/L sub DE ratio and the crossover voltage.

Anomalous Dynamics of a Lipid Recognition Protein on a Membrane Surface

PubMed Central

Yamamoto, Eiji; Kalli, Antreas C.; Akimoto, Takuma; Yasuoka, Kenji; Sansom, Mark S. P.

2015-01-01

Pleckstrin homology (PH) domains are lipid-binding modules present in peripheral membrane proteins which interact with phosphatidyl-inositol phosphates (PIPs) in cell membranes. We use multiscale molecular dynamics simulations to characterize the localization and anomalous dynamics of the DAPP1 PH domain on the surface of a PIP-containing lipid bilayer. Both translational and rotational diffusion of the PH domain on the lipid membrane surface exhibit transient subdiffusion, with an exponent α ≈ 0.5 for times of less than 10 ns. In addition to a PIP3 molecule at the canonical binding site of the PH domain, we observe additional PIP molecules in contact with the protein. Fluctuations in the number of PIPs associated with the PH domain exhibit 1/f noise. We suggest that the anomalous diffusion and long-term correlated interaction of the PH domain with the membrane may contribute to an enhanced probability of encounter with target complexes on cell membrane surfaces. PMID:26657413

Transformation of Pb(II) from Cerrusite to Chloropyromorphite in the Presence of Hydroxyapatite under Varying Conditions of pH

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

Ryan, J.A.; Zhang, P.

1998-10-14

Cerrusite (PbC03) is soluble under acidic conditions and considered to be a highly bioavailable soil Pb species. In this study, synthetic cerrusite and hydroxyapatite [Ca5(P04)30H] were reacted under constant and dynamic pH conditions with various P/Pb molar ratios in an attempt to evaluate the effect of reaction kinetics on the formation of chloropyromorphite (Pb5(P04)3Cl) and solubilization of Pb. Under constant pH conditions, dissolution rates of both cerrusite and apatite were rapid when pH was low. Complete conversion of Pb from cerrusite to chloropyromorphite occurred within 60 tin at pH 4 and below when the amount of phosphate in the addedmore » apatite was stoichoimetrically equal to that needed to transform all added Pb into chloropyromorphite. The concentration of soluble Pb depended upon the volubility of chloropyromorphite. The dissolution rates of apatite and cerrusite decreased with increasing pH, and the transformation was incomplete at pH 5 and above in the 60 rnin reaction period. The soluble Pb level, therefore, was determined by the volubility of cerrusite. In the dynamic pH system which simulated the gastrointestinal tract (GI tract) system, a complete transformation of Pb from cerrusite to chloropyromorphite was achieved due to the complete dissolution of apatite and cerrusite at the initial low pHs. Chloropyromorphite was the exclusive reaction product in both constant and dynamic pH systems as indicated by XRD analysis. The differences in transformation rate and the control of Pb volubility between the reactions occurring in constant and dynamic pH systems indicate the significance of kinetics in controlling the bioavailability of Pb and the potential for the reaction to occur during ingestion.« less

The normal squamocolumnar junction is circumferentially even and minimal irregularities are manifestations of gastroesophageal acid reflux.

PubMed

Guerrero Garcia Hall, Mats; Wenner, Jörgen; Öberg, Stefan

2017-03-01

The macroscopic appearance of the normal squamocolumnar junction (SCJ) is often described as serrated with short projections of columnar mucosa that extend into the esophagus. As studies of the normal SCJ are sparse, the aim of this study was to test the hypothesis that the normal SCJ is even and that irregularities are manifestations of acid reflux. Fifty asymptomatic subjects and 149 patients with symptoms suggestive of gastroesophageal reflux disease underwent endoscopy and 48-h pH monitoring with a pH electrode positioned immediately above the SCJ. The shape of the SCJ was assessed according to the Z-line appearance classification and correlated with clinical characteristics and the degree of esophageal acid exposure in the most distal esophagus. Even SCJs without irregularities were significantly more common in asymptomatic subjects compared with patients (50% versus 10%, p < .001) and were never found in patients with erosive esophagitis. The median degree of distal esophageal acid exposure in individuals with an even SCJ was within normal limits. With increasing degree of irregularity of the SCJ, the frequency and duration of reflux episodes, the degree of distal esophageal acid exposure, and the prevalence of abnormal acid exposure increased progressively and significantly. The shape of the normal SCJ is even and also minimal irregularities are a consequence of acid reflux, likely due to the formation of small areas of metaplastic columnar mucosa.

Functional asymmetry and plasticity of electrical synapses interconnecting neurons through a 36-state model of gap junction channel gating

PubMed Central

Kraujalis, Tadas; Maciunas, Kestutis

2017-01-01

We combined the Hodgkin–Huxley equations and a 36-state model of gap junction channel gating to simulate electrical signal transfer through electrical synapses. Differently from most previous studies, our model can account for dynamic modulation of junctional conductance during the spread of electrical signal between coupled neurons. The model of electrical synapse is based on electrical properties of the gap junction channel encompassing two fast and two slow gates triggered by the transjunctional voltage. We quantified the influence of a difference in input resistances of electrically coupled neurons and instantaneous conductance–voltage rectification of gap junctions on an asymmetry of cell-to-cell signaling. We demonstrated that such asymmetry strongly depends on junctional conductance and can lead to the unidirectional transfer of action potentials. The simulation results also revealed that voltage spikes, which develop between neighboring cells during the spread of action potentials, can induce a rapid decay of junctional conductance, thus demonstrating spiking activity-dependent short-term plasticity of electrical synapses. This conclusion was supported by experimental data obtained in HeLa cells transfected with connexin45, which is among connexin isoforms expressed in neurons. Moreover, the model allowed us to replicate the kinetics of junctional conductance under different levels of intracellular concentration of free magnesium ([Mg2+]i), which was experimentally recorded in cells expressing connexin36, a major neuronal connexin. We demonstrated that such [Mg2+]i-dependent long-term plasticity of the electrical synapse can be adequately reproduced through the changes of slow gate parameters of the 36-state model. This suggests that some types of chemical modulation of gap junctions can be executed through the underlying mechanisms of voltage gating. Overall, the developed model accounts for direction-dependent asymmetry, as well as for short- and long-term plasticity of electrical synapses. Our modeling results demonstrate that such complex behavior of the electrical synapse is important in shaping the response of coupled neurons. PMID:28384220

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

PubMed Central

Mustoe, Anthony M.; Brooks, Charles L.; Al-Hashimi, Hashim M.

2014-01-01

Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in higher order RNA junctions remains poorly understood. Here, we use a specialized coarse-grained molecular dynamics model to directly probe the thermodynamic contributions of topological constraints in defining the 3D architecture and dynamics of transfer RNA (tRNA). Topological constraints alone restrict tRNA's allowed conformational space by over an order of magnitude and strongly discriminate against formation of non-native tertiary contacts, providing a sequence independent source of folding specificity. Topological constraints also give rise to long-range correlations between the relative orientation of tRNA's helices, which in turn provides a mechanism for encoding thermodynamic cooperativity between distinct tertiary interactions. These aspects of topological constraints make it such that only several tertiary interactions are needed to confine tRNA to its native global structure and specify functionally important 3D dynamics. We further show that topological constraints are conserved across tRNA's different naturally occurring secondary structures. Taken together, our results emphasize the central role of secondary-structure-encoded topological constraints in defining RNA 3D structure, dynamics and folding. PMID:25217593

Ca2+-associated triphasic pH changes in mitochondria during brown adipocyte activation.

PubMed

Hou, Yanyan; Kitaguchi, Tetsuya; Kriszt, Rókus; Tseng, Yu-Hua; Raghunath, Michael; Suzuki, Madoka

2017-08-01

Brown adipocytes (BAs) are endowed with a high metabolic capacity for energy expenditure due to their high mitochondria content. While mitochondrial pH is dynamically regulated in response to stimulation and, in return, affects various metabolic processes, how mitochondrial pH is regulated during adrenergic stimulation-induced thermogenesis is unknown. We aimed to reveal the spatial and temporal dynamics of mitochondrial pH in stimulated BAs and the mechanisms behind the dynamic pH changes. A mitochondrial targeted pH-sensitive protein, mito-pHluorin, was constructed and transfected to BAs. Transfected BAs were stimulated by an adrenergic agonist, isoproterenol. The pH changes in mitochondria were characterized by dual-color imaging with indicators that monitor mitochondrial membrane potential and heat production. The mechanisms of pH changes were studied by examining the involvement of electron transport chain (ETC) activity and Ca 2+ profiles in mitochondria and the intracellular Ca 2+ store, the endoplasmic reticulum (ER). A triphasic mitochondrial pH change in BAs upon adrenergic stimulation was revealed. In comparison to a thermosensitive dye, we reveal that phases 1 and 2 of the pH increase precede thermogenesis, while phase 3, characterized by a pH decrease, occurs during thermogenesis. The mechanism of pH increase is partially related to ETC. In addition, the pH increase occurs concurrently with an increase in mitochondrial Ca 2+ . This Ca 2+ increase is contributed to by an influx from the ER, and it is further involved in mitochondrial pH regulation. We demonstrate that an increase in mitochondrial pH is implicated as an early event in adrenergically stimulated BAs. We further suggest that this pH increase may play a role in the potentiation of thermogenesis.

Diurnal cycles control the fate of contaminants at an Andean river confluence impacted by legacy mining

NASA Astrophysics Data System (ADS)

Pasten, P.; Guerra, P. A.; Simonson, K.; Bonilla, C.; Pizarro, G. E.; Escauriaza, C. R.; González, C.

2014-12-01

The importance of hydrologic-geochemical interactions in arid environments is a controlling factor in quality and quantity of water available for human consumption and agriculture. When acid drainage affects these watersheds, water quality is gravely degraded. Despite its effect on watersheds, the relationship between time changes in hydrological variables and water quality in arid regions has not been studied thoroughly. Temporal variations in acid drainage can control when the transport of toxic elements is increased. We performed field work at the Azufre River (pH 2, E.C~10.9 mS/cm) and Caracarani River (pH 8.7, E.C~1.2 mS/cm) confluence, located in the Northern Chilean Altiplano (at 4000 m asl). We registered stream flowrates (total flowrate~430 L/s), temperature and electric conductivity (E.C) hourly using in-stream data loggers during one year. We also measured turbidity and pH during one field survey at different distances from the junction, as a proxy of the formation of iron-aluminum particles that cycle trace elements in these environments. We found turbidity-pH diurnal cycles were caused by upstream hourly changes in upstream flowrate: when the Caracarani River flowrate reached its daily peak, particle formation occurred, while the dissolution of particles occurred when the Azufre River reached its maximum value. This last process occurred due to upstream freeze-thaw cycles. This study shows how the dynamics of natural confluences determines chemical transport. The formation of particles enriched in toxic elements can promote settling as a natural attenuation process, while their dissolution will produce their release and transport long distances downstream. It is important to consider time as an important variable in water quality monitoring and in water management infrastructure where pulses of contamination can have potentially negative effects in its use. Acknowledgements: Funding was provided by "Proyecto Fondecyt 1130936" and "CONICYT/FONDAP 15110020".

Synchronous Bioimaging of Intracellular pH and Chloride Based on LSS Fluorescent Protein.

PubMed

Paredes, Jose M; Idilli, Aurora I; Mariotti, Letizia; Losi, Gabriele; Arslanbaeva, Lyaysan R; Sato, Sebastian Sulis; Artoni, Pietro; Szczurkowska, Joanna; Cancedda, Laura; Ratto, Gian Michele; Carmignoto, Giorgio; Arosio, Daniele

2016-06-17

Ion homeostasis regulates critical physiological processes in the living cell. Intracellular chloride concentration not only contributes in setting the membrane potential of quiescent cells but it also plays a role in modulating the dynamic voltage changes during network activity. Dynamic chloride imaging demands new tools, allowing faster acquisition rates and correct accounting of concomitant pH changes. Joining a long-Stokes-shift red-fluorescent protein to a GFP variant with high sensitivity to pH and chloride, we obtained LSSmClopHensor, a genetically encoded fluorescent biosensor optimized for the simultaneous chloride and pH imaging and requiring only two excitation wavelengths (458 and 488 nm). LSSmClopHensor allowed us to monitor the dynamic changes of intracellular pH and chloride concentration during seizure like discharges in neocortical brain slices. Only cells with tightly controlled resting potential revealed a narrow distribution of chloride concentration peaking at about 5 and 8 mM, in neocortical neurons and SK-N-SH cells, respectively. We thus showed that LSSmClopHensor represents a new versatile tool for studying the dynamics of chloride and proton concentration in living systems.

Low-noise current amplifier based on mesoscopic Josephson junction.

PubMed

Delahaye, J; Hassel, J; Lindell, R; Sillanpää, M; Paalanen, M; Seppä, H; Hakonen, P

2003-02-14

We used the band structure of a mesoscopic Josephson junction to construct low-noise amplifiers. By taking advantage of the quantum dynamics of a Josephson junction, i.e., the interplay of interlevel transitions and the Coulomb blockade of Cooper pairs, we created transistor-like devices, Bloch oscillating transistors, with considerable current gain and high-input impedance. In these transistors, the correlated supercurrent of Cooper pairs is controlled by a small base current made up of single electrons. Our devices reached current and power gains on the order of 30 and 5, respectively. The noise temperature was estimated to be around 1 kelvin, but noise temperatures of less than 0.1 kelvin can be realistically achieved. These devices provide quantum-electronic building blocks that will be useful at low temperatures in low-noise circuit applications with an intermediate impedance level.

Phase dynamics of single long Josephson junction in MgB2 superconductor

NASA Astrophysics Data System (ADS)

Chimouriya, Shanker Pd.; Ghimire, Bal Ram; Kim, Ju H.

2018-05-01

A system of perturbed sine Gordon equations is derived to a superconductor-insulator-superconductor (SIS) long Joseph-son junction as an extension of the Ambegaokar-Baratoff relation, following the long route of path integral formalism. A computer simulation is performed by discretizing the equations using finite difference approximation and applied to the MgB2 superconductor with SiO2 as the junction material. The solution of unperturbed sG equation is taken as the initial profile for the simulation and observed how the perturbation terms play the role to modify it. It is found initial profile deformed as time goes on. The variation of total Josephson current has also been observed. It is found that, the perturbation terms play the role for phase frustration. The phase frustration achieves quicker for high tunneling current.

Nanomechanical DNA origami pH sensors.

PubMed

Kuzuya, Akinori; Watanabe, Ryosuke; Yamanaka, Yusei; Tamaki, Takuya; Kaino, Masafumi; Ohya, Yuichi

2014-10-16

Single-molecule pH sensors have been developed by utilizing molecular imaging of pH-responsive shape transition of nanomechanical DNA origami devices with atomic force microscopy (AFM). Short DNA fragments that can form i-motifs were introduced to nanomechanical DNA origami devices with pliers-like shape (DNA Origami Pliers), which consist of two levers of 170-nm long and 20-nm wide connected at a Holliday-junction fulcrum. DNA Origami Pliers can be observed as in three distinct forms; cross, antiparallel and parallel forms, and cross form is the dominant species when no additional interaction is introduced to DNA Origami Pliers. Introduction of nine pairs of 12-mer sequence (5'-AACCCCAACCCC-3'), which dimerize into i-motif quadruplexes upon protonation of cytosine, drives transition of DNA Origami Pliers from open cross form into closed parallel form under acidic conditions. Such pH-dependent transition was clearly imaged on mica in molecular resolution by AFM, showing potential application of the system to single-molecular pH sensors.

A novel mutation in the AGXT gene causing primary hyperoxaluria type I: genotype-phenotype correlation.

PubMed

M'Dimegh, Saoussen; Aquaviva-Bourdain, Cécile; Omezzine, Asma; M'Barek, Ibtihel; Souche, Geneviéve; Zellama, Dorsaf; Abidi, Kamel; Achour, Abdelattif; Gargah, Tahar; Abroug, Saoussen; Bouslama, Ali

2016-09-01

Primary hyperoxaluria type I (PH1) is an autosomal recessive metabolic disorder caused by inherited mutations in the AGXT gene encoding liver peroxisomal alanine : glyoxylate aminotransferase (AGT) which is deficient or mistargeted to mitochondria. PH1 shows considerable phenotypic and genotypic heterogeneity. The incidence and severity of PH1 varies in different geographic regions. DNA samples of the affected members from two unrelated Tunisian families were tested by amplifying and sequencing each of the AGXT exons and intron-exon junctions. We identified a novel frameshift mutation in the AGXT gene, the c.406_410dupACTGC resulting in a truncated protein (p.Gln137Hisfs*19). It is found in homozygous state in two nonconsanguineous unrelated families from Tunisia. These molecular findings provide genotype/phenotype correlations in the intrafamilial phenotypic and permit accurate carrier detection, and prenatal diagnosis. The novel p.Gln137Hisfs*19 mutation detected in our study extend the spectrum of known AGXT gene mutations in Tunisia.

Effect of baclofen on the acid pocket at the gastroesophageal junction.

PubMed

Scarpellini, E; Boecxstaens, V; Farré, R; Bisschops, R; Dewulf, D; Gasbarrini, A; Pauwels, A; Blondeau, K; Tack, J

2015-07-01

Previous studies established that a pocket of highly acidic gastric juice is present postprandially at the gastroesophageal junction in man. The GABA-B agonist baclofen inhibits postprandial reflux events through its effects on the lower esophageal sphincter (LES). The aim of the current study was to investigate whether baclofen would affect the location and the extent of the postprandial acid pocket in healthy volunteers. Twelve healthy volunteers underwent acid pocket studies on two different occasions, at least 1 week apart. LES position was determined preprandially with pull-through manometry. Dual pH electrode and manometry probe stepwise pull-through (1 cm/minute, LES-10 to +5 cm) was performed at 30-minute intervals for 150 minutes, with administration of placebo or baclofen 40 mg after the first and ingestion of a liquid meal after the second pull-through. After placebo, a significant drop in intragastric gastric pH was present at the gastroesophageal junction after the meal, reflecting the acid pocket, and this was associated with a drop in LES pressure. Baclofen did not affect the presence of the acid pocket, but prevented the postprandial drop in LES pressure, and the extent of the acid pocket above the upper margin of the manometrically located LES was significantly decreased by baclofen (1.6 ± 0.7 vs. 0.3 ± 0.4 cm at 60 minutes, 2.2 ± 0.6 vs. 0.2 ± 0.6 at 90 minutes, and 1.5 ± 0.5 vs. 0.7 ± 0.7 cm at 120 minutes, all P < 0.05). Baclofen does not alter the intragastric acid pocket, but limits its extension into the distal esophagus, probably through an increase in postprandial LES pressure. © 2014 International Society for Diseases of the Esophagus.

A miniature integrated multimodal sensor for measuring pH, EC and temperature for precision agriculture.

PubMed

Futagawa, Masato; Iwasaki, Taichi; Murata, Hiroaki; Ishida, Makoto; Sawada, Kazuaki

2012-01-01

Making several simultaneous measurements with different kinds of sensors at the same location in a solution is difficult because of crosstalk between the sensors. In addition, because the conditions at different locations in plant beds differ, in situ measurements in agriculture need to be done in small localized areas. We have fabricated a multimodal sensor on a small Si chip in which a pH sensor was integrated with electrical conductivity (EC) and temperature sensors. An ISFET with a Si(3)N(4) membrane was used for the pH sensor. For the EC sensor, the electrical conductivity between platinum electrodes was measured, and the temperature sensor was a p-n junction diode. These are some of the most important measurements required for controlling the conditions in plant beds. The multimodal sensor can be inserted into a plant bed for in situ monitoring. To confirm the absence of crosstalk between the sensors, we made simultaneous measurements of pH, EC, and temperature of a pH buffer solution in a plant bed. When the solution was diluted with hot or cold water, the real time measurements showed changes to the EC and temperature, but no change in pH. We also demonstrated that our sensor was capable of simultaneous in situ measurements in rock wool without being affected by crosstalk.

A Miniature Integrated Multimodal Sensor for Measuring pH, EC and Temperature for Precision Agriculture

PubMed Central

Futagawa, Masato; Iwasaki, Taichi; Murata, Hiroaki; Ishida, Makoto; Sawada, Kazuaki

2012-01-01

Making several simultaneous measurements with different kinds of sensors at the same location in a solution is difficult because of crosstalk between the sensors. In addition, because the conditions at different locations in plant beds differ, in situ measurements in agriculture need to be done in small localized areas. We have fabricated a multimodal sensor on a small Si chip in which a pH sensor was integrated with electrical conductivity (EC) and temperature sensors. An ISFET with a Si3N4 membrane was used for the pH sensor. For the EC sensor, the electrical conductivity between platinum electrodes was measured, and the temperature sensor was a p-n junction diode. These are some of the most important measurements required for controlling the conditions in plant beds. The multimodal sensor can be inserted into a plant bed for in situ monitoring. To confirm the absence of crosstalk between the sensors, we made simultaneous measurements of pH, EC, and temperature of a pH buffer solution in a plant bed. When the solution was diluted with hot or cold water, the real time measurements showed changes to the EC and temperature, but no change in pH. We also demonstrated that our sensor was capable of simultaneous in situ measurements in rock wool without being affected by crosstalk. PMID:22969403

Spectrophotometric Calibration of pH Electrodes in Seawater Using Purified m-Cresol Purple

PubMed Central

2012-01-01

This work examines the use of purified meta-cresol purple (mCP) for direct spectrophotometric calibration of glass pH electrodes in seawater. The procedures used in this investigation allow for simple, inexpensive electrode calibrations over salinities of 20–40 and temperatures of 278.15–308.15 K without preparation of synthetic Tris seawater buffers. The optimal pH range is ∼7.0–8.1. Spectrophotometric calibrations enable straightforward, quantitative distinctions between Nernstian and non-Nernstian electrode behavior. For the electrodes examined in this study, both types of behavior were observed. Furthermore, calibrations performed in natural seawater allow direct determination of the influence of salinity on electrode performance. The procedures developed in this study account for salinity-induced variations in liquid junction potentials that, if not taken into account, would create pH inconsistencies of 0.028 over a 10-unit change in salinity. Spectrophotometric calibration can also be used to expeditiously determine the intercept potential (i.e., the potential corresponding to pH 0) of an electrode that has reliably demonstrated Nernstian behavior. Titrations to ascertain Nernstian behavior and salinity effects can be undertaken relatively infrequently (∼weekly to monthly). One-point determinations of intercept potential should be undertaken frequently (∼daily) to monitor for stable electrode behavior and ensure accurate potentiometric pH determinations. PMID:22463815

Gap-junction coupling and ATP-sensitive potassium channels in human β -cell clusters: Effects on emergent dynamics

NASA Astrophysics Data System (ADS)

Loppini, A.; Pedersen, M. G.; Braun, M.; Filippi, S.

2017-09-01

The importance of gap-junction coupling between β cells in pancreatic islets is well established in mouse. Such ultrastructural connections synchronize cellular activity, confine biological heterogeneity, and enhance insulin pulsatility. Dysfunction of coupling has been associated with diabetes and altered β -cell function. However, the role of gap junctions between human β cells is still largely unexplored. By using patch-clamp recordings of β cells from human donors, we previously estimated electrical properties of these channels by mathematical modeling of pairs of human β cells. In this work we revise our estimate by modeling triplet configurations and larger heterogeneous clusters. We find that a coupling conductance in the range 0.005 -0.020 nS/pF can reproduce experiments in almost all the simulated arrangements. We finally explore the consequence of gap-junction coupling of this magnitude between β cells with mutant variants of the ATP-sensitive potassium channels involved in some metabolic disorders and diabetic conditions, translating studies performed on rodents to the human case. Our results are finally discussed from the perspective of therapeutic strategies. In summary, modeling of more realistic clusters with more than two β cells slightly lowers our previous estimate of gap-junction conductance and gives rise to patterns that more closely resemble experimental traces.

MicroRNA Intercellular Transfer and Bioelectrical Regulation of Model Multicellular Ensembles by the Gap Junction Connectivity.

PubMed

Cervera, Javier; Meseguer, Salvador; Mafe, Salvador

2017-08-17

We have studied theoretically the microRNA (miRNA) intercellular transfer through voltage-gated gap junctions in terms of a biophysically grounded system of coupled differential equations. Instead of modeling a specific system, we use a general approach describing the interplay between the genetic mechanisms and the single-cell electric potentials. The dynamics of the multicellular ensemble are simulated under different conditions including spatially inhomogeneous transcription rates and local intercellular transfer of miRNAs. These processes result in spatiotemporal changes of miRNA, mRNA, and ion channel protein concentrations that eventually modify the bioelectrical states of small multicellular domains because of the ensemble average nature of the electrical potential. The simulations allow a qualitative understanding of the context-dependent nature of the effects observed when specific signaling molecules are transferred through gap junctions. The results suggest that an efficient miRNA intercellular transfer could permit the spatiotemporal control of small cellular domains by the conversion of single-cell genetic and bioelectric states into multicellular states regulated by the gap junction interconnectivity.

SQUID magnetometers for low-frequency applications

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

Ryhaenen, T.; Seppae, H.; Ilmoniemi, R.

1989-09-01

The authors present a novel formulation for SQUID operation, which enables them to evaluate and compare the sensitivity and applicability of different devices. SQUID magnetometers for low-frequency applications are analyzed, taking into account the coupling circuits and electronics. They discuss nonhysteretic and hysteretic single-junction rf SQUIDs, but the main emphasis is on the dynamics, sensitivity, and coupling considerations of dc-SQUID magnetometers. A short review of current ideas on thin-film, dc-SQUID design presents the problems in coupling and the basic limits of sensitivity. The fabrication technology of tunnel-junction devices is discussed with emphasis on how it limits critical current densities, specificmore » capacitances of junctions, minimum linewidths, conductor separations, etc. Properties of high-temperature superconductors are evaluated on the basis of recently published results on increased flux creep, low density of current carriers, and problems in fabricating reliable junctions. The optimization of electronics for different types of SQUIDs is presented. Finally, the most important low-frequency applications of SQUIDs in biomagnetism, metrology, geomagnetism, and some physics experiments demonstrate the various possibilities that state-of-the-art SQUIDs can provide.« less

Direct determination of minority carrier diffusion lengths at axial GaAs nanowire p-n junctions.

PubMed

Gutsche, Christoph; Niepelt, Raphael; Gnauck, Martin; Lysov, Andrey; Prost, Werner; Ronning, Carsten; Tegude, Franz-Josef

2012-03-14

Axial GaAs nanowire p-n diodes, possibly one of the core elements of future nanowire solar cells and light emitters, were grown via the Au-assisted vapor-liquid-solid mode, contacted by electron beam lithography, and investigated using electron beam induced current measurements. The minority carrier diffusion lengths and dynamics of both, electrons and holes, were determined directly at the vicinity of the p-n junction. The generated photocurrent shows an exponential decay on both sides of the junction and the extracted diffusion lengths are about 1 order of magnitude lower compared to bulk material due to surface recombination. Moreover, the observed strong diameter-dependence is well in line with the surface-to-volume ratio of semiconductor nanowires. Estimating the surface recombination velocities clearly indicates a nonabrupt p-n junction, which is in essential agreement with the model of delayed dopant incorporation in the Au-assisted vapor-liquid-solid mechanism. Surface passivation using ammonium sulfide effectively reduces the surface recombination and thus leads to higher minority carrier diffusion lengths. © 2012 American Chemical Society

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.

PubMed

Chen, Wei; Shen, Jana K

2014-10-15

Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma. Copyright © 2014 Wiley Periodicals, Inc.

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics †

PubMed Central

Chen, Wei; Shen, Jana K.

2014-01-01

Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: 1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? 2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK a values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via co-titrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle-mesh Ewald, considering the known artifacts due to charge-compensating background plasma. PMID:25142416

Actin cable dynamics and Rho/Rock orchestrate a polarized cytoskeletal architecture in the early steps of assembling a stratified epithelium.

PubMed

Vaezi, Alec; Bauer, Christoph; Vasioukhin, Valeri; Fuchs, Elaine

2002-09-01

To enable stratification and barrier function, the epidermis must permit self-renewal while maintaining adhesive connections. By generating K14-GFP-actin mice to monitor actin dynamics in cultured primary keratinocytes, we uncovered a role for the actin cytoskeleton in establishing cellular organization. During epidermal sheet formation, a polarized network of nascent intercellular junctions and radial actin cables assemble in the apical plane of the monolayer. These actin fibers anchor to a central actin-myosin network, creating a tension-based plane of cytoskeleton across the apical surface of the sheet. Movement of the sheet surface relative to its base expands the zone of intercellular overlap, catalyzing new sites for nascent intercellular junctions. This polarized cytoskeleton is dependent upon alpha-catenin, Rho, and Rock, and its regulation may be important for wound healing and/or stratification, where coordinated tissue movements are involved.

Regulation of tight junction permeability with switch-like speed.

PubMed

Beyenbach, Klaus W

2003-09-01

The case is made that tight junctions can undergo large reversible conductance changes in a matter of seconds and yet preserve their permselectivity. The diuretic peptide leucokinin transforms (renal) Malpighian tubules of the yellow fever mosquito from a moderately tight epithelium to a leaky epithelium by increasing the chloride-conductance of the paracellular shunt pathway. The nine-fold increase in the paracellular chloride-conductance brings about a non-selective stimulation of transepithelial sodium chloride and potassium chloride secretion, as expected from a conductance increase in the pathway taken by the counterion of sodium and potassium. The leucokinin signaling pathway consists in part of a receptor coupled G-protein, phospholipase C, inositol-1,4,5-trisphosphate, and increased intracellular calcium concentration that bring about the increase in the paracellular, tight junction chloride-conductance. As the conductance of the tight junction pathway increases it becomes more selective for the transepithelial passage of chloride. Epithelial cells in Malpighian tubules taper to tight junctions at their lateral edges exposing them directly to apical and serosal solutions. Furthermore, evolutionary pressures to excrete salt and water at high rates without the aid of glomerular filtration have led to powerful mechanisms of tubular secretion, capable of diuresis when the mosquito is challenged with the volume expansion of a blood meal. The tubular diuresis is mediated in part by increasing the paracellular chloride conductance. Thus, anatomical and physiological specializations in Malpighian tubules combine to yield the evidence for the dynamic hormonal regulation of the tight junction pathway.

Spatiotemporal pH dynamics in concentration polarization near ion-selective membranes.

PubMed

Andersen, Mathias B; Rogers, David M; Mai, Junyu; Schudel, Benjamin; Hatch, Anson V; Rempe, Susan B; Mani, Ali

2014-07-08

We present a detailed analysis of the transient pH dynamics for a weak, buffered electrolyte subject to voltage-driven transport through an ion-selective membrane. We show that pH fronts emanate from the concentration polarization zone next to the membrane and that these propagating fronts change the pH in the system several units from its equilibrium value. The analysis is based on a 1D model using the unsteady Poisson-Nernst-Planck equations with nonequilibrium chemistry and without assumptions of electroneutrality or asymptotically thin electric double layers. Nonequilibrium chemical effects, especially for water splitting, are shown to be important for the dynamical and spatiotemporal evolution of the pH fronts. Nonetheless, the model also shows that at steady state the assumption of chemical equilibrium can still lead to good approximations of the global pH distribution. Moreover, our model shows that the transport of the hydronium ion in the extended space charge region is governed by a balance between electromigration and water self-ionization. On the basis of this observation, we present a simple model showing that the net flux of the hydronium ion is proportional to the length of the extended space charge region and the water self-ionization rate. To demonstrate these effects in practice, we have adopted the experiment of Mai et al. (Mai, J.; Miller, H.; Hatch, A. V. Spatiotemporal Mapping of Concentration Polarization Induced pH Changes at Nanoconstrictions. ACS Nano 2012, 6, 10206) as a model problem, and by including the full chemistry and transport, we show that the present model can capture the experimentally observed pH fronts. Our model can, among other things, be used to predict and engineer pH dynamics, which can be essential to the performance of membrane-based systems for biochemical separation and analysis.

GSK3- and PRMT-1–dependent modifications of desmoplakin control desmoplakin–cytoskeleton dynamics

PubMed Central

Albrecht, Lauren V.; Zhang, Lichao; Shabanowitz, Jeffrey; Purevjav, Enkhsaikhan; Towbin, Jeffrey A.; Hunt, Donald F.

2015-01-01

Intermediate filament (IF) attachment to intercellular junctions is required for skin and heart integrity, but how the strength and dynamics of this attachment are modulated during normal and pathological remodeling is poorly understood. We show that glycogen synthase kinase 3 (GSK3) and protein arginine methyltransferase 1 (PRMT-1) cooperate to orchestrate a series of posttranslational modifications on the IF-anchoring protein desmoplakin (DP) that play an essential role in coordinating cytoskeletal dynamics and cellular adhesion. Front-end electron transfer dissociation mass spectrometry analyses of DP revealed six novel serine phosphorylation sites dependent on GSK3 signaling and four novel arginine methylation sites including R2834, the mutation of which has been associated with arrhythmogenic cardiomyopathy (AC). Inhibition of GSK3 or PRMT-1 or overexpression of the AC-associated mutant R2834H enhanced DP–IF associations and delayed junction assembly. R2834H blocked the GSK3 phosphorylation cascade and reduced DP–GSK3 interactions in cultured keratinocytes and in the hearts of transgenic R2834H DP mice. Interference with this regulatory machinery may contribute to skin and heart diseases. PMID:25733715

Short-time dynamics of molecular junctions after projective measurement

NASA Astrophysics Data System (ADS)

Tang, Gaomin; Xing, Yanxia; Wang, Jian

2017-08-01

In this work, we study the short-time dynamics of a molecular junction described by Anderson-Holstein model using full-counting statistics after projective measurement. The coupling between the central quantum dot (QD) and two leads was turned on at remote past and the system is evolved to steady state at time t =0 , when we perform the projective measurement in one of the lead. Generating function for the charge transfer is expressed as a Fredholm determinant in terms of Keldysh nonequilibrium Green's function in the time domain. It is found that the current is not constant at short times indicating that the measurement does perturb the system. We numerically compare the current behaviors after the projective measurement with those in the transient regime where the subsystems are connected at t =0 . The universal scaling for high-order cumulants is observed for the case with zero QD occupation due to the unidirectional transport at short times. The influences of electron-phonon interaction on short-time dynamics of electric current, shot noise, and differential conductance are analyzed.

Terahertz Josephson spectral analysis and its applications

NASA Astrophysics Data System (ADS)

Snezhko, A. V.; Gundareva, I. I.; Lyatti, M. V.; Volkov, O. Y.; Pavlovskiy, V. V.; Poppe, U.; Divin, Y. Y.

2017-04-01

Principles of Hilbert-transform spectral analysis (HTSA) are presented and advantages of the technique in the terahertz (THz) frequency range are discussed. THz HTSA requires Josephson junctions with high values of characteristic voltages I c R n and dynamics described by a simple resistively shunted junction (RSJ) model. To meet these requirements, [001]- and [100]-tilt YBa2Cu3O7-x bicrystal junctions with deviations from the RSJ model less than 1% have been developed. Demonstrators of Hilbert-transform spectrum analyzers with various cryogenic environments, including integration into Stirling coolers, are described. Spectrum analyzers have been characterized in the spectral range from 50 GHz to 3 THz. Inside a power dynamic range of five orders, an instrumental function of the analyzers has been found to have a Lorentz form around a single frequency of 1.48 THz with a spectral resolution as low as 0.9 GHz. Spectra of THz radiation from optically pumped gas lasers and semiconductor frequency multipliers have been studied with these spectrum analyzers and the regimes of these radiation sources were optimized for a single-frequency operation. Future applications of HTSA will be related with quick and precise spectral characterization of new radiation sources and identification of substances in the THz frequency range.

Modelling wound closure in an epithelial cell sheet using the cellular Potts model.

PubMed

Noppe, Adrian R; Roberts, Anthony P; Yap, Alpha S; Gomez, Guillermo A; Neufeld, Zoltan

2015-10-01

We use a two-dimensional cellular Potts model to represent the behavior of an epithelial cell layer and describe its dynamics in response to a microscopic wound. Using an energy function to describe properties of the cells, we found that the interaction between contractile tension along cell-cell junctions and cell-cell adhesion plays an important role not only in determining the dynamics and morphology of cells in the monolayer, but also in influencing whether or not a wound in the monolayer will close. Our results suggest that, depending on the balance between cell-cell adhesion and junctional tension, mechanics of the monolayer can either correspond to a hard or a soft regime that determines cell morphology and polygonal organization in the monolayer. Moreover, the presence of a wound in a hard regime, where junctional tension is significant, can lead to two results: (1) wound closure or (2) an initial increase and expansion of the wound area towards an equilibrium value. Theoretical approximations and simulations allowed us to determine the thresholds in the values of cell-cell adhesion and initial wound size that allow the system to lead to wound closure. Overall, our results suggest that around the site of injury, changes in the balance between contraction and adhesion determine whether or not non-monotonous wound closure occurs.

Ultralow power artificial synapses using nanotextured magnetic Josephson junctions.

PubMed

Schneider, Michael L; Donnelly, Christine A; Russek, Stephen E; Baek, Burm; Pufall, Matthew R; Hopkins, Peter F; Dresselhaus, Paul D; Benz, Samuel P; Rippard, William H

2018-01-01

Neuromorphic computing promises to markedly improve the efficiency of certain computational tasks, such as perception and decision-making. Although software and specialized hardware implementations of neural networks have made tremendous accomplishments, both implementations are still many orders of magnitude less energy efficient than the human brain. We demonstrate a new form of artificial synapse based on dynamically reconfigurable superconducting Josephson junctions with magnetic nanoclusters in the barrier. The spiking energy per pulse varies with the magnetic configuration, but in our demonstration devices, the spiking energy is always less than 1 aJ. This compares very favorably with the roughly 10 fJ per synaptic event in the human brain. Each artificial synapse is composed of a Si barrier containing Mn nanoclusters with superconducting Nb electrodes. The critical current of each synapse junction, which is analogous to the synaptic weight, can be tuned using input voltage spikes that change the spin alignment of Mn nanoclusters. We demonstrate synaptic weight training with electrical pulses as small as 3 aJ. Further, the Josephson plasma frequencies of the devices, which determine the dynamical time scales, all exceed 100 GHz. These new artificial synapses provide a significant step toward a neuromorphic platform that is faster, more energy-efficient, and thus can attain far greater complexity than has been demonstrated with other technologies.

Ultralow power artificial synapses using nanotextured magnetic Josephson junctions

PubMed Central

Schneider, Michael L.; Donnelly, Christine A.; Russek, Stephen E.; Baek, Burm; Pufall, Matthew R.; Hopkins, Peter F.; Dresselhaus, Paul D.; Benz, Samuel P.; Rippard, William H.

2018-01-01

Neuromorphic computing promises to markedly improve the efficiency of certain computational tasks, such as perception and decision-making. Although software and specialized hardware implementations of neural networks have made tremendous accomplishments, both implementations are still many orders of magnitude less energy efficient than the human brain. We demonstrate a new form of artificial synapse based on dynamically reconfigurable superconducting Josephson junctions with magnetic nanoclusters in the barrier. The spiking energy per pulse varies with the magnetic configuration, but in our demonstration devices, the spiking energy is always less than 1 aJ. This compares very favorably with the roughly 10 fJ per synaptic event in the human brain. Each artificial synapse is composed of a Si barrier containing Mn nanoclusters with superconducting Nb electrodes. The critical current of each synapse junction, which is analogous to the synaptic weight, can be tuned using input voltage spikes that change the spin alignment of Mn nanoclusters. We demonstrate synaptic weight training with electrical pulses as small as 3 aJ. Further, the Josephson plasma frequencies of the devices, which determine the dynamical time scales, all exceed 100 GHz. These new artificial synapses provide a significant step toward a neuromorphic platform that is faster, more energy-efficient, and thus can attain far greater complexity than has been demonstrated with other technologies. PMID:29387787

Improvement of the Performance of an Electrocoagulation Process System Using Fuzzy Control of pH.

PubMed

Demirci, Yavuz; Pekel, Lutfiye Canan; Altinten, Ayla; Alpbaz, Mustafa

2015-12-01

The removal efficiencies of electrocoagulation (EC) systems are highly dependent on the initial value of pH. If an EC system has an acidic influent, the pH of the effluent increases during the treatment process; conversely, if such a system has an alkaline influent, the pH of the effluent decreases during the treatment process. Thus, changes in the pH of the wastewater affect the efficiency of the EC process. In this study, we investigated the dynamic effects of pH. To evaluate approaches for preventing increases in the pH of the system, the MATLAB/Simulink program was used to develop and evaluate an on-line computer-based system for pH control. The aim of this work was to study Proportional-Integral-Derivative (PID) control and fuzzy control of the pH of a real textile wastewater purification process using EC. The performances and dynamic behaviors of these two control systems were evaluated based on determinations of COD, colour, and turbidity removal efficiencies.

Development of RF Sensor Based on Two-cell SQUID

DTIC Science & Technology

2012-07-01

according to (8) is proportional to the reduced drive detuning, ωp0 is the resonant frequency for small oscillations, i.e. the plasma frequency of the...0/2 Φ= cnc IRπω (16) where Rn is the normal resistance of the Josephson junction in the SQUID, and L the inductance of the...17.7 μA, normal resistance 110.9 Ω, plasma frequency ωp 124 GHz and characteristic frequency 948 GHz. While the loop inductance of SQUID was 60 pH

The analysis of ion-selective field-effect transistor operation in chemical sensors

NASA Astrophysics Data System (ADS)

Hotra, Zenon; Holyaka, Roman; Hladun, Michael; Humenuk, Iryna

2003-09-01

In this paper we present the research results of influence of substrate potential in ion-selective field-effect transistors (ISFET) on output signal of chemical sensors, e.g. PH-meters. It is shown that the instability of substrate-source p-n junction bias in well-known chemical sensors, which use grounded reference electrode - ISFET gate, affect on sensor characteristics in negative way. The analytical description and research results of 'substrate effect' on ISFET characteristics are considered.

Generation of constant-amplitude radio-frequency sweeps at a tunnel junction for spin resonance STM

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

Paul, William; Lutz, Christopher P.; Heinrich, Andreas J.

2016-07-15

We describe the measurement and successful compensation of the radio-frequency transfer function of a scanning tunneling microscope over a wide frequency range (15.5–35.5 GHz) and with high dynamic range (>50 dB). The precise compensation of cabling resonances and attenuations is critical for the production of constant-voltage frequency sweeps for electric-field driven electron spin resonance (ESR) experiments. We also demonstrate that a well-calibrated tunnel junction voltage is necessary to avoid spurious ESR peaks that can arise due to a non-flat transfer function.

Markovian Dynamics of Josephson Parametric Amplification

NASA Astrophysics Data System (ADS)

Kaiser, Waldemar; Haider, Michael; Russer, Johannes A.; Russer, Peter; Jirauschek, Christian

2017-09-01

In this work, we derive the dynamics of the lossy DC pumped non-degenerate Josephson parametric amplifier (DCPJPA). The main element in a DCPJPA is the superconducting Josephson junction. The DC bias generates the AC Josephson current varying the nonlinear inductance of the junction. By this way the Josephson junction acts as the pump oscillator as well as the time varying reactance of the parametric amplifier. In quantum-limited amplification, losses and noise have an increased impact on the characteristics of an amplifier. We outline the classical model of the lossy DCPJPA and derive the available noise power spectral densities. A classical treatment is not capable of including properties like spontaneous emission which is mandatory in case of amplification at the quantum limit. Thus, we derive a quantum mechanical model of the lossy DCPJPA. Thermal losses are modeled by the quantum Langevin approach, by coupling the quantized system to a photon heat bath in thermodynamic equilibrium. The mode occupation in the bath follows the Bose-Einstein statistics. Based on the second quantization formalism, we derive the Heisenberg equations of motion of both resonator modes. We assume the dynamics of the system to follow the Markovian approximation, i.e. the system only depends on its actual state and is memory-free. We explicitly compute the time evolution of the contributions to the signal mode energy and give numeric examples based on different damping and coupling constants. Our analytic results show, that this model is capable of including thermal noise into the description of the DC pumped non-degenerate Josephson parametric amplifier.

Llgl1 Connects Cell Polarity with Cell-Cell Adhesion in Embryonic Neural Stem Cells.

PubMed

Jossin, Yves; Lee, Minhui; Klezovitch, Olga; Kon, Elif; Cossard, Alexia; Lien, Wen-Hui; Fernandez, Tania E; Cooper, Jonathan A; Vasioukhin, Valera

2017-06-05

Malformations of the cerebral cortex (MCCs) are devastating developmental disorders. We report here that mice with embryonic neural stem-cell-specific deletion of Llgl1 (Nestin-Cre/Llgl1 fl/fl ), a mammalian ortholog of the Drosophila cell polarity gene lgl, exhibit MCCs resembling severe periventricular heterotopia (PH). Immunohistochemical analyses and live cortical imaging of PH formation revealed that disruption of apical junctional complexes (AJCs) was responsible for PH in Nestin-Cre/Llgl1 fl/fl brains. While it is well known that cell polarity proteins govern the formation of AJCs, the exact mechanisms remain unclear. We show that LLGL1 directly binds to and promotes internalization of N-cadherin, and N-cadherin/LLGL1 interaction is inhibited by atypical protein kinase C-mediated phosphorylation of LLGL1, restricting the accumulation of AJCs to the basolateral-apical boundary. Disruption of the N-cadherin-LLGL1 interaction during cortical development in vivo is sufficient for PH. These findings reveal a mechanism responsible for the physical and functional connection between cell polarity and cell-cell adhesion machineries in mammalian cells. Copyright © 2017 Elsevier Inc. All rights reserved.

A test of the hypothesis that oxalate secretion produces proximal tubule crystallization in primary hyperoxaluria type I

PubMed Central

Evan, Andrew P.; Coe, Fredric L.; Lingeman, James E.; Krambeck, Amy; Sommers, Andre; Phillips, Carrie L.; Milliner, Dawn

2013-01-01

The sequence of events by which primary hyperoxaluria type 1 (PH1) causes renal failure is unclear. We hypothesize that proximal tubule (PT) is vulnerable because oxalate secretion raises calcium oxalate (CaOx) supersaturation (SS) there, leading to crystal formation and cellular injury. We studied cortical and papillary biopsies from two PH1 patients with preserved renal function, and seven native kidneys removed from four patients at the time of transplant, after short-term (2) or longer term (2) dialysis. In these patients, and another five PH1 patients without renal failure, we calculated oxalate secretion, and estimated PT CaOx SS. Plasma oxalate was elevated in all PH1 patients and inverse to creatinine clearance. Renal secretion of oxalate was present in all PH1 but rare in controls. PT CaOx SS was >1 in all nonpyridoxine-responsive PH1 before transplant and most marked in patients who developed end stage renal disease (ESRD). PT from PH1 with preserved renal function had birefringent crystals, confirming the presence of CaOx SS, but had no evidence of cortical inflammation or scarring by histopathology or hyaluronan staining. PH1 with short ESRD showed CaOx deposition and hyaluronan staining particularly at the corticomedullary junction in distal PT while cortical collecting ducts were spared. Longer ESRD showed widespread cortical CaOx, and in both groups papillary tissue had marked intratubular CaOx deposits and fibrosis. CaOx SS in PT causes CaOx crystal formation, and CaOx deposition in distal PT appears to be associated with ESRD. Minimizing PT CaOx SS may be important for preserving renal function in PH1. PMID:24089413

The inverse hall-petch relation in nanocrystalline metals: A discrete dislocation dynamics analysis

NASA Astrophysics Data System (ADS)

Quek, Siu Sin; Chooi, Zheng Hoe; Wu, Zhaoxuan; Zhang, Yong Wei; Srolovitz, David J.

2016-03-01

When the grain size in polycrystalline materials is reduced to the nanometer length scale (nanocrystallinity), observations from experiments and atomistic simulations suggest that the yield strength decreases (softening) as the grain size is decreased. This is in contrast to the Hall-Petch relation observed in larger sized grains. We incorporated grain boundary (GB) sliding and dislocation emission from GB junctions into the classical DDD framework, and recovered the smaller is weaker relationship observed in nanocrystalline materials. This current model shows that the inverse Hall-Petch behavior can be obtained through a relief of stress buildup at GB junctions from GB sliding by emitting dislocations from the junctions. The yield stress is shown to vary with grain size, d, by a d 1 / 2 relationship when grain sizes are very small. However, pure GB sliding alone without further plastic accomodation by dislocation emission is grain size independent.

Modeling Bloch oscillations in nanoscale Josephson junctions.

PubMed

Vora, Heli; Kautz, R L; Nam, S W; Aumentado, J

2017-08-01

Bloch oscillations in nanoscale Josephson junctions with a Coulomb charging energy comparable to the Josephson coupling energy are explored within the context of a model previously considered by Geigenmüller and Schön that includes Zener tunneling and treats quasiparticle tunneling as an explicit shot-noise process. The dynamics of the junction quasicharge are investigated numerically using both Monte Carlo and ensemble approaches to calculate voltage-current characteristics in the presence of microwaves. We examine in detail the origin of harmonic and subharmonic Bloch steps at dc biases I = ( n/m )2 ef induced by microwaves of frequency f and consider the optimum parameters for the observation of harmonic ( m = 1) steps. We also demonstrate that the GS model allows a detailed semiquantitative fit to experimental voltage-current characteristics previously obtained at the Chalmers University of Technology, confirming and strengthening the interpretation of the observed microwave-induced steps in terms of Bloch oscillations.

Modeling Bloch oscillations in nanoscale Josephson junctions

PubMed Central

Vora, Heli; Kautz, R. L.; Nam, S. W.; Aumentado, J.

2018-01-01

Bloch oscillations in nanoscale Josephson junctions with a Coulomb charging energy comparable to the Josephson coupling energy are explored within the context of a model previously considered by Geigenmüller and Schön that includes Zener tunneling and treats quasiparticle tunneling as an explicit shot-noise process. The dynamics of the junction quasicharge are investigated numerically using both Monte Carlo and ensemble approaches to calculate voltage-current characteristics in the presence of microwaves. We examine in detail the origin of harmonic and subharmonic Bloch steps at dc biases I = (n/m)2ef induced by microwaves of frequency f and consider the optimum parameters for the observation of harmonic (m = 1) steps. We also demonstrate that the GS model allows a detailed semiquantitative fit to experimental voltage-current characteristics previously obtained at the Chalmers University of Technology, confirming and strengthening the interpretation of the observed microwave-induced steps in terms of Bloch oscillations. PMID:29577106

Conductance enhancement due to interface magnons in electron-beam evaporated MgO magnetic tunnel junctions with CoFeB free layer deposited at different pressure

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

Guo, P.; Yu, G. Q.; Wei, H. X.

Electron-beam evaporated MgO-based magnetic tunnel junctions have been fabricated with the CoFeB free layer deposited at Ar pressure from 1 to 4 mTorr, and their tunneling process has been studied as a function of temperature and bias voltage. By changing the growth pressure, the junction dynamic conductance dI/dV, inelastic electron tunneling spectrum d²I/dV², and tunneling magnetoresistance vary with temperature. Moreover, the low-energy magnon cutoff energy E {sub C} derived from the conductance versus temperature curve agrees with interface magnon energy obtained directly from the inelastic electron tunneling spectrum, which demonstrates that interface magnons are involved in the electron tunneling process,more » opening an additional conductance channel and thus enhancing the total conductance.« less

Non-linear wave phenomena in Josephson elements for superconducting electronics

NASA Astrophysics Data System (ADS)

Christiansen, P. L.; Parmentier, R. D.; Skovgaard, O.

1985-07-01

The long and intermediate length Josephson tunnel junction oscillator with overlap geometry of linear and circular configuration, is investigated by computational solution of the perturbed sine-Gordon equation model and by experimental measurements. The model predicts the experimental results very well. Line oscillators as well as ring oscillators are treated. For long junctions soliton perturbation methods are developed and turn out to be efficient prediction tools, also providing physical understanding of the dynamics of the oscillator. For intermediate length junctions expansions in terms of linear cavity modes reduce computational costs. The narrow linewidth of the electromagnetic radiation (typically 1 kHz of a line at 10 GHz) is demonstrated experimentally. Corresponding computer simulations requiring a relative accuracy of less than 10 to the -7th power are performed on supercomputer CRAY-1-S. The broadening of linewidth due to external microradiation and internal thermal noise is determined.

Ventilatory effects of gap junction blockade in the RTN in awake rats.

PubMed

Hewitt, Amy; Barrie, Rachel; Graham, Michael; Bogus, Kara; Leiter, J C; Erlichman, Joseph S

2004-12-01

We tested the hypothesis that carbenoxolone, a pharmacological inhibitor of gap junctions, would reduce the ventilatory response to CO(2) when focally perfused within the retrotrapezoid nucleus (RTN). We tested this hypothesis by measuring minute ventilation (V(E)), tidal volume (V(T)), and respiratory frequency (F(R)) responses to increasing concentrations of inspired CO(2) (Fi(CO(2)) = 0-8%) in rats during wakefulness. We confirmed that the RTN was chemosensitive by perfusing the RTN unilaterally with either acetazolamide (AZ; 10 microM) or hypercapnic artificial cerebrospinal fluid equilibrated with 50% CO(2) (pH approximately 6.5). Focal perfusion of AZ or hypercapnic aCSF increased V(E), V(T), and F(R) during exposure to room air. Carbenoxolone (300 microM) focally perfused into the RTN decreased V(E) and V(T) in animals <11 wk of age, but V(E) and V(T) were increased in animals >12 wk of age. Glyzyrrhizic acid, a congener of carbenoxolone, did not change V(E), V(T), or F(R) when focally perfused into the RTN. Carbenoxolone binds to the mineralocorticoid receptor, but spironolactone (10 microM) did not block the disinhibition of V(E) or V(T) in older animals when combined with carbenoxolone. Thus the RTN is a CO(2) chemosensory site in all ages tested, but the function of gap junctions in the chemosensory process varies substantially among animals of different ages: gap junctions amplify the ventilatory response to CO(2) in younger animals, but appear to inhibit the ventilatory response to CO(2) in older animals.

Alternative splicing regulated by butyrate in bovine epithelial cells.

PubMed

Wu, Sitao; Li, Congjun; Huang, Wen; Li, Weizhong; Li, Robert W

2012-01-01

As a signaling molecule and an inhibitor of histone deacetylases (HDACs), butyrate exerts its impact on a broad range of biological processes, such as apoptosis and cell proliferation, in addition to its critical role in energy metabolism in ruminants. This study examined the effect of butyrate on alternative splicing in bovine epithelial cells using RNA-seq technology. Junction reads account for 11.28 and 12.32% of total mapped reads between the butyrate-treated (BT) and control (CT) groups. 201,326 potential splicing junctions detected were supported by ≥ 3 junction reads. Approximately 94% of these junctions conformed to the consensus sequence (GT/AG) while ~3% were GC/AG junctions. No AT/AC junctions were observed. A total of 2,834 exon skipping events, supported by a minimum of 3 junction reads, were detected. At least 7 genes, their mRNA expression significantly affected by butyrate, also had exon skipping events differentially regulated by butyrate. Furthermore, COL5A3, which was induced 310-fold by butyrate (FDR <0.001) at the gene level, had a significantly higher number of junction reads mapped to Exon#8 (Donor) and Exon#11 (Acceptor) in BT. This event had the potential to result in the formation of a COL5A3 mRNA isoform with 2 of the 69 exons missing. In addition, 216 differentially expressed transcript isoforms regulated by butyrate were detected. For example, Isoform 1 of ORC1 was strongly repressed by butyrate while Isoform 2 remained unchanged. Butyrate physically binds to and inhibits all zinc-dependent HDACs except HDAC6 and HDAC10. Our results provided evidence that butyrate also regulated deacetylase activities of classical HDACs via its transcriptional control. Moreover, thirteen gene fusion events differentially affected by butyrate were identified. Our results provided a snapshot into complex transcriptome dynamics regulated by butyrate, which will facilitate our understanding of the biological effects of butyrate and other HDAC inhibitors.

Dynamic electrical response of solar cells

NASA Technical Reports Server (NTRS)

Catani, J. P.

1981-01-01

The dynamic response of a solar generator is of primary importance as much for the design and development of electrical power conditioning hardware as for the analysis of electromagnetic compatibility. A mathematical model of photo-batteries was developed on the basis of impedance measurements performed under differing conditions of temperature, light intensity, before and after irradiation. This model was compared with that derived from PN junction theory and to static measurements. These dynamic measurements enabled the refinement of an integration method capable of determining, under normal laboratory conditions, the dynamic response of a generator to operational lighting conditions.

A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations

PubMed Central

Alberini, Giulio; Benfenati, Fabio

2017-01-01

Tight-junctions between epithelial cells of biological barriers are specialized molecular structures that regulate the flux of solutes across the barrier, parallel to cell walls. The tight-junction backbone is made of strands of transmembrane proteins from the claudin family, but the molecular mechanism of its function is still not completely understood. Recently, the crystal structure of a mammalian claudin-15 was reported, displaying for the first time the detailed features of transmembrane and extracellular domains. Successively, a structural model of claudin-15-based paracellular channels has been proposed, suggesting a putative assembly that illustrates how claudins associate in the same cell (via cis interactions) and across adjacent cells (via trans interactions). Although very promising, the model offers only a static conformation, with residues missing in the most important extracellular regions and potential steric clashes. Here we present detailed atomic models of paracellular single and double pore architectures, obtained from the putative assembly and refined via structural modeling and all-atom molecular dynamics simulations in double membrane bilayer and water environment. Our results show an overall stable configuration of the complex with a fluctuating pore size. Extracellular residue loops in trans interaction are able to form stable contacts and regulate the size of the pore, which displays a stationary radius of 2.5–3.0 Å at the narrowest region. The side-by-side interactions of the cis configuration are preserved via stable hydrogen bonds, already predicted by cysteine crosslinking experiments. Overall, this work introduces an improved version of the claudin-15-based paracellular channel model that strengthens its validity and that can be used in further computational studies to understand the structural features of tight-junctions regulation. PMID:28863193

Unique pH dynamics in GABAergic synaptic vesicles illuminates the mechanism and kinetics of GABA loading.

PubMed

Egashira, Yoshihiro; Takase, Miki; Watanabe, Shoji; Ishida, Junji; Fukamizu, Akiyoshi; Kaneko, Ryosuke; Yanagawa, Yuchio; Takamori, Shigeo

2016-09-20

GABA acts as the major inhibitory neurotransmitter in the mammalian brain, shaping neuronal and circuit activity. For sustained synaptic transmission, synaptic vesicles (SVs) are required to be recycled and refilled with neurotransmitters using an H(+) electrochemical gradient. However, neither the mechanism underlying vesicular GABA uptake nor the kinetics of GABA loading in living neurons have been fully elucidated. To characterize the process of GABA uptake into SVs in functional synapses, we monitored luminal pH of GABAergic SVs separately from that of excitatory glutamatergic SVs in cultured hippocampal neurons. By using a pH sensor optimal for the SV lumen, we found that GABAergic SVs exhibited an unexpectedly higher resting pH (∼6.4) than glutamatergic SVs (pH ∼5.8). Moreover, unlike glutamatergic SVs, GABAergic SVs displayed unique pH dynamics after endocytosis that involved initial overacidification and subsequent alkalization that restored their resting pH. GABAergic SVs that lacked the vesicular GABA transporter (VGAT) did not show the pH overshoot and acidified further to ∼6.0. Comparison of luminal pH dynamics in the presence or absence of VGAT showed that VGAT operates as a GABA/H(+) exchanger, which is continuously required to offset GABA leakage. Furthermore, the kinetics of GABA transport was slower (τ > 20 s at physiological temperature) than that of glutamate uptake and may exceed the time required for reuse of exocytosed SVs, allowing reuse of incompletely filled vesicles in the presence of high demand for inhibitory transmission.

Desipramine prevents cardiac gap junction uncoupling.

PubMed

Jozwiak, Joanna; Dietze, Anna; Grover, Rajiv; Savtschenko, Alex; Etz, Christian; Mohr, Friedrich W; Dhein, Stefan

2012-11-01

Uncoupling of cardiac gap junction channels is an important arrhythmogenic mechanism in ischemia/reperfusion. Antiarrhythmic peptide AAP10 (H-Gly-Ala-Gly-Hyp-Pro-Tyr-CONH(2)) has been shown to prevent acidosis-induced uncoupling and ischemia-related increase in dispersion. Previous structure-effect investigations and subsequent computer modeling studies indicated that the tricyclic antidepressant desipramine may exert similar effects as AAP10. We assessed the binding of (14)C-AAP10 to membranes of rabbit cardiac ventricles and its displacement with desipramine in a classical radioligand binding and competition study. Gap junction currents were measured between isolated pairs of human atrial cardiomyocytes under normal and acidotic (pH 6.3) conditions with or without 1 μmol/l desipramine using dual whole-cell voltage clamp. The effect of 1 μmol/l desipramine was assessed in isolated rabbit hearts (Langendorff technique) undergoing local ischemia by coronary occlusion with 256-channel electrophysiological mapping and subsequent analysis of connexin43 (Cx43) expression, phosphorylation (Western blot), and subcellular localization (immunohistology). We found saturable (14)C-AAP10 binding to cardiac membranes (K (D), 0.29 ± 0.11 nmol/l; B (max), 42.5 ± 7.2 pmol/mg) which could be displaced by desipramine with a K (D.High) = 0.14 μmol/l and a K (D.Low) = 22 μmol/l. Acidosis reduced the gap junction conductance in human cardiomyocyte pairs from 24.1 ± 4.7 to 11.5 ± 2.5 nS, which could be significantly reversed by desipramine (26.6 ± 4.8 nS). In isolated hearts, ischemia resulted in significantly increased dispersion of activation-recovery intervals, loss of membrane Cx43, and dephosphorylation of Cx43, which all could be prevented by desipramine. Desipramine seems to prevent the uncoupling of cardiac gap junctions and ischemia-related increase in dispersion.

Carbon Nanotube Based Molecular Electronics

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Saini, Subhash; Menon, Madhu

1998-01-01

Carbon nanotubes and the nanotube heterojunctions have recently emerged as excellent candidates for nanoscale molecular electronic device components. Experimental measurements on the conductivity, rectifying behavior and conductivity-chirality correlation have also been made. While quasi-one dimensional simple heterojunctions between nanotubes with different electronic behavior can be generated by introduction of a pair of heptagon-pentagon defects in an otherwise all hexagon graphene sheet. Other complex 3- and 4-point junctions may require other mechanisms. Structural stability as well as local electronic density of states of various nanotube junctions are investigated using a generalized tight-binding molecular dynamics (GDBMD) scheme that incorporates non-orthogonality of the orbitals. The junctions investigated include straight and small angle heterojunctions of various chiralities and diameters; as well as more complex 'T' and 'Y' junctions which do not always obey the usual pentagon-heptagon pair rule. The study of local density of states (LDOS) reveal many interesting features, most prominent among them being the defect-induced states in the gap. The proposed three and four pointjunctions are one of the smallest possible tunnel junctions made entirely of carbon atoms. Furthermore the electronic behavior of the nanotube based device components can be taylored by doping with group III-V elements such as B and N, and BN nanotubes as a wide band gap semiconductor has also been realized in experiments. Structural properties of heteroatomic nanotubes comprising C, B and N will be discussed.

Single-molecule analysis of diffusion and trapping of STIM1 and Orai1 at endoplasmic reticulum–plasma membrane junctions

PubMed Central

Wu, Minnie M.; Covington, Elizabeth D.; Lewis, Richard S.

2014-01-01

Following endoplasmic reticulum (ER) Ca2+ depletion, STIM1 and Orai1 complexes assemble autonomously at ER–plasma membrane (PM) junctions to trigger store-operated Ca2+ influx. One hypothesis to explain this process is a diffusion trap in which activated STIM1 diffusing in the ER becomes trapped at junctions through interactions with the PM, and STIM1 then traps Orai1 in the PM through binding of its calcium release-activated calcium activation domain. We tested this model by analyzing STIM1 and Orai1 diffusion using single-particle tracking, photoactivation of protein ensembles, and Monte Carlo simulations. In resting cells, STIM1 diffusion is Brownian, while Orai1 is slightly subdiffusive. After store depletion, both proteins slow to the same speeds, consistent with complex formation, and are confined to a corral similar in size to ER–PM junctions. While the escape probability at high STIM:Orai expression ratios is <1%, it is significantly increased by reducing the affinity of STIM1 for Orai1 or by expressing the two proteins at comparable levels. Our results provide direct evidence that STIM-Orai complexes are trapped by their physical connections across the junctional gap, but also reveal that the complexes are surprisingly dynamic, suggesting that readily reversible binding reactions generate free STIM1 and Orai1, which engage in constant diffusional exchange with extrajunctional pools. PMID:25057023

MRCK-1 drives apical constriction in C. elegans by linking developmental patterning to force generation

PubMed Central

Marston, Daniel J.; Higgins, Christopher D.; Peters, Kimberly A.; Cupp, Timothy D.; Dickinson, Daniel J.; Pani, Ariel M.; Moore, Regan P.; Cox, Amanda H.; Kiehart, Daniel P.; Goldstein, Bob

2016-01-01

Summary Apical constriction is a change in cell shape that drives key morphogenetic events including gastrulation and neural tube formation. Apical force-producing actomyosin networks drive apical constriction by contracting while connected to cell-cell junctions. The mechanisms by which developmental patterning regulates these actomyosin networks and associated junctions with spatial precision are not fully understood. Here, we identify a myosin light chain kinase MRCK-1 as a key regulator of C. elegans gastrulation that integrates spatial and developmental patterning information. We show that MRCK-1 is required for activation of contractile actomyosin dynamics and elevated cortical tension in the apical cell cortex of endodermal precursor cells. MRCK-1 is apically localized by active Cdc42 at the external, cell-cell contact-free surfaces of apically constricting cells, downstream of cell fate determination mechanisms. We establish that the junctional components α-catenin, β-catenin, and cadherin become highly enriched at the apical junctions of apically-constricting cells, and that MRCK-1 and myosin activity are required in vivo for this enrichment. Taken together, our results define mechanisms that position a myosin activator to a specific cell surface where it both locally increases cortical tension and locally enriches junctional components to facilitate apical constriction. These results reveal crucial links that can tie spatial information to local force generation to drive morphogenesis. PMID:27451898

pH dynamics in sewers and its modeling.

PubMed

Sharma, Keshab; Ganigue, Ramon; Yuan, Zhiguo

2013-10-15

pH variation in sewers has a significant effect on hydrogen sulfide production and emissions, and hence its accurate prediction is critical for the optimization of mitigation strategies. In this study, the nature and dynamics of pH variation in a sewer system is examined. Three sewer systems collecting domestic wastewater were monitored, with pH in all cases showing large diurnal variations. pH in fresh sewage in all three cases had a very similar trend with maximum pH in the range of 8.5-8.7. pH variation in fresh sewage followed the same pattern as the sewage flow rate, suggesting that sewage pH is influenced by household water use. Nitrogen content of the wastewater was found to be the most influential factor causing pH variation in fresh sewage, with the total ammonium concentration variation well correlated with the pH variation. A methodology for predicting pH variation in sewers is developed and calibration protocols proposed. The methodology, which is based on the concept of charge balance, was validated using titration curves and field pH data. Measurement of the total ammonium concentration in fresh sewage was found necessary and adequate for the calibration of the charge balance-based pH model. Copyright © 2013 Elsevier Ltd. All rights reserved.

Internal Electric Field Modulation in Molecular Electronic Devices by Atmosphere and Mobile Ions.

PubMed

Chandra Mondal, Prakash; Tefashe, Ushula M; McCreery, Richard L

2018-06-13

The internal potential profile and electric field are major factors controlling the electronic behavior of molecular electronic junctions consisting of ∼1-10 nm thick layers of molecules oriented in parallel between conducting contacts. The potential profile is assumed linear in the simplest cases, but can be affected by internal dipoles, charge polarization, and electronic coupling between the contacts and the molecular layer. Electrochemical processes in solutions or the solid state are entirely dependent on modification of the electric field by electrolyte ions, which screen the electrodes and form the ionic double layers that are fundamental to electrode kinetics and widespread applications. The current report investigates the effects of mobile ions on nominally solid-state molecular junctions containing aromatic molecules covalently bonded between flat, conducting carbon surfaces, focusing on changes in device conductance when ions are introduced into an otherwise conventional junction design. Small changes in conductance were observed when a polar molecule, acetonitrile, was present in the junction, and a large decrease of conductance was observed when both acetonitrile (ACN) and lithium ions (Li + ) were present. Transient experiments revealed that conductance changes occur on a microsecond-millisecond time scale, and are accompanied by significant alteration of device impedance and temperature dependence. A single molecular junction containing lithium benzoate could be reversibly transformed from symmetric current-voltage behavior to a rectifier by repetitive bias scans. The results are consistent with field-induced reorientation of acetonitrile molecules and Li + ion motion, which screen the electrodes and modify the internal potential profile and provide a potentially useful means to dynamically alter junction electronic behavior.

Multicomponent order parameter superconductivity of Sr2RuO4 revealed by topological junctions

NASA Astrophysics Data System (ADS)

Anwar, M. S.; Ishiguro, R.; Nakamura, T.; Yakabe, M.; Yonezawa, S.; Takayanagi, H.; Maeno, Y.

2017-06-01

Single crystals of the Sr2RuO4 -Ru eutectic system are known to exhibit enhanced superconductivity at 3 K in addition to the bulk superconductivity of Sr2RuO4 at 1.5 K. The 1.5 K phase is believed to be a spin-triplet, chiral p -wave state with a multicomponent order parameter, giving rise to chiral domain structure. In contrast, the 3 K phase is attributable to enhanced superconductivity of Sr2RuO4 in the strained interface region between Ru inclusion of a few to tens of micrometers in size and the surrounding Sr2RuO4 . We investigate the dynamic behavior of a topological junction, where a superconductor is surrounded by another superconductor. Specifically, we fabricated Nb/Ru/Sr2RuO4 topological superconducting junctions, in which the difference in phase winding between the s -wave superconductivity in Ru microislands induced from Nb and the superconductivity of Sr2RuO4 mainly governs the junction behavior. Comparative results of the asymmetry, hysteresis, and noise in junctions with different sizes, shapes, and configurations of Ru inclusions are explained by the chiral domain-wall motion in these topological junctions. Furthermore, a striking difference between the 1.5 and 3 K phases is clearly revealed: the large noise in the 1.5 K phase sharply disappears in the 3 K phase. These results confirm the multicomponent order-parameter superconductivity of the bulk Sr2RuO4 , consistent with the chiral p -wave state, and the proposed nonchiral single-component superconductivity of the 3 K phase.

Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity

PubMed Central

Yamamoto, Eiji; Akimoto, Takuma; Kalli, Antreas C.; Yasuoka, Kenji; Sansom, Mark S. P.

2017-01-01

Pleckstrin homology (PH) domains are membrane-binding lipid recognition proteins that interact with phosphatidylinositol phosphate (PIP) molecules in eukaryotic cell membranes. Diffusion of PH domains plays a critical role in biological reactions on membrane surfaces. Although diffusivity can be estimated by long-time measurements, it lacks information on the short-time diffusive nature. We reveal two diffusive properties of a PH domain bound to the surface of a PIP-containing membrane using molecular dynamics simulations. One is fractional Brownian motion, attributed to the motion of the lipids with which the PH domain interacts. The other is temporally fluctuating diffusivity; that is, the short-time diffusivity of the bound protein changes substantially with time. Moreover, the diffusivity for short-time measurements is intrinsically different from that for long-time measurements. This fluctuating diffusivity results from dynamic changes in interactions between the PH domain and PIP molecules. Our results provide evidence that the complexity of protein-lipid interactions plays a crucial role in the diffusion of proteins on biological membrane surfaces. Changes in the diffusivity of PH domains and related membrane-bound proteins may in turn contribute to the formation/dissolution of protein complexes in membranes. PMID:28116358

Evidence for less irritation to the peritoneal membrane in rats dialyzed with solutions low in glucose degradation products.

PubMed

Wieczorowska-Tobis, Katarzyna; Brelinska, Renata; Witowski, Janusz; Passlick-Deetjen, Jutta; Schaub, Thomas P; Schilling, Holger; Breborowicz, Andrzej

2004-01-01

Acidic pH and the presence of glucose degradation products (GDP) are believed to compromise the biocompatibility of peritoneal dialysis fluids (PDF). The present study examines the effects of long-term exposure to GDP and low pH by comparing conventional PDF and a new, neutral pH, low GDP solution. All experiments were performed using a chronic infusion model of dialysis in nonuremic rats. The animals were treated for 6 weeks with 2 daily injections of 4.25% glucose-containing PDF. The following PDF were tested: CAPD3 (single-chamber bag, low pH, high GDP), CAPD3 pH 7.4 (single-chamber bag, neutral pH, high GDP), CAPD3-Balance (double-chamber bag, neutral pH, low GDP). All test solutions were obtained from Fresenius Medical Care, Bad Homburg, Germany. After 6 weeks of exposure, peritoneal permeability to water, urea, creatinine, glucose, and sodium, assessed by peritoneal equilibration test, was similar in all groups. However, compared to other PDF, dialysis with CAPD3-Balance was associated with reduced concentrations of protein and hyaluronan in the dialysate, decreased peritoneal eosinophilia, and reduced dialysate levels of chemokines CCL2/MCP-1 and CCL5/RANTES. Morphologic changes in the peritoneal membrane of CAPD3-Balance-treated animals were much less pronounced and included reduced vascular density, preservation of the mesothelial monolayer and intercellular junction, and no reduplication of the submesothelial basement membrane. A new generation of PDF with physiologic pH and low GDP level produce less irritation to the peritoneal membrane and better preserve its structural integrity. This effect seems to be related predominantly to minimized GDP concentrations.

Presynaptic pH and vesicle fusion in Drosophila larvae neurones.

PubMed

Caldwell, Lesley; Harries, Peter; Sydlik, Sebastian; Schwiening, Christof J

2013-11-01

Both intracellular pH (pHi) and synaptic cleft pH change during neuronal activity yet little is known about how these pH shifts might affect synaptic transmission by influencing vesicle fusion. To address this we imaged pH- and Ca(2+) -sensitive fluorescent indicators (HPTS, Oregon green) in boutons at neuromuscular junctions. Electrical stimulation of motor nerves evoked presynaptic Ca(2+) i rises and pHi falls (∼0.1 pH units) followed by recovery of both Ca(2+) i and pHi. The plasma-membrane calcium ATPase (PMCA) inhibitor, 5(6)-carboxyeosin diacetate, slowed both the calcium recovery and the acidification. To investigate a possible calcium-independent role for the pHi shifts in modulating vesicle fusion we recorded post-synaptic miniature end-plate potential (mEPP) and current (mEPC) frequency in Ca(2+) -free solution. Acidification by propionate superfusion, NH(4)(+) withdrawal, or the inhibition of acid extrusion on the Na(+)/H(+) exchanger (NHE) induced a rise in miniature frequency. Furthermore, the inhibition of acid extrusion enhanced the rise induced by propionate addition and NH(4)(+) removal. In the presence of NH(4)(+), 10 out of 23 cells showed, after a delay, one or more rises in miniature frequency. These findings suggest that Ca(2+) -dependent pHi shifts, caused by the PMCA and regulated by NHE, may stimulate vesicle release. Furthermore, in the presence of membrane permeant buffers, exocytosed acid or its equivalents may enhance release through positive feedback. This hitherto neglected pH signalling, and the potential feedback role of vesicular acid, could explain some important neuronal excitability changes associated with altered pH and its buffering. Copyright © 2013 Wiley Periodicals, Inc.

Self-Assembly Assisted Fabrication of Dextran-Based Nanohydrogels with Reduction-Cleavable Junctions for Applications as Efficient Drug Delivery Systems

PubMed Central

Wang, Hao; Dai, Tingting; Zhou, Shuyan; Huang, Xiaoxiao; Li, Songying; Sun, Kang; Zhou, Guangdong; Dou, Hongjing

2017-01-01

In order to overcome the key challenge in improving both fabrication efficiency and their drug delivery capability of anti-cancer drug delivery systems (ACDDS), here polyacrylic acid (PAA) grafted dextran (Dex) nanohydrogels (NGs) with covalent crosslinked structure bearing redox sensitive disulfide crosslinking junctions (Dex-SS-PAA) were synthesized efficiently through a one-step self-assembly assisted methodology (SAA). The Dex-SS-PAA were subsequently conjugated with doxorubicin through an acid-labile hydrazone bond (Dex-SS-PAA-DOX). The in vitro drug release behavior, anti-cancer effects in vivo, and biosafety of the as-prepared acid- and redox-dual responsive biodegradable NGs were systematically investigated. The results revealed that the Dex-SS-PAA-DOX exhibited pH- and redox-controlled drug release, greatly reduced the toxicity of free DOX, while exhibiting a strong ability to inhibit the growth of MDA-MB-231 tumors. Our study demonstrated that the Dex-SS-PAA-DOX NGs are very promising candidates as ACDDS for anti-cancer therapeutics. PMID:28071743

All solution-processed lead halide perovskite-BiVO4 tandem assembly for photolytic solar fuels production.

PubMed

Chen, Yong-Siou; Manser, Joseph S; Kamat, Prashant V

2015-01-21

The quest for economic, large-scale hydrogen production has motivated the search for new materials and device designs capable of splitting water using only energy from the sun. Here we introduce an all solution-processed tandem water splitting assembly composed of a BiVO4 photoanode and a single-junction CH3NH3PbI3 hybrid perovskite solar cell. This unique configuration allows efficient solar photon management, with the metal oxide photoanode selectively harvesting high energy visible photons, and the underlying perovskite solar cell capturing lower energy visible-near IR wavelengths in a single-pass excitation. Operating without external bias under standard AM 1.5G illumination, the photoanode-photovoltaic architecture, in conjunction with an earth-abundant cobalt phosphate catalyst, exhibits a solar-to-hydrogen conversion efficiency of 2.5% at neutral pH. The design of low-cost tandem water splitting assemblies employing single-junction hybrid perovskite materials establishes a potentially promising new frontier for solar water splitting research.

Self-Assembly Assisted Fabrication of Dextran-Based Nanohydrogels with Reduction-Cleavable Junctions for Applications as Efficient Drug Delivery Systems

NASA Astrophysics Data System (ADS)

Wang, Hao; Dai, Tingting; Zhou, Shuyan; Huang, Xiaoxiao; Li, Songying; Sun, Kang; Zhou, Guangdong; Dou, Hongjing

2017-01-01

In order to overcome the key challenge in improving both fabrication efficiency and their drug delivery capability of anti-cancer drug delivery systems (ACDDS), here polyacrylic acid (PAA) grafted dextran (Dex) nanohydrogels (NGs) with covalent crosslinked structure bearing redox sensitive disulfide crosslinking junctions (Dex-SS-PAA) were synthesized efficiently through a one-step self-assembly assisted methodology (SAA). The Dex-SS-PAA were subsequently conjugated with doxorubicin through an acid-labile hydrazone bond (Dex-SS-PAA-DOX). The in vitro drug release behavior, anti-cancer effects in vivo, and biosafety of the as-prepared acid- and redox-dual responsive biodegradable NGs were systematically investigated. The results revealed that the Dex-SS-PAA-DOX exhibited pH- and redox-controlled drug release, greatly reduced the toxicity of free DOX, while exhibiting a strong ability to inhibit the growth of MDA-MB-231 tumors. Our study demonstrated that the Dex-SS-PAA-DOX NGs are very promising candidates as ACDDS for anti-cancer therapeutics.

There are four dynamically and functionally distinct populations of E-cadherin in cell junctions

PubMed Central

Erami, Zahra; Timpson, Paul; Yao, Wu; Zaidel-Bar, Ronen; Anderson, Kurt I.

2015-01-01

ABSTRACT E-cadherin is a trans-membrane tumor suppressor responsible for epithelial cell adhesion. E-cadherin forms adhesive clusters through combined extra-cellular cis- and trans-interactions and intracellular interaction with the actin cytoskeleton. Here we identify four populations of E-cadherin within cell junctions based on the molecular interactions which determine their mobility and adhesive properties. Adhesive and non-adhesive populations of E-cadherin each consist of mobile and immobile fractions. Up to half of the E-cadherin immobilized in cell junctions is non-adhesive. Incorporation of E-cadherin into functional adhesions require all three adhesive interactions, with deletion of any one resulting in loss of effective cell-cell adhesion. Interestingly, the only interaction which could independently slow the diffusion of E-cadherin was the tail-mediated intra-cellular interaction. The adhesive and non-adhesive mobile fractions of E-cadherin can be distinguished by their sensitivity to chemical cross-linking with adhesive clusters. Our data define the size, mobility, and adhesive properties of four distinct populations of E-cadherin within cell junctions, and support association with the actin cytoskeleton as the first step in adhesion formation. PMID:26471767

Electron transport and noise spectroscopy in organic magnetic tunnel junctions with PTCDA and Alq3 barriers

NASA Astrophysics Data System (ADS)

Martinez, Isidoro; Cascales, Juan Pedro; Hong, Jhen-Yong; Lin, Minn-Tsong; Prezioso, Mirko; Riminucci, Alberto; Dediu, Valentin A.; Aliev, Farkhad G.

2016-10-01

The possible influence of internal barrier dynamics on spin, charge transport and their fluctuations in organic spintronics remains poorly understood. Here we present investigation of the electron transport and low frequency noise at temperatures down to 0.3K in magnetic tunnel junctions with an organic PTCDA barriers with thickness up to 5 nm in the tunneling regime and with 200 nm thick Alq3 barrier in the hopping regime. We observed high tunneling magneto-resistance at low temperatures (15-40%) and spin dependent super-poissonian shot noise in organic magnetic tunnel junctions (OMTJs) with PTCDA. The Fano factor exceeds 1.5-2 values which could be caused by interfacial states controlled by spin dependent bunching in the tunneling events through the molecules.1 The bias dependence of the low frequency noise in OMTJs with PTCDA barriers which includes both 1/f and random telegraph noise activated at specific biases will also be discussed. On the other hand, the organic junctions with ferromagnetic electrodes and thick Alq3 barriers present sub-poissonian shot noise which depends on the temperature, indicative of variable range hopping.

Hissar-Alai and the Pamirs: Junction and Position in the System of Mobile Belts of Central Asia

NASA Astrophysics Data System (ADS)

Leonov, M. G.; Rybin, A. K.; Batalev, V. Yu.; Matyukov, V. E.; Shchelochkov, G. G.

2018-01-01

The position of the Pamirs and the Hissar-Alai mountainous system in the structure of Central Asia and features of their junction are considered. It is shown that their outer contours and tectonic infrastructure are significantly distinct in the planar pattern: latitudinally linear and arched for the Hissar-Alai and the Pamirs, respectively. These structures logically match those of the Central Asian and Alpine-Himalayan belts, respectively. The Pamir orogen is a relatively autonomous structural element of the crust, which is located discordantly relative to the country lithospheric blocks. Most of the Pamirs (at least, the Northern and Central) probably form a giant allochthon on the ancient basement of the Tarim and Afghan-Tajik blocks. The junction zone of these two "hard" crustal segments is reflected in the transverse Transpamir threshold, which is expressed in the relief, deep structure, and seismicity. The specific geological structure of the junction zone of the Pamirs and Hissar-Alai (systems of the Tarim, Alai, and Afghan-Tajik troughs) is shown. It suggested that this zone is a damper, which significantly neutralizes the dynamic influence of the Pamir and the southernmost elements of the Pamir-Punjab syntax on Hissar-Alai structures.

Clinical and laboratory studies of the antacid and raft-forming properties of Rennie alginate suspension.

PubMed

Tytgat, G N; Simoneau, G

2006-03-15

Acid pockets at the gastro-oesophageal junction escape buffering from meals in the stomach. Combining high-dose antacid with alginate may therefore be of benefit in gastro-oesophageal reflux disease. To characterize the antacid and raft-forming properties of Rennie alginate suspension (containing high-dose antacid and alginate; Bayer Consumer Care, Bladel, the Netherlands). The in vitro acid-neutralizing capacity of Rennie algniate was compared with Gaviscon (Reckitt Benckiser, Slough, UK) by pH-recorded HCl titration. Alginate raft weight formed in vitro at different pH was used to evaluate the pH dependency of raft formation with each product. A double-blind, placebo-controlled, randomized crossover study also compared the antacid activity of Rennie alginate vs. placebo in vivo using continuous intragastric pH monitoring in 12 healthy fasting volunteers. Compared with Gaviscon, Rennie alginate had a higher acid-neutralizing capacity, greater maximum pH and longer duration of antacid activity in vitro. However, the two products produced comparable alginate rafts at each pH evaluated. In vivo, Rennie alginate provided rapid, effective and long-lasting acid neutralization, with an onset of action of <5 min, and duration of action of almost 90 min. The dual mode of action of Rennie alginate offers an effective treatment option for mild symptomatic gastro-oesophageal reflux disease particularly considering recent findings regarding 'acid pockets'.

Ion Separation using a Y-Junction Carbon Nanotube

NASA Astrophysics Data System (ADS)

Park, Jae Hyun; Sinnott, Susan; Aluru, Narayana

2005-11-01

Using molecular dynamics simulations, we show that a Y-junction carbon nanotube can be used to separate potassium and chloride ions from a KCl solution. The system consists of a KCl solution chamber connected to an (8,8) carbon nanotube, which acts as the stem. Two carbon nanotube branches of sizes (5,5) and (6,6) are connected to the (8,8) nanotube forming the Y-junction. Uncharged (5,5) and (6,6) carbon nanotubes show close to zero occupancy for transport of potassium and chloride ions. By functionalizing a (5,5) carbon nanotube with a negative charge, we show that we can selectively transport potassium ions. Similarly, by functionalizing a (6,6) carbon nanotube with a positive charge, we can selectively transport chloride ions. By performing molecular dynamics simulations on the entire system comprising the two branches, stem and the KCl solution chamber, we show that perfect ion separation is observed when (5,5) and (6,6) nanotubes are charged with σw,(5,5)=-0.181 C/m^2 and σw,(6,6)=+0.143 C/m^2, respectively, whereas for the system with σw,(5,5)=-0.168 C/m^2 and σw,(6,6)=+0.131 C/m^2 the separation is not perfect because of the formation of ion pairs. We discuss the formation and control of ion pairing, which is a common phenomenon in confined nanochannels.

Ankyrin-G Inhibits Endocytosis of Cadherin Dimers.

PubMed

Cadwell, Chantel M; Jenkins, Paul M; Bennett, Vann; Kowalczyk, Andrew P

2016-01-08

Dynamic regulation of endothelial cell adhesion is central to vascular development and maintenance. Furthermore, altered endothelial adhesion is implicated in numerous diseases. Therefore, normal vascular patterning and maintenance require tight regulation of endothelial cell adhesion dynamics. However, the mechanisms that control junctional plasticity are not fully understood. Vascular endothelial cadherin (VE-cadherin) is an adhesive protein found in adherens junctions of endothelial cells. VE-cadherin mediates adhesion through trans interactions formed by its extracellular domain. Trans binding is followed by cis interactions that laterally cluster the cadherin in junctions. VE-cadherin is linked to the actin cytoskeleton through cytoplasmic interactions with β- and α-catenin, which serve to increase adhesive strength. Furthermore, p120-catenin binds to the cytoplasmic tail of cadherin and stabilizes it at the plasma membrane. Here we report that induced cis dimerization of VE-cadherin inhibits endocytosis independent of both p120 binding and trans interactions. However, we find that ankyrin-G, a protein that links membrane proteins to the spectrin-actin cytoskeleton, associates with VE-cadherin and inhibits its endocytosis. Ankyrin-G inhibits VE-cadherin endocytosis independent of p120 binding. We propose a model in which ankyrin-G associates with and inhibits the endocytosis of VE-cadherin cis dimers. Our findings support a novel mechanism for regulation of VE-cadherin endocytosis through ankyrin association with cadherin engaged in lateral interactions. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Co-percolation to tune conductive behaviour in dynamical metallic nanowire networks.

PubMed

Fairfield, J A; Rocha, C G; O'Callaghan, C; Ferreira, M S; Boland, J J

2016-11-03

Nanowire networks act as self-healing smart materials, whose sheet resistance can be tuned via an externally applied voltage stimulus. This memristive response occurs due to modification of junction resistances to form a connectivity path across the lowest barrier junctions in the network. While most network studies have been performed on expensive noble metal nanowires like silver, networks of inexpensive nickel nanowires with a nickel oxide coating can also demonstrate resistive switching, a common feature of metal oxides with filamentary conduction. However, networks made from solely nickel nanowires have high operation voltages which prohibit large-scale material applications. Here we show, using both experiment and simulation, that a heterogeneous network of nickel and silver nanowires allows optimization of the activation voltage, as well as tuning of the conduction behavior to be either resistive switching, memristive, or a combination of both. Small percentages of silver nanowires, below the percolation threshold, induce these changes in electrical behaviour, even for low area coverage and hence very transparent films. Silver nanowires act as current concentrators, amplifying conductivity locally as shown in our computational dynamical activation framework for networks of junctions. These results demonstrate that a heterogeneous nanowire network can act as a cost-effective adaptive material with minimal use of noble metal nanowires, without losing memristive behaviour that is essential for smart sensing and neuromorphic applications.

Fast, clash-free RNA conformational morphing using molecular junctions

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

Heliou, Amelie; Budday, Dominik; Fonseca, Rasmus

Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groupsmore » of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.« less

Fast, clash-free RNA conformational morphing using molecular junctions

DOE PAGES

Heliou, Amelie; Budday, Dominik; Fonseca, Rasmus; ...

2017-03-13

Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groupsmore » of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.« less

A High Grain Diet Dynamically Shifted the Composition of Mucosa-Associated Microbiota and Induced Mucosal Injuries in the Colon of Sheep.

PubMed

Wang, Yue; Xu, Lei; Liu, Junhua; Zhu, Weiyun; Mao, Shengyong

2017-01-01

This study investigated the dynamic shifts in mucosa-associated microbiota composition and mucosal morphology in the colon of sheep fed a high grain (HG) diet. A total of 20 male sheep were randomly assigned to four groups ( n = 5 for each). The sheep in first group received hay diet. The animals in other 3 groups were fed an HG diet for 7 (HG7), 14 (HG14), or 28 (HG28) days, respectively. Colonic digesta samples were collected to determine the pH and the concentrations of volatile fatty acid (VFA) and lactate. The colonic mucosa was sampled to characterize the bacterial communities using Illumina MiSeq sequencing and to determine mRNA expression levels of cytokines and tight junction protein genes using quantitative real-time PCR. As time advanced, results revealed that colonic pH linearly decreased ( P = 0.007), and the concentrations of total VFA linearly increased ( P < 0.001). Microbial analysis showed that an HG diet linearly reduced ( P < 0.050) the diversity and richness of the colonic microbiota. The principal coordinate analysis results showed that the colonic mucosa-associated bacterial communities of the four groups significantly shifted with number of days fed an HG diet. At the genus level, HG feeding significantly increased the relative abundance of some taxa including Prevotella , Coprococcus , Roseburia , and Clostridium_sensu_stricto_1 , and decreased the proportion of Treponema, and the percentage of these taxa was not affected by days fed an HG diet. The microscopic examination showed that HG feeding caused the mucosal epithelial injury. The RT-PCR results showed that the mRNA expression of claudin-1 ( P = 0.038), IL-1β ( P = 0.045), IL-6 ( P = 0.050), and TNF-α ( P = 0.020) increased linearly with number of days fed an HG diet. The correlation analysis revealed significant correlation between the colonic mucosal mRNA expression of cytokines and mucosal bacterial composition. Generally, HG feeding increased colonic fermentation and altered colonic mucosal bacterial communities, which eventually caused colonic mucosal damage and led to colonic dysfunction, and these changes occurred gradually over at least 4 weeks.

A High Grain Diet Dynamically Shifted the Composition of Mucosa-Associated Microbiota and Induced Mucosal Injuries in the Colon of Sheep

PubMed Central

Wang, Yue; Xu, Lei; Liu, Junhua; Zhu, Weiyun; Mao, Shengyong

2017-01-01

This study investigated the dynamic shifts in mucosa-associated microbiota composition and mucosal morphology in the colon of sheep fed a high grain (HG) diet. A total of 20 male sheep were randomly assigned to four groups (n = 5 for each). The sheep in first group received hay diet. The animals in other 3 groups were fed an HG diet for 7 (HG7), 14 (HG14), or 28 (HG28) days, respectively. Colonic digesta samples were collected to determine the pH and the concentrations of volatile fatty acid (VFA) and lactate. The colonic mucosa was sampled to characterize the bacterial communities using Illumina MiSeq sequencing and to determine mRNA expression levels of cytokines and tight junction protein genes using quantitative real-time PCR. As time advanced, results revealed that colonic pH linearly decreased (P = 0.007), and the concentrations of total VFA linearly increased (P < 0.001). Microbial analysis showed that an HG diet linearly reduced (P < 0.050) the diversity and richness of the colonic microbiota. The principal coordinate analysis results showed that the colonic mucosa-associated bacterial communities of the four groups significantly shifted with number of days fed an HG diet. At the genus level, HG feeding significantly increased the relative abundance of some taxa including Prevotella, Coprococcus, Roseburia, and Clostridium_sensu_stricto_1, and decreased the proportion of Treponema, and the percentage of these taxa was not affected by days fed an HG diet. The microscopic examination showed that HG feeding caused the mucosal epithelial injury. The RT-PCR results showed that the mRNA expression of claudin-1 (P = 0.038), IL-1β (P = 0.045), IL-6 (P = 0.050), and TNF-α (P = 0.020) increased linearly with number of days fed an HG diet. The correlation analysis revealed significant correlation between the colonic mucosal mRNA expression of cytokines and mucosal bacterial composition. Generally, HG feeding increased colonic fermentation and altered colonic mucosal bacterial communities, which eventually caused colonic mucosal damage and led to colonic dysfunction, and these changes occurred gradually over at least 4 weeks. PMID:29123511

Structural Dynamic Assessment of the GN2 Piping System for NASA's New and Powerful Reverberant Acoustic Test Facility

NASA Technical Reports Server (NTRS)

McNelis, Mark E.; Staab, Lucas D.; Akers, James C.; Hughes, William O.; Chang, Li C.; Hozman, Aron D.; Henry, Michael W.

2012-01-01

The National Aeronautics and Space Administration (NASA) Glenn Research Center (GRC) has led the design and build of the new world-class vibroacoustic test capabilities at the NASA GRC's Plum Brook Station in Sandusky, Ohio, USA from 2007 to 2011. SAIC-Benham has completed construction of a new reverberant acoustic test facility to support the future testing needs of NASA's space exploration program and commercial customers. The large Reverberant Acoustic Test Facility (RATF) is approximately 101,000 cubic feet in volume and was designed to operate at a maximum empty chamber acoustic overall sound pressure level (OASPL) of 163 dB. This combination of size and acoustic power is unprecedented amongst the world s known active reverberant acoustic test facilities. Initial checkout acoustic testing was performed on March 2011 by SAIC-Benham at test levels up to 161 dB OASPL. During testing, several branches of the gaseous nitrogen (GN2) piping system, which supply the fluid to the noise generating acoustic modulators, failed at their T-junctions connecting the 12 in. supply line to their respective 4 in. branch lines. The problem was initially detected when the oxygen sensors in the horn room indicated a lower than expected oxygen level from which was inferred GN2 leaks in the piping system. In subsequent follow up inspections, cracks were identified in the failed T-junction connections through non-destructive evaluation testing. Through structural dynamic modeling of the piping system, the root cause of the T-junction connection failures was determined. The structural dynamic assessment identified several possible corrective design improvements to the horn room piping system. The effectiveness of the chosen design repairs were subsequently evaluated in September 2011 during acoustic verification testing to 161 dB OASPL.

Structural Dynamic Assessment of the GN2 Piping System for NASA's New and Powerful Reverberant Acoustic Test Facility

NASA Technical Reports Server (NTRS)

McNelis, Mark E.; Staab, Lucas D.; Akers, James C.; Hughes, WIlliam O.; Chang, Li, C.; Hozman, Aron D.; Henry, Michael W.

2012-01-01

The National Aeronautics and Space Administration (NASA) Glenn Research Center (GRC) has led the design and build of the new world-class vibroacoustic test capabilities at the NASA GRC's Plum Brook Station in Sandusky, Ohio, USA from 2007-2011. SAIC-Benham has completed construction of a new reverberant acoustic test facility to support the future testing needs of NASA's space exploration program and commercial customers. The large Reverberant Acoustic Test Facility (RATF) is approximately 101,000 cu ft in volume and was designed to operate at a maximum empty chamber acoustic overall sound pressure level (OASPL) of 163 dB. This combination of size and acoustic power is unprecedented amongst the world's known active reverberant acoustic test facilities. Initial checkout acoustic testing was performed on March 2011 by SAIC-Benham at test levels up to 161 dB OASPL. During testing, several branches of the gaseous nitrogen (GN2) piping system, which supply the fluid to the noise generating acoustic modulators, failed at their "t-junctions" connecting the 12 inch supply line to their respective 4 inch branch lines. The problem was initially detected when the oxygen sensors in the horn room indicated a lower than expected oxygen level from which was inferred GN2 leaks in the piping system. In subsequent follow up inspections, cracks were identified in the failed "t-junction" connections through non-destructive evaluation testing . Through structural dynamic modeling of the piping system, the root cause of the "t-junction" connection failures was determined. The structural dynamic assessment identified several possible corrective design improvements to the horn room piping system. The effectiveness of the chosen design repairs were subsequently evaluated in September 2011 during acoustic verification testing to 161 dB OASPL.

Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors

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

Malaby, Andrew W.; Das, Sanchaita; Chakravarthy, Srinivas

Membrane dynamic processes including vesicle biogenesis depend on Arf guanosine triphosphatase (GTPase) activation by guanine nucleotide exchange factors (GEFs) containing a catalytic Sec7 domain and a membrane-targeting module such as a pleckstrin homology (PH) domain. The catalytic output of cytohesin family Arf GEFs is controlled by autoinhibitory interactions that impede accessibility of the exchange site in the Sec7 domain. These restraints can be relieved through activator Arf-GTP binding to an allosteric site comprising the PH domain and proximal autoinhibitory elements (Sec7-PH linker and C-terminal helix). Small-angle X-ray scattering and negative-stain electron microscopy were used to investigate the structural organization andmore » conformational dynamics of cytohesin-3 (Grp1) in autoinhibited and active states. The results support a model in which hinge dynamics in the autoinhibited state expose the activator site for Arf-GTP binding, while subsequent C-terminal helix unlatching and repositioning unleash conformational entropy in the Sec7-PH linker to drive exposure of the exchange site.« less

The effect of intact talin and talin tail fragment on actin filament dynamics and structure depends on pH and ionic strength.

PubMed

Goldmann, W H; Hess, D; Isenberg, G

1999-03-01

We employed quasi-elastic light scattering and electron microscopy to investigate the influence of intact talin and talin tail fragment on actin filament dynamics and network structure. Using these methods, we confirm previous reports that intact talin induces cross-linking as well as filament shortening on actin networks. We now show that the effect of intact talin as well as talin tail fragment on actin networks is controlled by pH and ionic strength. At pH 7.5, actin filament dynamics in the presence of intact talin and talin tail fragment are characterized by a rapid decay of the dynamic structure factor and by a square root power law for the stretched exponential decay which is in contrast with the theory for pure actin solutions. At pH 6 and low ionic strength, intact talin cross-links actin filaments more tightly than talin tail fragment. Talin head fragment showed no effect on actin networks, indicating that the actin binding sites reside probably exclusively within the tail domain.

The Cytoplasmic Adaptor Protein Dok7 Activates the Receptor Tyrosine Kinase MuSK via Dimerization

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

Bergamin, E.; Hallock, P; Burden, S

Formation of the vertebrate neuromuscular junction requires, among others proteins, Agrin, a neuronally derived ligand, and the following muscle proteins: LRP4, the receptor for Agrin; MuSK, a receptor tyrosine kinase (RTK); and Dok7 (or Dok-7), a cytoplasmic adaptor protein. Dok7 comprises a pleckstrin-homology (PH) domain, a phosphotyrosine-binding (PTB) domain, and C-terminal sites of tyrosine phosphorylation. Unique among adaptor proteins recruited to RTKs, Dok7 is not only a substrate of MuSK, but also an activator of MuSK's kinase activity. Here, we present the crystal structure of the Dok7 PH-PTB domains in complex with a phosphopeptide representing the Dok7-binding site on MuSK.more » The structure and biochemical data reveal a dimeric arrangement of Dok7 PH-PTB that facilitates trans-autophosphorylation of the kinase activation loop. The structure provides the molecular basis for MuSK activation by Dok7 and for rationalizing several Dok7 loss-of-function mutations found in patients with congenital myasthenic syndromes.« less

Nuclear Magnetic Resonance Structures of GCN4p Are Largely Conserved When Ion Pairs Are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix.

PubMed

Kaplan, Anne R; Brady, Megan R; Maciejewski, Mark W; Kammerer, Richard A; Alexandrescu, Andrei T

2017-03-21

To understand the roles ion pairs play in stabilizing coiled coils, we determined nuclear magnetic resonance structures of GCN4p at three pH values. At pH 6.6, all acidic residues are fully charged; at pH 4.4, they are half-charged, and at pH 1.5, they are protonated and uncharged. The α-helix monomer and coiled coil structures of GCN4p are largely conserved, except for a loosening of the coiled coil quaternary structure with a decrease in pH. Differences going from neutral to acidic pH include (i) an unwinding of the coiled coil superhelix caused by the loss of interchain ion pair contacts, (ii) a small increase in the separation of the monomers in the dimer, (iii) a loosening of the knobs-into-holes packing motifs, and (iv) an increased separation between oppositely charged residues that participate in ion pairs at neutral pH. Chemical shifts (HN, N, C', Cα, and Cβ) of GCN4p display a seven-residue periodicity that is consistent with α-helical structure and is invariant with pH. By contrast, periodicity in hydrogen exchange rates at neutral pH is lost at acidic pH as the exchange mechanism moves into the EX1 regime. On the basis of 1 H- 15 N nuclear Overhauser effect relaxation measurements, the α-helix monomers experience only small increases in picosecond to nanosecond backbone dynamics at acidic pH. By contrast, 13 C rotating frame T 1 relaxation (T 1ρ ) data evince an increase in picosecond to nanosecond side-chain dynamics at lower pH, particularly for residues that stabilize the coiled coil dimerization interface through ion pairs. The results on the structure and dynamics of GCNp4 over a range of pH values help rationalize why a single structure at neutral pH poorly predicts the pH dependence of the unfolding stability of the coiled coil.

Dynamical electron-phonon coupling, G W self-consistency, and vertex effect on the electronic band gap of ice and liquid water

NASA Astrophysics Data System (ADS)

Ziaei, Vafa; Bredow, Thomas

2017-06-01

We study the impact of dynamical electron-phonon (el-ph) effects on the electronic band gap of ice and liquid water by accounting for frequency-dependent Fan contributions in the el-ph mediated self-energy within the many-body perturbation theory (MBPT). We find that the dynamical el-ph coupling effects greatly reduce the static el-ph band-gap correction of the hydrogen-rich molecular ice crystal from-2.46 to -0.23 eV in great contrast to the result of Monserrat et al. [Phys. Rev. B 92, 140302 (2015), 10.1103/PhysRevB.92.140302]. This is of particular importance as otherwise the static el-ph gap correction would considerably reduce the electronic band gap, leading to considerable underestimation of the intense peaks of optical absorption spectra of ice which would be in great disagreement to experimental references. By contrast, the static el-ph gap correction of liquid water is very moderate (-0.32 eV), and inclusion of dynamical effects slightly reduces the gap correction to -0.19 eV. Further, we determine the diverse sensitivity of ice and liquid water to the G W self-consistency and show that the energy-only self-consistent approach (GnWn ) exhibits large implicit vertex character in comparison to the quasiparticle self-consistent approach, for which an explicit calculation of vertex corrections is necessary for good agreement with experiment.

Monitoring protein hydrolysis by pepsin using pH-stat: In vitro gastric digestions in static and dynamic pH conditions.

PubMed

Mat, Damien J L; Cattenoz, Thomas; Souchon, Isabelle; Michon, Camille; Le Feunteun, Steven

2018-01-15

This study intends to demonstrate that acid titration at low pH is very well adapted to the monitoring of pepsin activity. After a description of the underlying principles, this approach was used during in vitro gastric digestions of a model of complex food containing 15wt% of whey proteins, according to both static (2h at pH = 3, Infogest protocol) and dynamic pH conditions (from pH 6.3 down to 2 in 1h). Pepsin activity was quantitatively assessed in all experiments through the calculation of degrees of hydrolysis (DH). Final values of 3.7 and 3.0% were obtained in static and dynamic pH conditions, respectively, and validated using an independent method. Results also show that about 92% of the peptides were detected at pH = 3, and 100% for pH≤2.5. Overall, the proposed approach proved to be very worthy to study protein hydrolysis during in vitro gastric digestions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Time dependent and temperature dependent properties of the forward voltage characteristic of InGaN high power LEDs

NASA Astrophysics Data System (ADS)

Fulmek, P. L.; Haumer, P.; Wenzl, F. P.; Nemitz, W.; Nicolics, J.

2017-03-01

Estimating the junction temperature and its dynamic behavior in dependence of various operating conditions is an important issue, since these properties influence the optical characteristics as well as the aging processes of a light-emitting diode (LED). Particularly for high-power LEDs and pulsed operation, the dynamic behavior and the resulting thermal cycles are of interest. The forward voltage method relies on the existence of a time-independent unique triple of forward-voltage, forward-current, and junction temperature. These three figures should as well uniquely define the optical output power and spectrum, as well as the loss power of the LED, which is responsible for an increase of the junction temperature. From transient FEM-simulations one may expect an increase of the temperature of the active semiconductor layer of some 1/10 K within the first 10 μs. Most of the well-established techniques for junction temperature measurement via forward voltage method evaluate the measurement data several dozens of microseconds after switching on or switching off and estimate the junction temperature by extrapolation towards the time of switching. In contrast, the authors developed a measurement procedure with the focus on the first microseconds after switching. Besides a fast data acquisition system, a precise control of the switching process is required, i.e. a precisely defined current pulse amplitude with fast rise-time and negligible transient by-effects. We start with a short description of the measurement setup and the newly developed control algorithm for the generation of short current pulses. The thermal characterization of the LED chip during the measurement procedures is accomplished by an IR thermography system and transient finite element simulations. The same experimental setup is used to investigate the optical properties of the LED in an Ulbricht-sphere. Our experiments are performed on InGaN LED chips mounted on an Al based insulated metal substrate (IMS), giving a comprehensive picture of the transient behavior of the forward voltage of this type of high power LED.

Dynamic behavior of Yarrowia lipolytica in response to pH perturbations: dependence of the stress response on the culture mode.

PubMed

Timoumi, Asma; Cléret, Mégane; Bideaux, Carine; Guillouet, Stéphane E; Allouche, Yohan; Molina-Jouve, Carole; Fillaudeau, Luc; Gorret, Nathalie

2017-01-01

Yarrowia lipolytica, a non-conventional yeast with a promising biotechnological potential, is able to undergo metabolic and morphological changes in response to environmental conditions. The effect of pH perturbations of different types (pulses, Heaviside) on the dynamic behavior of Y. lipolytica W29 strain was characterized under two modes of culture: batch and continuous. In batch cultures, different pH (4.5, 5.6 (optimal condition), and 7) were investigated in order to identify the pH inducing a stress response (metabolic and/or morphologic) in Y. lipolytica. Macroscopic behavior (kinetic parameters, yields, viability) of the yeast was slightly affected by pH. However, contrary to the culture at pH 5.6, a filamentous growth was induced in batch experiments at pH 4.5 and 7. Proportions of the filamentous subpopulation reached 84 and 93 % (v/v) under acidic and neutral conditions, respectively. Given the significant impact of neutral pH on morphology, pH perturbations from 5.6 to 7 were subsequently assayed in batch and continuous bioreactors. For both process modes, the growth dynamics remained fundamentally unaltered during exposure to stress. Nevertheless, morphological behavior of the yeast was dependent on the culture mode. Specifically, in batch bioreactors where cells proliferated at their maximum growth rate, mycelia were mainly formed. Whereas, in continuous cultures at controlled growth rates (from 0.03 to 0.20 h -1 ) even closed to the maximum growth rate of the stain (0.24 h -1 ), yeast-like forms predominated. This pointed out differences in the kinetic behavior of filamentous and yeast subpopulations, cell age distribution, and pH adaptive mechanisms between both modes of culture.

Flying over decades

NASA Astrophysics Data System (ADS)

Hoeller, Judith; Issler, Mena; Imamoglu, Atac

Levy flights haven been extensively used in the past three decades to describe non-Brownian motion of particles. In this presentation I give an overview on how Levy flights have been used across several disciplines, ranging from biology to finance to physics. In our publication we describe how a single electron spin 'flies' when captured in quantum dot using the central spin model. At last I motivate the use of Levy flights for the description of anomalous diffusion in modern experiments, concretely to describe the lifetimes of quasi-particles in Josephson junctions. Finished PhD at ETH in Spring 2015.

Ring modulators with enhanced efficiency based on standing-wave operation on a field-matched, interdigitated p-n junction.

PubMed

Pavanello, Fabio; Zeng, Xiaoge; Wade, Mark T; Popović, Miloš A

2016-11-28

We propose ring modulators based on interdigitated p-n junctions that exploit standing rather than traveling-wave resonant modes to improve modulation efficiency, insertion loss and speed. Matching the longitudinal nodes and antinodes of a standing-wave mode with high (contacts) and low (depletion regions) carrier density regions, respectively, simultaneously lowers loss and increases sensitivity significantly. This approach permits further to relax optical constraints on contacts placement and can lead to lower device capacitance. Such structures are well-matched to fabrication in advanced microelectronics CMOS processes. Device architectures that exploit this concept are presented along with their benefits and drawbacks. A temporal coupled mode theory model is used to investigate the static and dynamic response. We show that modulation efficiencies or loss Q factors up to 2 times higher than in previous traveling-wave geometries can be achieved leading to much larger extinction ratios. Finally, we discuss more complex doping geometries that can improve carrier dynamics for higher modulation speeds in this context.

Chaotic electrical activity of living β-cells in the mouse pancreatic islet

NASA Astrophysics Data System (ADS)

Kanno, Takahiro; Miyano, Takaya; Tokuda, Isao; Galvanovskis, Juris; Wakui, Makoto

2007-02-01

To test for chaotic dynamics of the insulin producing β-cell and explore its biological role, we observed the action potentials with the perforated patch clamp technique, for isolated cells as well as for intact cells of the mouse pancreatic islet. The time series obtained were analyzed using nonlinear diagnostic algorithms associated with the surrogate method. The isolated cells exhibited short-term predictability and visible determinism, in the steady state response to 10 mM glucose, while the intact cells did not. In the latter case, determinism became visible after the application of a gap junction inhibitor. This tendency was enhanced by the stimulation with tolbutamide. Our observations suggest that, thanks to the integration of individual chaotic dynamics via gap junction coupling, the β-cells will lose memory of fluctuations occurring at any instant in their electrical activity more rapidly with time. This is likely to contribute to the functional stability of the islet against uncertain perturbations.

Crossing Over from Attractive to Repulsive Interactions in a Tunneling Bosonic Josephson Junction.

PubMed

Spagnolli, G; Semeghini, G; Masi, L; Ferioli, G; Trenkwalder, A; Coop, S; Landini, M; Pezzè, L; Modugno, G; Inguscio, M; Smerzi, A; Fattori, M

2017-06-09

We explore the interplay between tunneling and interatomic interactions in the dynamics of a bosonic Josephson junction. We tune the scattering length of an atomic ^{39}K Bose-Einstein condensate confined in a double-well trap to investigate regimes inaccessible to other superconducting or superfluid systems. In the limit of small-amplitude oscillations, we study the transition from Rabi to plasma oscillations by crossing over from attractive to repulsive interatomic interactions. We observe a critical slowing down in the oscillation frequency by increasing the strength of an attractive interaction up to the point of a quantum phase transition. With sufficiently large initial oscillation amplitude and repulsive interactions, the system enters the macroscopic quantum self-trapping regime, where we observe coherent undamped oscillations with a self-sustained average imbalance of the relative well population. The exquisite agreement between theory and experiments enables the observation of a broad range of many body coherent dynamical regimes driven by tunable tunneling energy, interactions and external forces, with applications spanning from atomtronics to quantum metrology.

Quantum dynamics of a Josephson junction driven cavity mode system in the presence of voltage bias noise

NASA Astrophysics Data System (ADS)

Wang, Hui; Blencowe, M. P.; Armour, A. D.; Rimberg, A. J.

2017-09-01

We give a semiclassical analysis of the average photon number as well as photon number variance (Fano factor F ) for a Josephson junction (JJ) embedded microwave cavity system, where the JJ is subject to a fluctuating (i.e., noisy) bias voltage with finite dc average. Through the ac Josephson effect, the dc voltage bias drives the effectively nonlinear microwave cavity mode into an amplitude squeezed state (F <1 ), as has been established previously [Armour et al., Phys. Rev. Lett. 111, 247001 (2013), 10.1103/PhysRevLett.111.247001], but bias noise acts to degrade this squeezing. We find that the sensitivity of the Fano factor to bias voltage noise depends qualitatively on which stable fixed point regime the system is in for the corresponding classical nonlinear steady-state dynamics. Furthermore, we show that the impact of voltage bias noise is most significant when the cavity is excited to states with large average photon number.

Grain Refinement Kinetics in a Low Alloyed Cu–Cr–Zr Alloy Subjected to Large Strain Deformation

PubMed Central

Morozova, Anna; Borodin, Elijah; Bratov, Vladimir; Zherebtsov, Sergey; Kaibyshev, Rustam

2017-01-01

This paper investigates the microstructural evolution and grain refinement kinetics of a solution-treated Cu–0.1Cr–0.06Zr alloy during equal channel angular pressing (ECAP) at a temperature of 673 K via route BC. The microstructural change during plastic deformation was accompanied by the formation of the microband and an increase in the misorientations of strain-induced subboundaries. We argue that continuous dynamic recrystallization refined the initially coarse grains, and discuss the dynamic recrystallization kinetics in terms of grain/subgrain boundary triple junction evolution. A modified Johnson–Mehl–Avrami–Kolmogorov relationship with a strain exponent of about 1.49 is used to express the strain dependence of the triple junctions of high-angle boundaries. Severe plastic deformation by ECAP led to substantial strengthening of the Cu–0.1Cr–0.06Zr alloy. The yield strength increased from 60 MPa in the initial state to 445 MPa after a total strain level of 12. PMID:29210990

Epitaxial regrowth of silicon for the fabrication of radial junction nanowire solar cells

NASA Astrophysics Data System (ADS)

Kendrick, Chito E.; Eichfeld, Sarah M.; Ke, Yue; Weng, Xiaojun; Wang, Xin; Mayer, Theresa S.; Redwing, Joan M.

2010-08-01

Radial p-n silicon nanowire (SiNW) solar cells are of interest as a potential pathway to increase the efficiency of crystalline silicon photovoltaics by reducing the junction length and surface reflectivity. Our studies have focused on the use of vapor-liquid-solid (VLS) growth in combination with chemical vapor deposition (CVD) processing for the fabrication of radial p-n junction SiNW array solar cells. High aspect ratio p-type SiNW arrays were initially grown on gold-coated (111) Si substrates by CVD using SiCl4 as the source gas and B2H6 as the p-type dopant source. The epitaxial re-growth of n-type Si shell layers on the Si nanowires was then investigated using SiH4 as the source gas and PH3 as the dopant. Highly conformal coatings were achieved on nanowires up to 25 μm in length. The microstructure of the Si shell layer changed from polycrystalline to single crystal as the deposition temperature was raised from 650oC to 950oC. Electrical test structures were fabricated by aligning released SiNWs onto pre-patterned substrates via fieldassisted assembly followed by selective removal of the n-type shell layer and contact deposition. Current-voltage measurements of the radial p-n SiNWs diodes fabricated with re-grown Si shell layers at 950°C demonstrate rectifying behavior with an ideality factor of 1.93. Under illumination from an AM1.5g spectrum and efficiency for this single SiNW radial p-n junction was determined to be 1.8%, total wire diameter was 985 nm.

Hydrodynamically induced oscillations and traffic dynamics in 1D microfludic networks

NASA Astrophysics Data System (ADS)

Bartolo, Denis; Jeanneret, Raphael

2011-03-01

We report on the traffic dynamics of particles driven through a minimal microfluidic network. Even in the minimal network consisting in a single loop, the traffic dynamics has proven to yield complex temporal patterns, including periodic, multi-periodic or chaotic sequences. This complex dynamics arises from the strongly nonlinear hydrodynamic interactions between the particles, that takes place at a junction. To better understand the consequences of this nontrivial coupling, we combined theoretical, numerical and experimental efforts and solved the 3-body problem in a 1D loop network. This apparently simple dynamical system revealed a rich and unexpected dynamics, including coherent spontaneous oscillations along closed orbits. Striking similarities between Hamiltonian systems and this driven dissipative system will be explained.

Application of Satellite Geodesy in Analyzing the Accelerated Movement of the Back-arc Rifting in the Izu Bonin Islands, Japan

NASA Astrophysics Data System (ADS)

Arisa, D.; Heki, K.

2014-12-01

The Izu-Bonin islands lies along the convergent boundary between the subducting Pacific plate (PA) and the overriding Philippine Sea plate (PH) in the western Pacific. Nishimura (2011) found that the back-arc rifting goes on behind the Izu arc by studying the horizontal velocities of GNSS stations on the Izu islands. Here we show that this rifting has accelerated in 2004 using GNSS data at Aogashima, Hachijoujima, and Mikurajima stations. The back-arc rifting behind the Izu islands can be seen as the increasing distance between stations in the Izu-Bonin islands and stations located in the stable part of PH. We found that their movement showed clear acceleration around the third quarter of 2004. Obtaining the Euler vector of the PH is necessary to analyzed the movement of each stations relative to the other stations on the same plate. The analyzing of GPS timeseries leads us to one initial conclusion that some accelerated movement started to occur in the third quarter of 2004. This event was closely related to the earthquake on May 29, 2004 in Nankai Trough and September 5, 2004 earthquake near the triple junction of Sagami Trough. The analyzing process help us to understand that this accelerated movement was not the afterslip of any of these earthquakes, but it was triggering these area to move faster and further than it was. We first rule out the best possible cause by constraining the onset time of the accelerated movement, and correlating it with the earthquakes. May 29, 2004 earthquake (M6.5) at the PA-PH boundary clearly lacked the jump which should mark the onset of the eastward slow movement. Moreover, additional velocity vectors do not converge to the epicenter, and onset time that minimizes the post-fit residual is significantly later than May. We therefore conclude that accelerated movement started in 2004 was not due to the afterslip of interplate earthquake in May 29. On the next step we found that the onset time coincides with the occurrence of September 5, 2004 We found that the accelerated movement vectors of these islands are almost parallel with each other, and perpendicular to the rift axis. We hypothesize that the seismic wave radiated from the epicenter of this earthquake dynamically triggered the acceleration of the back arc opening in the Izu Arc.

pH-responsive supramolecular self-assembly of well-defined zwitterionic ABC miktoarm star terpolymers.

PubMed

Liu, Hao; Li, Changhua; Liu, Hewen; Liu, Shiyong

2009-04-21

We report the first example of the synthesis and pH-responsive supramolecular self-assembly of double hydrophilic ABC miktoarm star terpolymers. Well-defined ABC miktoarm star terpolymers consisting of poly(ethylene glycol), poly(tert-butyl methacrylate), and poly(2-(diethylamino)ethyl methacrylate) arms [PEG(-b-PtBMA)-b-PDEA] were synthesized via the combination of consecutive click reactions and atom transfer radical polymerization (ATRP), starting from a trifunctional core molecule, 1-azido-3-chloro-2-propanol (ACP). The click reaction of monoalkynyl-terminated PEG with an excess of ACP afforded difunctional PEG bearing a chlorine and a secondary hydroxyl moiety at the chain end, PEG113(-Cl)-OH (1). After azidation with NaN3, PEG-based macroinitiator PEG113(-N3)-Br (3) was prepared by the esterification of PEG113(-N3)-OH (2) with 2-bromoisobutyryl bromide and then employed in the ATRP of tert-butyl methacrylate (tBMA). The obtained PEG(-N3)-b-PtBMA copolymers (4) possessed an azido moiety at the diblock junction point. The preparation of PEG(-b-PtBMA)-b-PDEA miktoarm star terpolymers was then achieved via the click reaction of 4 with an excess of monoalkynyl-terminated PDEA. The obtained miktoarm star terpolymers were successfully converted into PEG(-b-PMAA)-b-PDEA, where PMAA is poly(methacrylic acid). In aqueous solution, PEG(-b-PMAA)-b-PDEA zwitterionic ABC miktoarm star terpolymers can self-assemble into three types of micellar aggregates by simply adjusting solution pH at room temperature. Above pH 8, PDEA-core micelles stabilized by PEG/ionized PMAA hybrid coronas were formed due to the insolubility of PDEA block. In the range of pH 5-7, micelles possessing polyion complex cores formed as a result of charge compensation between partially ionized PMAA and partially protonated PDEA sequences. At pH<4, hydrogen bonding interactions between fully protonated PMAA and PEG led to the formation of another type of micellar aggregates possessing hydrogen-bonded complex cores stabilized by protonated PDEA coronas. The fully reversible pH-responsive formation of three types of aggregates were characterized by 1H NMR, dynamic and static laser light scattering (LLS), and transmission electron microscopy (TEM).

Structure and properties of native and unfolded lysing enzyme from T. harzianum: Chemical and pH denaturation.

PubMed

Bey, Houda; Gtari, Wala; Aschi, Adel; Othman, Tahar

2016-11-01

The effect of chemical denaturants and pH on the change of the conformation of the protein Lysing Enzyme from Trichoderma Harzianum has been investigated by dynamic light scattering (DLS) and turbidimetry. Chemical denaturants are frequently used to describe the mechanisms of folding and transition states. We have analyzed the pH effect on the properties and particle size of the protein. The compaction factor CI has shown that the protein is weakly disordered. The molecular dynamics simulations confirm, at neutral pH, that the protein has a low net charge and high hydrophobicity. Copyright © 2016 Elsevier B.V. All rights reserved.

Femtosecond coherent nuclear dynamics of excited tetraphenylethylene: Ultrafast transient absorption and ultrafast Raman loss spectroscopic studies.

PubMed

Kayal, Surajit; Roy, Khokan; Umapathy, Siva

2018-01-14

Ultrafast torsional dynamics plays an important role in the photoinduced excited state dynamics. Tetraphenylethylene (TPE), a model system for the molecular motor, executes interesting torsional dynamics upon photoexcitation. The photoreaction of TPE involves ultrafast internal conversion via a nearly planar intermediate state (relaxed state) that further leads to a twisted zwitterionic state. Here, we report the photoinduced structural dynamics of excited TPE during the course of photoisomerization in the condensed phase by ultrafast Raman loss (URLS) and femtosecond transient absorption (TA) spectroscopy. TA measurements on the S 1 state reveal step-wise population relaxation from the Franck-Condon (FC) state → relaxed state → twisted state, while the URLS study provides insights on the vibrational dynamics during the course of the reaction. The TA spectral dynamics and vibrational Raman amplitudes within 1 ps reveal vibrational wave packet propagating from the FC state to the relaxed state. Fourier transformation of this oscillation leads to a ∼130 cm -1 low-frequency phenyl torsional mode. Two vibrational marker bands, C et =C et stretching (∼1512 cm -1 ) and C ph =C ph stretching (∼1584 cm -1 ) modes, appear immediately after photoexcitation in the URLS spectra. The initial red-shift of the C ph =C ph stretching mode with a time constant of ∼400 fs (in butyronitrile) is assigned to the rate of planarization of excited TPE. In addition, the C et =C et stretching mode shows initial blue-shift within 1 ps followed by frequency red-shift, suggesting that on the sub-picosecond time scale, structural relaxation is dominated by phenyl torsion rather than the central C et =C et twist. Furthermore, the effect of the solvent on the structural dynamics is discussed in the context of ultrafast nuclear dynamics and solute-solvent coupling.

Not only … but also: REM sleep creates and NREM Stage 2 instantiates landmark junctions in cortical memory networks.

PubMed

Llewellyn, Sue; Hobson, J Allan

2015-07-01

This article argues both rapid eye movement (REM) and non-rapid eye movement (NREM) sleep contribute to overnight episodic memory processes but their roles differ. Episodic memory may have evolved from memory for spatial navigation in animals and humans. Equally, mnemonic navigation in world and mental space may rely on fundamentally equivalent processes. Consequently, the basic spatial network characteristics of pathways which meet at omnidirectional nodes or junctions may be conserved in episodic brain networks. A pathway is formally identified with the unidirectional, sequential phases of an episodic memory. In contrast, the function of omnidirectional junctions is not well understood. In evolutionary terms, both animals and early humans undertook tours to a series of landmark junctions, to take advantage of resources (food, water and shelter), whilst trying to avoid predators. Such tours required memory for emotionally significant landmark resource-place-danger associations and the spatial relationships amongst these landmarks. In consequence, these tours may have driven the evolution of both spatial and episodic memory. The environment is dynamic. Resource-place associations are liable to shift and new resource-rich landmarks may be discovered, these changes may require re-wiring in neural networks. To realise these changes, REM may perform an associative, emotional encoding function between memory networks, engendering an omnidirectional landmark junction which is instantiated in the cortex during NREM Stage 2. In sum, REM may preplay associated elements of past episodes (rather than replay individual episodes), to engender an unconscious representation which can be used by the animal on approach to a landmark junction in wake. Copyright © 2015 Elsevier Inc. All rights reserved.

Gap junction blockade induces apoptosis in human endometrial stromal cells.

PubMed

Yu, Jie; Berga, Sarah L; Zou, Wei; Sun, He-Ying; Johnston-MacAnanny, Erika; Yalcinkaya, Tamer; Sidell, Neil; Bagchi, Indrani C; Bagchi, Milan K; Taylor, Robert N

2014-07-01

One of the most dynamic adult human tissues is the endometrium. Through coordinated, cyclical proliferation, differentiation, leukocyte recruitment, apoptosis, and desquamation, the uterine lining is expanded and shed monthly, unless pregnancy is established. Errors in these steps potentially cause endometrial dysfunction, abnormal uterine bleeding, failed embryonic implantation, infertility, or endometrial carcinoma. Our prior studies showed that gap junctions comprised of Gap junction alpha-1 (GJA1) protein, also known as connexin 43 (CX43), subunits are critical to endometrial stromal cell differentiation. The current studies were undertaken to explore the mechanism of endometrial dysfunction when gap junction intercellular communication (GJIC) is disrupted. Gap junction blockade by two distinct GJIC inhibitors, 18α-glycyrrhetinic acid (AGA) and octanol (OcOH), suppressed proliferation and induced apoptosis in endometrial stromal cells, as manifested by reduced biomarkers of cell viability, increased TUNEL staining, caspase-3 activation, sub-G1 chromosomal DNA complement, as well as shortened telomere length. Unexpectedly, we also observed that the chemical inhibitors blocked CX43 gene expression. Moreover, when endometrial stromal cells were induced to undergo hormonal decidualization, following a 7-day exposure to 10 nM 17β-estradiol + 100 nM progesterone + 0.5 mM dibutyryl cAMP, characteristic epithelioid changes in cell shape and secretion of prolactin were blunted in the presence of AGA or OcOH, recapitulating effects of RNA interference of CX43. Our findings indicate that endometrial stromal cell proliferation and maintenance of decidualized endometrial function are GJIC-dependent, and that disruption of gap junctions induces endometrial stromal cell apoptosis. These observations may have important implications for several common clinical endometrial pathologies. © 2014 Wiley Periodicals, Inc.

Imaging Ca2+ nanosparks in heart with a new targeted biosensor.

PubMed

Shang, Wei; Lu, Fujian; Sun, Tao; Xu, Jiejia; Li, Lin-Lin; Wang, Yanru; Wang, Gang; Chen, Liangyi; Wang, Xianhua; Cannell, Mark B; Wang, Shi-Qiang; Cheng, Heping

2014-01-31

In cardiac dyads, junctional Ca2+ directly controls the gating of the ryanodine receptors (RyRs), and is itself dominated by RyR-mediated Ca2+ release from the sarcoplasmic reticulum. Existing probes do not report such local Ca2+ signals because of probe diffusion, so a junction-targeted Ca2+ sensor should reveal new information on cardiac excitation-contraction coupling and its modification in disease states. To investigate Ca2+ signaling in the nanoscopic space of cardiac dyads by targeting a new sensitive Ca2+ biosensor (GCaMP6f) to the junctional space. By fusing GCaMP6f to the N terminus of triadin 1 or junctin, GCaMP6f-triadin 1/junctin was targeted to dyadic junctions, where it colocalized with t-tubules and RyRs after adenovirus-mediated gene transfer. This membrane protein-tagged biosensor displayed ≈4× faster kinetics than native GCaMP6f. Confocal imaging revealed junctional Ca2+ transients (Ca2+ nanosparks) that were ≈50× smaller in volume than conventional Ca2+ sparks (measured with diffusible indicators). The presence of the biosensor did not disrupt normal Ca2+ signaling. Because no indicator diffusion occurred, the amplitude and timing of release measurements were improved, despite the small recording volume. We could also visualize coactivation of subclusters of RyRs within a single junctional region, as well as quarky Ca2+ release events. This new, targeted biosensor allows selective visualization and measurement of nanodomain Ca2+ dynamics in intact cells and can be used to give mechanistic insights into dyad RyR operation in health and in disease states such as when RyRs become orphaned.

Effect of pH on the stability of hemochromatosis factor E: a combined spectroscopic and molecular dynamics simulation-based study.

PubMed

Khan, Parvez; Shandilya, Ashutosh; Jayaram, B; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

2017-05-01

Hereditary hemochromatosis is an iron overburden condition, which is mainly governed by hereditary hemochromatosis factor E (HFE), a member of major histocompatibility complex class I. To understand the effect of pH on the structure and stability of HFE, we have cloned, expressed, and purified the HFE in the bacterial system and performed circular dichroism, fluorescence, and absorbance measurements at a wide pH range (pH 3.0-11.0). We found that HFE remains stable in the pH range 7.5-11.0 and gets completely acid denatured at low pH values. In this work, we also analyzed the contribution of salt bridges to the stability of HFE. We further performed molecular dynamics simulations for 80 ns at different pH values. An excellent agreement was observed between results from biophysical and MD simulation studies. At lower pH, HFE undergoes denaturation and may be driven toward a degradation pathway, such as ubiquitination. Hence, HFE is not available to bind again with transferrin receptor1 to negatively regulate iron homeostasis. Further we postulated that, might be low pH of cancerous cells helps them to meet their high iron requirement.

Effect of pH on structure, function, and stability of mitochondrial carbonic anhydrase VA.

PubMed

Idrees, Danish; Shahbaaz, Mohd; Bisetty, Krishna; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

2017-02-01

Mitochondrial carbonic anhydrase VA (CAVA) catalyzes the hydration of carbon dioxide to produce proton and bicarbonate which is primarily expressed in the mitochondrial matrix of liver, and involved in numerous physiological processes including lipogenesis, insulin secretion from pancreatic cells, ureagenesis, gluconeogenesis, and neuronal transmission. To understand the effect of pH on the structure, function, and stability of CAVA, we employed spectroscopic techniques such as circular dichroism, fluorescence, and absorbance measurements in wide range of pH (from pH 2.0 to pH 11.5). CAVA showed an aggregation at acidic pH range from pH 2.0 to pH 5.0. However, it remains stable and maintains its secondary structure in the pH range, pH 7.0-pH 11.5. Furthermore, this enzyme has an appreciable activity at more than pH 7.0 (7.0 < pH ≤ 11.5) with maximum activity at pH 9.0. The maximal values of k cat and k cat /K m at pH 9.0 are 3.7 × 10 6  s -1 and 5.5 × 10 7  M -1  s -1 , respectively. However, this enzyme loses its activity in the acidic pH range. We further performed 20-ns molecular dynamics simulation of CAVA to see the dynamics at different pH values. An excellent agreement was observed between in silico and in vitro studies. This study provides an insight into the activity of CAVA in the pH range of subcellular environment.

Electronic Properties of Carbon Nanotubes and Junctions

NASA Technical Reports Server (NTRS)

Anantram, M. P.; Han, Jie; Yang, Liu; Govindan, T. R.; Jaffe, R.; Saini, Subhash (Technical Monitor)

1998-01-01

Metallic and semiconducting Single Wall Carbon Nanotubes (CNT) have recently been characterized using scanning tunneling microscopy (STM) and the manipulation of individual CNT has been demonstrated. These developments make the prospect of using CNT as molecular wires and possibly as electronic devices an even more interesting one. We have been modeling various electronic properties such as the density of states and the transmission coefficient of CNT wires and junctions. These studies involve first calculating the stability of junctions using molecular dynamics simulations and then calculating the electronic properties using a pi-electron tight binding Hamiltonian. We have developed the expertise to calculate the electronic properties of both finite-sized CNT and CNT systems with semi-infinite boundary conditions. In this poster, we will present an overview of some of our results. The electronic application of CNT that is most promising at this time is their use as molecular wires. The conductance can however be greatly reduced because of reflection due to defects and contacts. We have modeled the transmission through CNT in the presence of two types of defects: weak uniform disorder and strong isolated scatterers. We find that the conductance is affected in significantly different manners due to these defects Junctions of CNT have also been imaged using STM. This makes it essential to derive rules for the formation of junctions between tubes of different chirality, study their relative energies and electronic properties. We have generalized the rules for connecting two different CNT and have calculated the transmission and density of states through CNT junctions. Metallic and semiconducting CNT can be joined to form a stable junction and their current versus voltage characteristics are asymmetric. CNT are deformed by the application of external forces including interactions with a substrate or other CNT. In many experiments, these deformation are expected to occur naturally. We will present some preliminary results of our calculations of the modification of CNT electronic properties as a result of deformations.

Parameter-free driven Liouville-von Neumann approach for time-dependent electronic transport simulations in open quantum systems

DOE PAGES

Zelovich, Tamar; Hansen, Thorsten; Liu, Zhen-Fei; ...

2017-03-02

A parameter-free version of the recently developed driven Liouville-von Neumann equation [T. Zelovich et al., J. Chem. Theory Comput. 10(8), 2927-2941 (2014)] for electronic transport calculations in molecular junctions is presented. The single driving rate, appearing as a fitting parameter in the original methodology, is replaced by a set of state-dependent broadening factors applied to the different single-particle lead levels. These broadening factors are extracted explicitly from the self-energy of the corresponding electronic reservoir and are fully transferable to any junction incorporating the same lead model. Furthermore, the performance of the method is demonstrated via tight-binding and extended Hückel calculationsmore » of simple junction models. Our analytic considerations and numerical results indicate that the developed methodology constitutes a rigorous framework for the design of "black-box" algorithms to simulate electron dynamics in open quantum systems out of equilibrium.« less

Diversity of immunoglobulin lambda light chain gene usage over developmental stages in the horse.

PubMed

Tallmadge, Rebecca L; Tseng, Chia T; Felippe, M Julia B

2014-10-01

To further studies of neonatal immune responses to pathogens and vaccination, we investigated the dynamics of B lymphocyte development and immunoglobulin (Ig) gene diversity. Previously we demonstrated that equine fetal Ig VDJ sequences exhibit combinatorial and junctional diversity levels comparable to those of adult Ig VDJ sequences. Herein, RACE clones from fetal, neonatal, foal, and adult lymphoid tissue were assessed for Ig lambda light chain combinatorial, junctional, and sequence diversity. Remarkably, more lambda variable genes (IGLV) were used during fetal life than later stages and IGLV gene usage differed significantly with time, in contrast to the Ig heavy chain. Junctional diversity measured by CDR3L length was constant over time. Comparison of Ig lambda transcripts to germline revealed significant increases in nucleotide diversity over time, even during fetal life. These results suggest that the Ig lambda light chain provides an additional dimension of diversity to the equine Ig repertoire. Copyright © 2014 Elsevier Ltd. All rights reserved.

Modulation of Tight Junction Structure and Function by Kinases and Phosphatases Targeting Occludin

PubMed Central

Dörfel, Max Johannes; Huber, Otmar

2012-01-01

Tight junctions (TJs) typically represent the most apical contacts in epithelial and endothelial cell layers where they play an essential role in the separation of extracellular or luminal spaces from underlying tissues in the body. Depending on the protein composition, TJs define the barrier characteristics and in addition maintain cell polarity. Two major families of integral membrane proteins form the typical TJ strand network, the tight junction-associated MARVEL protein (TAMP) family members occludin, tricellulin, and MarvelD3 as well as a specific set of claudins. Occludin was the first identified member of these tetraspanins and is now widely accepted as a regulator of TJ assembly and function. Therefore, occludin itself has to be tightly regulated. Phosphorylation of occludin appears to be of central importance in this context. Here we want to summarize current knowledge on the kinases and phosphatases directly modifying occludin, and their role in the regulation of TJ structure, function, and dynamics. PMID:22315516

Nonadiabatic Josephson current pumping by chiral microwave irradiation

NASA Astrophysics Data System (ADS)

Venitucci, B.; Feinberg, D.; Mélin, R.; Douçot, B.

2018-05-01

Irradiating a Josephson junction with microwaves can operate not only on the amplitude but also on the phase of the Josephson current. This requires breaking time-inversion symmetry, which is achieved by introducing a phase lapse between the microwave components acting on the two sides of the junction. General symmetry arguments and the solution of a specific single-level quantum dot model show that this induces chirality in the Cooper pair dynamics due to the topology of the Andreev bound-state wave function. Another essential condition is to break electron-hole symmetry within the junction. A shift of the current-phase relation is obtained, which is controllable in sign and amplitude with the microwave phase and an electrostatic gate, thus producing a "chiral" Josephson transistor. The dot model is solved in the infinite-gap limit by Floquet theory and in the general case with Keldysh nonequilibrium Green's functions. The chiral current is nonadiabatic: it is extremal and changes sign close to resonant chiral transitions between the Andreev bound states.

Connecting Dissipation and Phase Slips in a Josephson Junction between Fermionic Superfluids.

PubMed

Burchianti, A; Scazza, F; Amico, A; Valtolina, G; Seman, J A; Fort, C; Zaccanti, M; Inguscio, M; Roati, G

2018-01-12

We study the emergence of dissipation in an atomic Josephson junction between weakly coupled superfluid Fermi gases. We find that vortex-induced phase slippage is the dominant microscopic source of dissipation across the Bose-Einstein condensate-Bardeen-Cooper-Schrieffer crossover. We explore different dynamical regimes by tuning the bias chemical potential between the two superfluid reservoirs. For small excitations, we observe dissipation and phase coherence to coexist, with a resistive current followed by well-defined Josephson oscillations. We link the junction transport properties to the phase-slippage mechanism, finding that vortex nucleation is primarily responsible for the observed trends of conductance and critical current. For large excitations, we observe the irreversible loss of coherence between the two superfluids, and transport cannot be described only within an uncorrelated phase-slip picture. Our findings open new directions for investigating the interplay between dissipative and superfluid transport in strongly correlated Fermi systems, and general concepts in out-of-equilibrium quantum systems.

Parameter-free driven Liouville-von Neumann approach for time-dependent electronic transport simulations in open quantum systems

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

Zelovich, Tamar; Hansen, Thorsten; Liu, Zhen-Fei

A parameter-free version of the recently developed driven Liouville-von Neumann equation [T. Zelovich et al., J. Chem. Theory Comput. 10(8), 2927-2941 (2014)] for electronic transport calculations in molecular junctions is presented. The single driving rate, appearing as a fitting parameter in the original methodology, is replaced by a set of state-dependent broadening factors applied to the different single-particle lead levels. These broadening factors are extracted explicitly from the self-energy of the corresponding electronic reservoir and are fully transferable to any junction incorporating the same lead model. Furthermore, the performance of the method is demonstrated via tight-binding and extended Hückel calculationsmore » of simple junction models. Our analytic considerations and numerical results indicate that the developed methodology constitutes a rigorous framework for the design of "black-box" algorithms to simulate electron dynamics in open quantum systems out of equilibrium.« less

Electric conductance of a mechanically strained molecular junction from first principles: Crucial role of structural relaxation and conformation sampling

NASA Astrophysics Data System (ADS)

Nguyen, Huu Chuong; Szyja, Bartłomiej M.; Doltsinis, Nikos L.

2014-09-01

Density functional theory (DFT) based molecular dynamics simulations have been performed of a 1,4-benzenedithiol molecule attached to two gold electrodes. To model the mechanical manipulation in typical break junction and atomic force microscopy experiments, the distance between two electrodes was incrementally increased up to the rupture point. For each pulling distance, the electric conductance was calculated using the DFT nonequilibrium Green's-function approach for a statistically relevant sample of configurations extracted from the simulation. With increasing mechanical strain, the formation of monoatomic gold wires is observed. The conductance decreases by three orders of magnitude as the initial twofold coordination of the thiol sulfur to the gold is reduced to a single S-Au bond at each electrode and the order in the electrodes is destroyed. Independent of the pulling distance, the conductance was found to fluctuate by at least two orders of magnitude depending on the instantaneous junction geometry.

Mouse rods signal through gap junctions with cones.

PubMed

Asteriti, Sabrina; Gargini, Claudia; Cangiano, Lorenzo

2014-01-01

Rod and cone photoreceptors are coupled by gap junctions (GJs), relatively large channels able to mediate both electrical and molecular communication. Despite their critical location in our visual system and evidence that they are dynamically gated for dark/light adaptation, the full impact that rod-cone GJs can have on cone function is not known. We recorded the photovoltage of mouse cones and found that the initial level of rod input increased spontaneously after obtaining intracellular access. This process allowed us to explore the underlying coupling capacity to rods, revealing that fully coupled cones acquire a striking rod-like phenotype. Calcium, a candidate mediator of the coupling process, does not appear to be involved on the cone side of the junctional channels. Our findings show that the anatomical substrate is adequate for rod-cone coupling to play an important role in vision and, possibly, in biochemical signaling among photoreceptors. DOI: http://dx.doi.org/10.7554/eLife.01386.001.

An intercellular polyamine transfer via gap junctions regulates proliferation and response to stress in epithelial cells

PubMed Central

Desforges, Bénédicte; Curmi, Patrick A.; Bounedjah, Ouissame; Nakib, Samir; Hamon, Loic; De Bandt, Jean-Pascal; Pastré, David

2013-01-01

In the organism, quiescent epithelial cells have the potential to resume cycling as a result of various stimuli, including wound healing or oxidative stress. Because quiescent cells have a low polyamine level, resuming their growth requires an increase of their intracellular polyamine levels via de novo polyamine synthesis or their uptake from plasma. Another alternative, explored here, is an intercellular exchange with polyamine-rich cycling cells via gap junctions. We show that polyamines promote gap junction communication between proliferating cells by promoting dynamical microtubule plus ends at the cell periphery and thus allow polyamine exchange between cells. In this way, cycling cells favor regrowth in adjacent cells deprived of polyamines. In addition, intercellular interactions mediated by polyamines can coordinate the translational response to oxidative stress through the formation of stress granules. Some putative in vivo consequences of polyamine-mediated intercellular interactions are also discussed regarding cancer invasiveness and tissue regeneration. PMID:23515223

Mouse rods signal through gap junctions with cones

PubMed Central

Asteriti, Sabrina; Gargini, Claudia; Cangiano, Lorenzo

2014-01-01

Rod and cone photoreceptors are coupled by gap junctions (GJs), relatively large channels able to mediate both electrical and molecular communication. Despite their critical location in our visual system and evidence that they are dynamically gated for dark/light adaptation, the full impact that rod–cone GJs can have on cone function is not known. We recorded the photovoltage of mouse cones and found that the initial level of rod input increased spontaneously after obtaining intracellular access. This process allowed us to explore the underlying coupling capacity to rods, revealing that fully coupled cones acquire a striking rod-like phenotype. Calcium, a candidate mediator of the coupling process, does not appear to be involved on the cone side of the junctional channels. Our findings show that the anatomical substrate is adequate for rod–cone coupling to play an important role in vision and, possibly, in biochemical signaling among photoreceptors. DOI: http://dx.doi.org/10.7554/eLife.01386.001 PMID:24399457

Connecting Dissipation and Phase Slips in a Josephson Junction between Fermionic Superfluids

NASA Astrophysics Data System (ADS)

Burchianti, A.; Scazza, F.; Amico, A.; Valtolina, G.; Seman, J. A.; Fort, C.; Zaccanti, M.; Inguscio, M.; Roati, G.

2018-01-01

We study the emergence of dissipation in an atomic Josephson junction between weakly coupled superfluid Fermi gases. We find that vortex-induced phase slippage is the dominant microscopic source of dissipation across the Bose-Einstein condensate-Bardeen-Cooper-Schrieffer crossover. We explore different dynamical regimes by tuning the bias chemical potential between the two superfluid reservoirs. For small excitations, we observe dissipation and phase coherence to coexist, with a resistive current followed by well-defined Josephson oscillations. We link the junction transport properties to the phase-slippage mechanism, finding that vortex nucleation is primarily responsible for the observed trends of conductance and critical current. For large excitations, we observe the irreversible loss of coherence between the two superfluids, and transport cannot be described only within an uncorrelated phase-slip picture. Our findings open new directions for investigating the interplay between dissipative and superfluid transport in strongly correlated Fermi systems, and general concepts in out-of-equilibrium quantum systems.

Coupling Two-Dimensional MoTe2 and InGaZnO Thin-Film Materials for Hybrid PN Junction and CMOS Inverters.

PubMed

Lee, Han Sol; Choi, Kyunghee; Kim, Jin Sung; Yu, Sanghyuck; Ko, Kyeong Rok; Im, Seongil

2017-05-10

We report the fabrication of hybrid PN junction diode and complementary (CMOS) inverters, where 2D p-type MoTe 2 and n-type thin film InGaZnO (IGZO) are coupled for each device process. IGZO thin film was initially patterned by conventional photolithography either for n-type material in a PN diode or for n-channel of top-gate field-effect transistors (FET) in CMOS inverter. The hybrid PN junction diode shows a good ideality factor of 1.57 and quite a high ON/OFF rectification ratio of ∼3 × 10 4 . Under photons, our hybrid PN diode appeared somewhat stable only responding to high-energy photons of blue and ultraviolet. Our 2D nanosheet-oxide film hybrid CMOS inverter exhibits voltage gains as high as ∼40 at 5 V, low power consumption less than around a few nW at 1 V, and ∼200 μs switching dynamics.

Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model

NASA Astrophysics Data System (ADS)

Li, Chunhua; Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin; Su, Jiguo; Zhang, Yang

2016-07-01

Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.

Regulation and impairments of dynamic desmosome and corneodesmosome remodeling.

PubMed

Kitajima, Yasuo

2013-04-30

Desmosomes and corneodesmosomes are the most important adhering junctions to provide strength for the epidermal sheet structure made of living keratinocytes and enucleated corneocytes, respectively. These junctions are connected directly with transmembrane desmosomal cadherins, desmogleins (Dsgs) and desmocollins (Dscs), mainly Dsg1/Dsc1 and Dsg3/Dsc3 in desmosomes and Dsg1/Dsc1 with corneodesmosin in corneodesmosomes. Dsgs and Dscs are associated with several proteins at their inner cytoplasmic domains to anchor keratin intermediate filaments. Desmosomes are not static, but dynamic units that undergo regular remodeling to allow for keratinocyte outward-migration in the epidermis. Recently, two mutually-reversible desmosomal adhesion states have been recognized, i.e., "stable hyper-adhesion (Ca 2+ -independent)" and "dynamic weak-adhesion (Ca 2+ -dependent)". A remarkable impairment of this remodeling is observed in pemphigus vulgaris (an autoimmune blistering disease), caused by anti-Dsg3 antibodies, generating a weak-adhesion desmosome state. Immediately after formation, corneodesmosomes normally commit to degradation, which is complicatedly regulated by proteolytic cleavage of their respective extracellular portion(s), via kallikrein-regulated peptidases and cathepsins. This proteolytic activity is in turn controlled by a variety of inhibitory agents, including protease inhibitors, cholesterol sulfate, and an acidic gradient. The impairment of protease control causes keratinization disorders. This review focuses on the dynamic regulation of desmosomes and corneodesmosomes in relation to keratinization disorders.

Exploring the limits of optical microscopy: live cell and superresolution fluorescence microscopy of HIV-1 Transfer Between T lymphocytes Across the Virological Synapse

NASA Astrophysics Data System (ADS)

McNerney, Gregory Paul

Human immunodeficiency virus 1 (HIV-1) is a human retrovirus that efficiently, albeit gradually, overruns the immune system. An already infected T lymphocyte can latch onto another T lymphocyte whereby creating a virological synapse (VS); this junction drives viral assembly and transfer to the target cell in batches in an efficient, protective manor. My Ph.D. doctoral thesis focused on studying this transmission mechanism using advanced optical imaging modalities and the fully infectious fluorescent clone HIV Gag-iGFP. T lymphocytes are non-adherent cells (˜10 um thick) and the viral transmission process is fairly dynamic, hence we employed a custom spinning disk confocal microscope that revealed many interesting characteristics of this cooperative event. This methodology has low throughput as cell contact and transfer is at random. Optical tweezers was then added to the microscope to directly initiate cell contact at will. To assess when viral maturation occurs post-transfer, an optical assay based off of Forster resonance energy transfer was developed to monitor maturation. Structured illumination microscopy was further used to image the process at higher resolution and it showed that viral particles are not entering existing degradative compartments. Non-HIV-1 applications of the optical technologies are also reviewed.

Controlling dynamical entanglement in a Josephson tunneling junction

NASA Astrophysics Data System (ADS)

Ziegler, K.

2017-12-01

We analyze the evolution of an entangled many-body state in a Josephson tunneling junction and its dependence on the number of bosons and interaction strength. A N00N state, which is a superposition of two complementary Fock states, appears in the evolution with sufficient probability only for a moderate many-body interaction on an intermediate time scale. This time scale is inversely proportional to the tunneling rate. Many-body interaction strongly supports entanglement: The probability for creating an entangled state decays exponentially with the number of particles without many-body interaction, whereas it decays only like the inverse square root of the number of particles in the presence of many-body interaction.

Juncture flow improvement for wing/pylon configurations by using CFD methodology

NASA Technical Reports Server (NTRS)

Gea, Lie-Mine; Chyu, Wei J.; Stortz, Michael W.; Chow, Chuen-Yen

1993-01-01

Transonic flow field around a fighter wing/pylon configuration was simulated by using an implicit upwinding Navier-Stokes flow solver (F3D) and overset grid technology (Chimera). Flow separation and local shocks near the wing/pylon junction were observed in flight and predicted by numerical calculations. A new pylon/fairing shape was proposed to improve the flow quality. Based on numerical results, the size of separation area is significantly reduced and the onset of separation is delayed farther downstream. A smoother pressure gradient is also obtained near the junction area. This paper demonstrates that computational fluid dynamics (CFD) methodology can be used as a practical tool for aircraft design.

Theory of the Bloch oscillating transistor

NASA Astrophysics Data System (ADS)

Hassel, J.; Seppä, H.

2005-01-01

The Bloch oscillating transistor (BOT) is a device in which single electron current through a normal tunnel junction enhances Cooper pair current in a mesoscopic Josephson junction, leading to signal amplification. In this article we develop a theory in which the BOT dynamics is described as a two-level system. The theory is used to predict current-voltage characteristics and small-signal response. The transition from stable operation into the hysteretic regime is studied. By identifying the two-level switching noise as the main source of fluctuations, the expressions for equivalent noise sources and the noise temperature are derived. The validity of the model is tested by comparing the results with simulations and experiments.

Computational Investigation of the pH Dependence of Loop Flexibility and Catalytic Function in Glycoside Hydrolases*

PubMed Central

Bu, Lintao; Crowley, Michael F.; Himmel, Michael E.; Beckham, Gregg T.

2013-01-01

Cellulase enzymes cleave glycosidic bonds in cellulose to produce cellobiose via either retaining or inverting hydrolysis mechanisms, which are significantly pH-dependent. Many fungal cellulases function optimally at pH ∼5, and their activities decrease dramatically at higher or lower pH. To understand the molecular-level implications of pH in cellulase structure, we use a hybrid, solvent-based, constant pH molecular dynamics method combined with pH-based replica exchange to determine the pKa values of titratable residues of a glycoside hydrolase (GH) family 6 cellobiohydrolase (Cel6A) and a GH family 7 cellobiohydrolase (Cel7A) from the fungus Hypocrea jecorina. For both enzymes, we demonstrate that a bound substrate significantly affects the pKa values of the acid residues at the catalytic center. The calculated pKa values of catalytic residues confirm their proposed roles from structural studies and are consistent with the experimentally measured apparent pKa values. Additionally, GHs are known to impart a strained pucker conformation in carbohydrate substrates in active sites for catalysis, and results from free energy calculations combined with constant pH molecular dynamics suggest that the correct ring pucker is stable near the optimal pH for both Cel6A and Cel7A. Much longer molecular dynamics simulations of Cel6A and Cel7A with fixed protonation states based on the calculated pKa values suggest that pH affects the flexibility of tunnel loops, which likely affects processivity and substrate complexation. Taken together, this work demonstrates several molecular-level effects of pH on GH enzymes important for cellulose turnover in the biosphere and relevant to biomass conversion processes. PMID:23504310

How Social Media Affects the Dynamics of Protest

DTIC Science & Technology

2014-12-01

AFFECTS THE DYNAMICS OF PROTEST by Ajay Seebaluck December 2014 Thesis Advisor: T. Camber Warren Second Reader: Leo Blanken THIS PAGE...December 2014 Author: Ajay Seebaluck Approved by: T. Camber Warren, Ph.D. Thesis Advisor Leo Blanken, Ph.D. Second Reader...thanks to Professor Warren Camber and Professor Blanken Leo for their continued encouragement and tutelage. This thesis would not have been possible

The Josephson Effect and e/h

ERIC Educational Resources Information Center

Clarke, John

1970-01-01

Discusses the theory of the Josephson Effect, the derivation of the Josephson voltage-frequency relation, and methods of measuring the fundamental constatn ratio e/h. Various types of Josephson junctions are described. The impact of the measurement of e/h upin the fundamental constants and quantum electro-dynamics is briefly discussed.…

The Nature of Dynamic Arteriolar Vasoreactivity: A Mini-Review and A classification Scheme

DTIC Science & Technology

1993-06-08

small veins. In this videomicroscopy study we always examined a junction of a true transverse (TR) and a true terminal (TE) arteriole within the muscle...by LDF), comparisons of vascular wall behavior were made from intravital videomicroscopy records. Vasoreactive behavior of the microvessels was

Epidural varix at the cervicothoracic junction: unusual cause of quadriplegia: a case report.

PubMed

Bapat, Mihir; Metkar, Umesh

2006-02-01

A case report describing an unusual incident of quadriplegia in a young adult male caused by an epidural varix at the cervicothoracic junction. To report an unusual case of quadriplegia caused by an epidural varix at the cervicothoracic junction. Epidural varices are dilated tortuous elongated veins inside the central canal. In degenerative spinal stenosis, these varices are a result of venous stagnation and contribute to the pathogenesis of radicular pain. In the absence of stenosis, primary varicosities develop as a result of dynamic obstruction to venous outflow during spinal movements. A primary epidural varix can produce neurologic deficit similar to a space occupying lesion within the spinal canal. The myeloradiculopathy is of a slow progressive nature. A young man presented with an acute onset flaccid quadriplegia in the absence of significant trauma. Magnetic resonance imaging revealed an extradural space occupying lesion at the cervicothoracic junction that was diagnosed as an isolated epidural varix during surgery. No neurologic recovery occurred. Postoperative magnetic resonance imaging revealed a syrinx in the cervicothoracic cord. In the absence of other precipitating factors, the cord injury was attributed to the epidural varix. A temporary impedance to the venous outflow with the increase in the venous pressure has been hypothesized as the mechanism of cord injury.

TWO INNEXINS OF Spodoptera litura INFLUENCES HEMICHANNEL AND GAP JUNCTION FUNCTIONS IN CELLULAR IMMUNE RESPONSES.

PubMed

Pang, Zunyu; Li, Ming; Yu, Dongshuai; Yan, Zhang; Liu, Xinyi; Ji, Xinglai; Yang, Yang; Hu, Jiansheng; Luo, Kaijun

2015-09-01

Insect cellular immune responses include encapsulation, nodule formation, and phagocytosis. Hemichannels and gap junctions are involved in these cellular actions. Innexins (Inxs: analogous to the vertebrate connexins) form hemichannels and gap junctions, but the molecular mechanisms underlying their biology is still unclear. In this article, we reported a steady-state level of Inxs (SpliInxs) in hemocytes of Spodoptera litura, which formed nonfunctional hemichannels on the cell surface to maintain normal metabolism. We also reported that two innnexins (SpliInx2 and SpliInx3) were expressed significantly higher in hemocytes compared to other tissues, suggesting that they play important roles in hemocytes. Amino acid analysis found that two cysteine residues in two extracellular loops provided the capability for SpliInx2 and SpliInx3 hemichannels to dock into gap junctions. Western blotting demonstrated that both extracellular and intracellular loops of SpliInx3 and the extracellular loops of SpliInx2 might undergo posttranslational modification during the formation of a steady-state hemichannel. During hemichannel formation, SpliInx2 presented as one isoform, while SpliInx3 presented as three isoforms. These results provide fundamental knowledge for further study of how steady-state levels of SpliInxs are dynamically adjusted to perform cellular immune responses under immune challenge. © 2015 Wiley Periodicals, Inc.

Simulating botulinum neurotoxin with constant pH molecular dynamics in Generalized Born implicit solvent

NASA Astrophysics Data System (ADS)

Chen, Yongzhi; Chen, Xin; Deng, Yuefan

2007-07-01

A new method was proposed by Mongan et al. for constant pH molecular dynamics simulation and was implemented in AMBER 8 package. Protonation states are modeled with different charge sets, and titrating residues are sampled from a Boltzmann distribution of protonation states. The simulation periodically adopts Monte Carlo sampling based on Generalized Born (GB) derived energies. However, when this approach was applied to a bio-toxin, Botulinum Neurotoxin Type A (BoNT/A) at pH 4.4, 4.7, 5.0, 6.8 and 7.2, the pK predictions yielded by the method were inconsistent with the experimental values. The systems being simulated were divergent. Furthermore, the system behaviors in a very weak acidic solution (pH 6.8) and in a very weak basic solution (pH 7.2) were significantly different from the neutral case (pH 7.0). Hence, we speculate this method may require further study for modeling large biomolecule.

Influence of pH on dynamics of microbial enhanced oil recovery processes using biosurfactant producing Pseudomonas putida: Mathematical modelling and numerical simulation.

PubMed

Sivasankar, P; Suresh Kumar, G

2017-01-01

In present work, the influence of reservoir pH conditions on dynamics of microbial enhanced oil recovery (MEOR) processes using Pseudomonas putida was analysed numerically from the developed mathematical model for MEOR processes. Further, a new strategy to improve the MEOR performance has also been proposed. It is concluded from present study that by reversing the reservoir pH from highly acidic to low alkaline condition (pH 5-8), flow and mobility of displaced oil, displacement efficiency, and original oil in place (OOIP) recovered gets significantly enhanced, resulting from improved interfacial tension (IFT) reduction by biosurfactants. At pH 8, maximum of 26.1% of OOIP was recovered with higher displacement efficiency. The present study introduces a new strategy to increase the recovery efficiency of MEOR technique by characterizing the biosurfactants for IFT min /IFT max values for different pH conditions and subsequently, reversing the reservoir pH conditions at which the IFT min /IFT max value is minimum. Copyright © 2016 Elsevier Ltd. All rights reserved.

A low pH does not determine the community dynamics of spontaneously developed backslopped liquid wheat sourdoughs but does influence their metabolite kinetics.

PubMed

Van Kerrebroeck, Simon; Bastos, Francisca Casanova C; Harth, Henning; De Vuyst, Luc

2016-12-19

This study dealt with the influence of a crucial pH value of 4.0 on the microbiota of spontaneously fermented backslopped liquid wheat sourdoughs. Two spontaneously fermented wheat sourdough fermentation experiments were carried out, one without control of the pH and one with the pH kept constant at pH4.0, both during nine backslopping steps. In each case, two additional backslopping steps were carried out, with the pH kept constant at 4.0 and with free pH, respectively. Keeping the pH constant at 4.0 changed the microbial community dynamics and metabolite kinetics of the sourdough fermentations. A slower prevalence of sourdough-specific Kazachstania yeasts occurred. Nevertheless, in both experiments, Lactobacillus fermentum, Lb. plantarum/pentosus/paraplantarum, and Kazachstania exigua/bulderi/barnettii prevailed ultimately. The lactic acid and ethanol concentration profiles were affected positively by keeping the pH constant at a minimum of 4.0 as well as the l- and d-lactic acid ratio profile, a potential biological marker for sourdough stability and maturity. Also, the concentration and diversity of acetate esters and their precursors, in particular isoamyl acetate and isoamyl alcohol, were affected negatively by the pH control, indicating the role of pH stress in the sourdough aroma formation. Copyright © 2016 Elsevier B.V. All rights reserved.

Influence of binding pH and protein solubility on the dynamic binding capacity in hydrophobic interaction chromatography.

PubMed

Baumann, Pascal; Baumgartner, Kai; Hubbuch, Jürgen

2015-05-29

Hydrophobic interaction chromatography (HIC) is one of the most frequently used purification methods in biopharmaceutical industry. A major drawback of HIC, however, is the rather low dynamic binding capacity (DBC) obtained when compared to e.g. ion exchange chromatography (IEX). The typical purification procedure for HIC includes binding at neutral pH, independently of the proteins nature and isoelectric point. Most approaches to process intensification are based on resin and salt screenings. In this paper a combination of protein solubility data and varying binding pH leads to a clear enhancement of dynamic binding capacity. This is shown for three proteins of acidic, neutral, and alkaline isoelectric points. High-throughput solubility screenings as well as miniaturized and parallelized breakthrough curves on Media Scout RoboColumns (Atoll, Germany) were conducted at pH 3-10 on a fully automated robotic workstation. The screening results show a correlation between the DBC and the operational pH, the protein's isoelectric point and the overall solubility. Also, an inverse relationship of DBC in HIC and the binding kinetics was observed. By changing the operational pH, the DBC could be increased up to 30% compared to the standard purification procedure performed at neutral pH. As structural changes of the protein are reported during HIC processes, the applied samples and the elution fractions were proven not to be irreversibly unfolded. Copyright © 2015 Elsevier B.V. All rights reserved.

Highly Stretchable Potentiometric pH Sensor Fabricated via Laser Carbonization and Machining of Carbon-Polyaniline Composite.

PubMed

Rahimi, Rahim; Ochoa, Manuel; Tamayol, Ali; Khalili, Shahla; Khademhosseini, Ali; Ziaie, Babak

2017-03-15

The development of stretchable sensors has recently attracted considerable attention. These sensors have been used in wearable and robotics applications, such as personalized health-monitoring, motion detection, and human-machine interfaces. Herein, we report on a highly stretchable electrochemical pH sensor for wearable point-of-care applications that consists of a pH-sensitive working electrode and a liquid-junction-free reference electrode, in which the stretchable conductive interconnections are fabricated by laser carbonizing and micromachining of a polyimide sheet bonded to an Ecoflex substrate. This method produces highly porous carbonized 2D serpentine traces that are subsequently permeated with polyaniline (PANI) as the conductive filler, binding material, and pH-sensitive membrane. The experimental and simulation results demonstrate that the stretchable serpentine PANI/C-PI interconnections with an optimal trace width of 0.3 mm can withstand elongations of up to 135% and are robust to more than 12 000 stretch-and-release cycles at 20% strain without noticeable change in the resistance. The pH sensor displays a linear sensitivity of -53 mV/pH (r 2 = 0.976) with stable performance in the physiological range of pH 4-10. The sensor shows excellent stability to applied longitudinal and transverse strains up to 100% in different pH buffer solutions with a minimal deviation of less than ±4 mV. The material biocompatibility is confirmed with NIH 3T3 fibroblast cells via PrestoBlue assays.

Investigating spin-transfer torques induced by thermal gradients in magnetic tunnel junctions by using micro-cavity ferromagnetic resonance

NASA Astrophysics Data System (ADS)

Cansever, H.; Narkowicz, R.; Lenz, K.; Fowley, C.; Ramasubramanian, L.; Yildirim, O.; Niesen, A.; Huebner, T.; Reiss, G.; Lindner, J.; Fassbender, J.; Deac, A. M.

2018-06-01

Similar to electrical currents flowing through magnetic multilayers, thermal gradients applied across the barrier of a magnetic tunnel junction may induce pure spin-currents and generate ‘thermal’ spin-transfer torques large enough to induce magnetization dynamics in the free layer. In this study, we describe a novel experimental approach to observe spin-transfer torques induced by thermal gradients in magnetic multilayers by studying their ferromagnetic resonance response in microwave cavities. Utilizing this approach allows for measuring the magnetization dynamics on micron/nano-sized samples in open-circuit conditions, i.e. without the need of electrical contacts. We performed first experiments on magnetic tunnel junctions patterned into 6  ×  9 µm2 ellipses from Co2FeAl/MgO/CoFeB stacks. We conducted microresonator ferromagnetic resonance (FMR) under focused laser illumination to induce thermal gradients in the layer stack and compared them to measurements in which the sample was globally heated from the backside of the substrate. Moreover, we carried out broadband FMR measurements under global heating conditions on the same extended films the microstructures were later on prepared from. The results clearly demonstrate the effect of thermal spin-torque on the FMR response and thus show that the microresonator approach is well suited to investigate thermal spin-transfer-driven processes for small temperatures gradients, far below the gradients required for magnetic switching.

Phosphorylation of histone H3(T118) alters nucleosome dynamics and remodeling

PubMed Central

North, Justin A.; Javaid, Sarah; Ferdinand, Michelle B.; Chatterjee, Nilanjana; Picking, Jonathan W.; Shoffner, Matthew; Nakkula, Robin J.; Bartholomew, Blaine; Ottesen, Jennifer J.; Fishel, Richard; Poirier, Michael G.

2011-01-01

Nucleosomes, the fundamental units of chromatin structure, are regulators and barriers to transcription, replication and repair. Post-translational modifications (PTMs) of the histone proteins within nucleosomes regulate these DNA processes. Histone H3(T118) is a site of phosphorylation [H3(T118ph)] and is implicated in regulation of transcription and DNA repair. We prepared H3(T118ph) by expressed protein ligation and determined its influence on nucleosome dynamics. We find H3(T118ph) reduces DNA–histone binding by 2 kcal/mol, increases nucleosome mobility by 28-fold and increases DNA accessibility near the dyad region by 6-fold. Moreover, H3(T118ph) increases the rate of hMSH2–hMSH6 nucleosome disassembly and enables nucleosome disassembly by the SWI/SNF chromatin remodeler. These studies suggest that H3(T118ph) directly enhances and may reprogram chromatin remodeling reactions. PMID:21576235

A genetically-encoded chloride and pH sensor for dissociating ion dynamics in the nervous system

PubMed Central

Raimondo, Joseph V.; Joyce, Bradley; Kay, Louise; Schlagheck, Theresa; Newey, Sarah E.; Srinivas, Shankar; Akerman, Colin J.

2013-01-01

Within the nervous system, intracellular Cl− and pH regulate fundamental processes including cell proliferation, metabolism, synaptic transmission, and network excitability. Cl− and pH are often co-regulated, and network activity results in the movement of both Cl− and H+. Tools to accurately measure these ions are crucial for understanding their role under physiological and pathological conditions. Although genetically-encoded Cl− and pH sensors have been described previously, these either lack ion specificity or are unsuitable for neuronal use. Here we present ClopHensorN—a new genetically-encoded ratiometric Cl− and pH sensor that is optimized for the nervous system. We demonstrate the ability of ClopHensorN to dissociate and simultaneously quantify Cl− and H+ concentrations under a variety of conditions. In addition, we establish the sensor's utility by characterizing activity-dependent ion dynamics in hippocampal neurons. PMID:24312004

A genetically-encoded chloride and pH sensor for dissociating ion dynamics in the nervous system.

PubMed

Raimondo, Joseph V; Joyce, Bradley; Kay, Louise; Schlagheck, Theresa; Newey, Sarah E; Srinivas, Shankar; Akerman, Colin J

2013-01-01

Within the nervous system, intracellular Cl(-) and pH regulate fundamental processes including cell proliferation, metabolism, synaptic transmission, and network excitability. Cl(-) and pH are often co-regulated, and network activity results in the movement of both Cl(-) and H(+). Tools to accurately measure these ions are crucial for understanding their role under physiological and pathological conditions. Although genetically-encoded Cl(-) and pH sensors have been described previously, these either lack ion specificity or are unsuitable for neuronal use. Here we present ClopHensorN-a new genetically-encoded ratiometric Cl(-) and pH sensor that is optimized for the nervous system. We demonstrate the ability of ClopHensorN to dissociate and simultaneously quantify Cl(-) and H(+) concentrations under a variety of conditions. In addition, we establish the sensor's utility by characterizing activity-dependent ion dynamics in hippocampal neurons.

Segmentation and Quantitative Analysis of Epithelial Tissues.

PubMed

Aigouy, Benoit; Umetsu, Daiki; Eaton, Suzanne

2016-01-01

Epithelia are tissues that regulate exchanges with the environment. They are very dynamic and can acquire virtually any shape; at the cellular level, they are composed of cells tightly connected by junctions. Most often epithelia are amenable to live imaging; however, the large number of cells composing an epithelium and the absence of informatics tools dedicated to epithelial analysis largely prevented tissue scale studies. Here we present Tissue Analyzer, a free tool that can be used to segment and analyze epithelial cells and monitor tissue dynamics.

Focal adhesion kinase is a regulator of F-actin dynamics

PubMed Central

Li, Stephen YT; Mruk, Dolores D; Cheng, C Yan

2013-01-01

During spermatogenesis, spermatogonia (2n, diploid) undergo a series of mitotic divisions as well as differentiation to become spermatocytes, which enter meiosis I to be followed by meiosis II to form round spermatids (1n, haploid), and then differentiate into spermatozoa (1n, haploid) via spermiogenesis. These events take place in the epithelium of the seminiferous tubule, involving extensive junction restructuring at the Sertoli-Sertoli and Sertoli-germ cell interface to allow the transport of developing germ cells across the epithelium. Although structural aspects of these cell-cell junctions have been studied, the underlying mechanism(s) that governs these events has yet to be explored. Earlier studies have shown that a non-receptor protein tyrosine kinase known as focal adhesion kinase (FAK) is a likely regulator of these events due to the stage-specific and spatiotemporal expression of its various phosphorylated/activated forms at the testis-specific anchoring junctions in the testis, as well as its association with actin regulatory proteins. Recent studies have shown that FAK, in particular its two activated phosphorylated forms p-FAK-Tyr407 and p-FAK-Tyr397, are crucial regulators in modulating junction restructuring at the Sertoli cell-cell interface at the blood-testis barrier (BTB) known as the basal ectoplasmic specialization (basal ES), as well as at the Sertoli-spermatid interface called apical ES during spermiogenesis via its effects on the filamentous (F)-actin organization at the ES. We herein summarize and critically evaluate the current knowledge regarding the physiological significance of FAK in regulating BTB and apical ES dynamics by governing the conversion of actin filaments at the ES from a “bundled” to a “de-bundled/branched” configuration and vice versa. We also provide a molecular model on the role of FAK in regulating these events based on the latest findings in the field. PMID:24381802

Nanoscale patterning controls inorganic-membrane interface structure

NASA Astrophysics Data System (ADS)

Almquist, Benjamin D.; Verma, Piyush; Cai, Wei; Melosh, Nicholas A.

2011-02-01

The ability to non-destructively integrate inorganic structures into or through biological membranes is essential to realizing full bio-inorganic integration, including arrayed on-chip patch-clamps, drug delivery, and biosensors. Here we explore the role of nanoscale patterning on the strength of biomembrane-inorganic interfaces. AFM measurements show that inorganic probes functionalized with hydrophobic bands with thicknesses complimentary to the hydrophobic lipid bilayer core exhibit strong attachment in the bilayer. As hydrophobic band thickness increases to 2-3 times the bilayer core the interfacial strength decreases, comparable to homogeneously hydrophobic probes. Analytical calculations and molecular dynamics simulations predict a transition between a `fused' interface and a `T-junction' that matches the experimental results, showing lipid disorder and defect formation for thicker bands. These results show that matching biological length scales leads to more intimate bio-inorganic junctions, enabling rational design of non-destructive membrane interfaces.The ability to non-destructively integrate inorganic structures into or through biological membranes is essential to realizing full bio-inorganic integration, including arrayed on-chip patch-clamps, drug delivery, and biosensors. Here we explore the role of nanoscale patterning on the strength of biomembrane-inorganic interfaces. AFM measurements show that inorganic probes functionalized with hydrophobic bands with thicknesses complimentary to the hydrophobic lipid bilayer core exhibit strong attachment in the bilayer. As hydrophobic band thickness increases to 2-3 times the bilayer core the interfacial strength decreases, comparable to homogeneously hydrophobic probes. Analytical calculations and molecular dynamics simulations predict a transition between a `fused' interface and a `T-junction' that matches the experimental results, showing lipid disorder and defect formation for thicker bands. These results show that matching biological length scales leads to more intimate bio-inorganic junctions, enabling rational design of non-destructive membrane interfaces. Electronic supplementary information (ESI) available: Breakthrough rate as a function of force plots for 5 nm, 10 nm and ∞-probes.. See DOI: 10.1039/c0nr00486c

Modular Nuclease-Responsive DNA Three-Way Junction-Based Dynamic Assembly of a DNA Device and Its Sensing Application.

PubMed

Zhu, Jing; Wang, Lei; Xu, Xiaowen; Wei, Haiping; Jiang, Wei

2016-04-05

Here, we explored a modular strategy for rational design of nuclease-responsive three-way junctions (TWJs) and fabricated a dynamic DNA device in a "plug-and-play" fashion. First, inactivated TWJs were designed, which contained three functional domains: the inaccessible toehold and branch migration domains, the specific sites of nucleases, and the auxiliary complementary sequence. The actions of different nucleases on their specific sites in TWJs caused the close proximity of the same toehold and branch migration domains, resulting in the activation of the TWJs and the formation of a universal trigger for the subsequent dynamic assembly. Second, two hairpins (H1 and H2) were introduced, which could coexist in a metastable state, initially to act as the components for the dynamic assembly. Once the trigger initiated the opening of H1 via TWJs-driven strand displacement, the cascade hybridization of hairpins immediately switched on, resulting in the formation of the concatemers of H1/H2 complex appending numerous integrated G-quadruplexes, which were used to obtain label-free signal readout. The inherent modularity of this design allowed us to fabricate a flexible DNA dynamic device and detect multiple nucleases through altering the recognition pattern slightly. Taking uracil-DNA glycosylase and CpG methyltransferase M.SssI as models, we successfully realized the butt joint between the uracil-DNA glycosylase and M.SssI recognition events and the dynamic assembly process. Furthermore, we achieved ultrasensitive assay of nuclease activity and the inhibitor screening. The DNA device proposed here will offer an adaptive and flexible tool for clinical diagnosis and anticancer drug discovery.

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

Li, Chunhua; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108; Lv, Dashuai

Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regionsmore » between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.« less

HdeB chaperone activity is coupled to its intrinsic dynamic properties

PubMed Central

Ding, Jienv; Yang, Chengfeng; Niu, Xiaogang; Hu, Yunfei; Jin, Changwen

2015-01-01

Enteric bacteria encounter extreme acidity when passing through hosts’ stomach. Since the bacterial periplasmic space quickly equilibrates with outer environment, an efficient acid resistance mechanism is essential in preventing irreversible protein denaturation/aggregation and maintaining bacteria viability. HdeB, along with its homolog HdeA, was identified as a periplasmic acid-resistant chaperone. Both proteins exist as homodimers and share similar monomeric structures under neutral pH, while showing different dimeric packing interfaces. Previous investigations show that HdeA functions through an acid-induced dimer-to-monomer transition and partial unfolding at low pH (pH 2–3), resulting in exposure of hydrophobic surfaces that bind substrate proteins. In contrast, HdeB appears to have a much higher optimal activation pH (pH 4–5), under which condition the protein maintains a well-folded dimer and the mechanism for its chaperone activity remains elusive. Herein, we present an NMR study of HdeB to investigate its dynamic properties. Our results reveal that HdeB undergoes significant micro- to milli-second timescale conformational exchanges at neutral to near-neutral pH, under the later condition it exhibits optimal activity. The current study indicates that HdeB activation is coupled to its intrinsic dynamics instead of structural changes, and therefore its functional mechanism is apparently different from HdeA. PMID:26593705

Highly Sensitive and Wide-Dynamic-Range Multichannel Optical-Fiber pH Sensor Based on PWM Technique.

PubMed

Khan, Md Rajibur Rahaman; Kang, Shin-Won

2016-11-09

In this study, we propose a highly sensitive multichannel pH sensor that is based on an optical-fiber pulse width modulation (PWM) technique. According to the optical-fiber PWM method, the received sensing signal's pulse width changes when the optical-fiber pH sensing-element of the array comes into contact with pH buffer solutions. The proposed optical-fiber PWM pH-sensing system offers a linear sensing response over a wide range of pH values from 2 to 12, with a high pH-sensing ability. The sensitivity of the proposed pH sensor is 0.46 µs/pH, and the correlation coefficient R² is approximately 0.997. Additional advantages of the proposed optical-fiber PWM pH sensor include a short/fast response-time of about 8 s, good reproducibility properties with a relative standard deviation (RSD) of about 0.019, easy fabrication, low cost, small size, reusability of the optical-fiber sensing-element, and the capability of remote sensing. Finally, the performance of the proposed PWM pH sensor was compared with that of potentiometric, optical-fiber modal interferometer, and optical-fiber Fabry-Perot interferometer pH sensors with respect to dynamic range width, linearity as well as response and recovery times. We observed that the proposed sensing systems have better sensing abilities than the above-mentioned pH sensors.

Highly Sensitive and Wide-Dynamic-Range Multichannel Optical-Fiber pH Sensor Based on PWM Technique

PubMed Central

Khan, Md. Rajibur Rahaman; Kang, Shin-Won

2016-01-01

In this study, we propose a highly sensitive multichannel pH sensor that is based on an optical-fiber pulse width modulation (PWM) technique. According to the optical-fiber PWM method, the received sensing signal’s pulse width changes when the optical-fiber pH sensing-element of the array comes into contact with pH buffer solutions. The proposed optical-fiber PWM pH-sensing system offers a linear sensing response over a wide range of pH values from 2 to 12, with a high pH-sensing ability. The sensitivity of the proposed pH sensor is 0.46 µs/pH, and the correlation coefficient R2 is approximately 0.997. Additional advantages of the proposed optical-fiber PWM pH sensor include a short/fast response-time of about 8 s, good reproducibility properties with a relative standard deviation (RSD) of about 0.019, easy fabrication, low cost, small size, reusability of the optical-fiber sensing-element, and the capability of remote sensing. Finally, the performance of the proposed PWM pH sensor was compared with that of potentiometric, optical-fiber modal interferometer, and optical-fiber Fabry–Perot interferometer pH sensors with respect to dynamic range width, linearity as well as response and recovery times. We observed that the proposed sensing systems have better sensing abilities than the above-mentioned pH sensors. PMID:27834865

Pgas, a Low-pH-Induced Promoter, as a Tool for Dynamic Control of Gene Expression for Metabolic Engineering of Aspergillus niger

PubMed Central

Yin, Xian; Shin, Hyun-Dong; Li, Jianghua; Du, Guocheng; Chen, Jian

2017-01-01

ABSTRACT The dynamic control of gene expression is important for adjusting fluxes in order to obtain desired products and achieve appropriate cell growth, particularly when the synthesis of a desired product drains metabolites required for cell growth. For dynamic gene expression, a promoter responsive to a particular environmental stressor is vital. Here, we report a low-pH-inducible promoter, Pgas, which promotes minimal gene expression at pH values above 5.0 but functions efficiently at low pHs, such as pH 2.0. First, we performed a transcriptional analysis of Aspergillus niger, an excellent platform for the production of organic acids, and we found that the promoter Pgas may act efficiently at low pH. Then, a gene for synthetic green fluorescent protein (sGFP) was successfully expressed by Pgas at pH 2.0, verifying the results of the transcriptional analysis. Next, Pgas was used to express the cis-aconitate decarboxylase (cad) gene of Aspergillus terreus in A. niger, allowing the production of itaconic acid at a titer of 4.92 g/liter. Finally, we found that Pgas strength was independent of acid type and acid ion concentration, showing dependence on pH only. IMPORTANCE The promoter Pgas can be used for the dynamic control of gene expression in A. niger for metabolic engineering to produce organic acids. This promoter may also be a candidate tool for genetic engineering. PMID:28087530

Temporo-parietal junction activity in theory-of-mind tasks: falseness, beliefs, or attention.

PubMed

Aichhorn, Markus; Perner, Josef; Weiss, Benjamin; Kronbichler, Martin; Staffen, Wolfgang; Ladurner, Gunther

2009-06-01

By combining the false belief (FB) and photo (PH) vignettes to identify theory-of-mind areas with the false sign (FS) vignettes, we re-establish the functional asymmetry between the left and right temporo-parietal junction (TPJ). The right TPJ (TPJ-R) is specially sensitive to processing belief information, whereas the left TPJ (TPJ-L) is equally responsible for FBs as well as FSs. Measuring BOLD at two time points in each vignette, at the time the FB-inducing information (or lack of information) is presented and at the time the test question is processed, made clear that the FB is processed spontaneously as soon as the relevant information is presented and not on demand for answering the question in contrast to extant behavioral data. Finally, a fourth, true belief vignette (TB) required teleological reasoning, that is, prediction of a rational action without any doubts being raised about the adequacy of the actor's information about reality. Activation by this vignette supported claims that the TPJ-R is activated by TBs as well as FBs.

Sparse short-distance connections enhance calcium wave propagation in a 3D model of astrocyte networks

PubMed Central

Lallouette, Jules; De Pittà, Maurizio; Ben-Jacob, Eshel; Berry, Hugues

2014-01-01

Traditionally, astrocytes have been considered to couple via gap-junctions into a syncytium with only rudimentary spatial organization. However, this view is challenged by growing experimental evidence that astrocytes organize as a proper gap-junction mediated network with more complex region-dependent properties. On the other hand, the propagation range of intercellular calcium waves (ICW) within astrocyte populations is as well highly variable, depending on the brain region considered. This suggests that the variability of the topology of gap-junction couplings could play a role in the variability of the ICW propagation range. Since this hypothesis is very difficult to investigate with current experimental approaches, we explore it here using a biophysically realistic model of three-dimensional astrocyte networks in which we varied the topology of the astrocyte network, while keeping intracellular properties and spatial cell distribution and density constant. Computer simulations of the model suggest that changing the topology of the network is indeed sufficient to reproduce the distinct ranges of ICW propagation reported experimentally. Unexpectedly, our simulations also predict that sparse connectivity and restriction of gap-junction couplings to short distances should favor propagation while long–distance or dense connectivity should impair it. Altogether, our results provide support to recent experimental findings that point toward a significant functional role of the organization of gap-junction couplings into proper astroglial networks. Dynamic control of this topology by neurons and signaling molecules could thus constitute a new type of regulation of neuron-glia and glia-glia interactions. PMID:24795613

Development of an economical, autonomous pHstat system for culturing phytoplankton under steady state or dynamic conditions.

PubMed

Golda, Rachel L; Golda, Mark D; Hayes, Jacqueline A; Peterson, Tawnya D; Needoba, Joseph A

2017-05-01

Laboratory investigations of physiological processes in phytoplankton require precise control of experimental conditions. Chemostats customized to control and maintain stable pH levels (pHstats) are ideally suited for investigations of the effects of pH on phytoplankton physiology, for example in context of ocean acidification. Here we designed and constructed a simple, flexible pHstat system and demonstrated its operational capabilities under laboratory culture conditions. In particular, the system is useful for simulating natural cyclic pH variability within aquatic ecosystems, such as diel fluctuations that result from metabolic activity or tidal mixing in estuaries. The pHstat system operates in two modes: (1) static/set point pH, which maintains pH at a constant level, or (2) dynamic pH, which generates regular, sinusoidal pH fluctuations by systematically varying pH according to user-defined parameters. The pHstat is self-regulating through the use of interchangeable electronically controlled reagent or gas-mediated pH-modification manifolds, both of which feature flow regulation by solenoid valves. Although effective pH control was achieved using both liquid reagent additions and gas-mediated methods, the liquid manifold exhibited tighter control (±0.03pH units) of the desired pH than the gas manifold (±0.10pH units). The precise control provided by this pHstat system, as well as its operational flexibility will facilitate studies that examine responses by marine microbiota to fluctuations in pH in aquatic ecosystems. Copyright © 2017 Elsevier B.V. All rights reserved.

Dynamics and Manipulation of Nanomagnets

NASA Astrophysics Data System (ADS)

Cai, Liufei

This thesis presents my work on the spin dynamics of nanomagnets and investigates the possibility of manipulating nanomagnets by various means. Most of the work has been published. Some has been submitted for publication. The structure of this thesis is as follows. In Chapter 1, I present the theory of manipulation of a nanomagnet by rotating ac fields whose frequency is time dependent. Theory has been developed that maps the problem onto Landau-Zener problem. For the linear frequency sweep the switching phase diagrams are obtained on the amplitude of the ac field and the frequency sweep rate. Switching conditions have been obtained numerically and analytically. For the nonlinear frequency sweep, the optimal time dependence of the frequency is obtained analytically with account of damping that gives the fastest controllable switching of the magnetization. In Chapter 2, interaction between a nanomagnet and a Josephson junction has been studied. The I-V curve of the Josephson junction in the proximity of a nanomagnet shows Shapiro-like steps due to the ac field generated by the precessing magnetic moment. Possibility of switching of the magnetic moment by a time-linear voltage in the Josephson junction is demonstrated. Realization of the optimal switching is suggested that employs two perpendicular Josephson junctions with time-dependent voltage signals. The result is shown to be robust against voltage noises. Quantum-mechanical coupling between the nanomagnet considered as a two-level system and a Josephson junction has been studied and quantum oscillations of the populations of the spin states have been computed. In Chapter 3, the switching dynamics of a nanomagnet embedded in a torsional oscillator that serves as a conducting wire for a spin current has been investigated. Generalized Slonczewski's equation is derived. The coupling of the nanomagnet, the torsional oscillator and the spin current generates a number of interesting phenomena. The mechanically-assisted magnetization switching is studied, in which the magnetization can be reversed by tilting the torsional oscillator. The effect of the torsional oscillator on the switching of the magnetization in the presence of spin-polarized current is computed. Combined effects of the spin current and a mechanical kick of the torsional oscillator have been studied. In Chapter 4, skyrmion dynamics and interaction of the skyrmion with an electron have been studied. Corrections to the spin texture of the skyrmion due to the crystal lattice have been computed. Due to the lattice effects the skyrmion collapses in clean ferromagnetic and anti-ferromagnetic materials. The lifetime of the skyrmion has been computed numerically and compared with analytical theory. In doped anti-ferromagnetic materials the weak attraction between a skyrmion and an electron may generate a bound state. In Chapter 5, experimental results of the NIST group on magnetic multilayer microcantilevers have been analyzed. Theoretical framework has been suggested that explains the observed strong damping effect of the platinum layer on the mechanical oscillations of Py-Pt bilayer cantilevers. The strong spin-orbit coupling of platinum is shown to impede the motion of the domain wall in permalloy and to dramatically increase the damping of the cantilever motion.

Dual-Ratiometric Fluorescent Nanoprobe for Visualizing the Dynamic Process of pH and Superoxide Anion Changes in Autophagy and Apoptosis.

PubMed

Yang, Limin; Chen, Yuanyuan; Yu, Zhengze; Pan, Wei; Wang, Hongyu; Li, Na; Tang, Bo

2017-08-23

Autophagy and apoptosis are closely associated with various pathological and physiological processes in cell cycles. Investigating the dynamic changes of intracellular active molecules in autophagy and apoptosis is of great significance for clarifying their inter-relationship and regulating mechanism in many diseases. In this study, we develop a dual-ratiometric fluorescent nanoprobe for quantitatively differentiating the dynamic process of superoxide anion (O 2 •- ) and pH changes in autophagy and apoptosis in HeLa cells. A rhodamine B-loaded mesoporous silica core was used as the reference, and fluorescence probes for pH and O 2 •- measurement were doped in the outer layer shell of SiO 2 . Then, chitosan and triphenylphosphonium were modified on the surface of SiO 2 . The experimental results showed that the nanoprobe is able to simultaneously and precisely visualize the changes of mitochondrial O 2 •- and pH in HeLa cells. The kinetics data revealed that the changes of pH and O 2 •- during autophagy and apoptosis in HeLa cells were significantly different. The pH value was decreased at the early stage of apoptosis and autophagy, whereas the O 2 •- level was enhanced at the early stage of apoptosis and almost unchanged at the initial stage of autophagy. At the late stage of apoptosis and autophagy, the concentration of O 2 •- was increased, whereas the pH was decreased at the late stage of autophagy and almost unchanged at the late stage of apoptosis. We hope that the present results provide useful information for studying the effects of O 2 •- and pH in autophagy and apoptosis in various pathological conditions and diseases.

The acid pocket: a target for treatment in reflux disease?

PubMed

Kahrilas, Peter J; McColl, Kenneth; Fox, Mark; O'Rourke, Lisa; Sifrim, Daniel; Smout, Andre J P M; Boeckxstaens, Guy

2013-07-01

The nadir esophageal pH of reflux observed during pH monitoring in the postprandial period is often more acidic than the concomitant intragastric pH. This paradox prompted the discovery of the "acid pocket", an area of unbuffered gastric acid that accumulates in the proximal stomach after meals and serves as the reservoir for acid reflux in healthy individuals and gastroesophageal reflux disease (GERD) patients. However, there are differentiating features between these populations in the size and position of the acid pocket, with GERD patients predisposed to upward migration of the proximal margin onto the esophageal mucosa, particularly when supine. This upward migration of acid, sometimes referred to as an "acid film", likely contributes to mucosal pathology in the region of the squamocolumnar junction. Furthermore, movement of the acid pocket itself to a supradiaphragmatic location with hiatus hernia increases the propensity for acid reflux by all conventional mechanisms. Consequently, the acid pocket is an attractive target for GERD therapy. It may be targeted in a global way with proton pump inhibitors that attenuate acid pocket development, or with alginate/antacid combinations that colocalize with the acid pocket and displace it distally, thereby demonstrating the potential for selective targeting of the acid pocket in GERD.

pH during non-synaptic epileptiform activity-computational simulations.

PubMed

Rodrigues, Antônio Márcio; Santos, Luiz Eduardo Canton; Covolan, Luciene; Hamani, Clement; de Almeida, Antônio-Carlos Guimarães

2015-09-02

The excitability of neuronal networks is strongly modulated by changes in pH. The origin of these changes, however, is still under debate. The high complexity of neural systems justifies the use of computational simulation to investigate mechanisms that are possibly involved. Simulated neuronal activity includes non-synaptic epileptiform events (NEA) induced in hippocampal slices perfused with high-K(+) and zero-Ca(2+), therefore in the absence of the synaptic circuitry. A network of functional units composes the NEA model. Each functional unit represents one interface of neuronal/extracellular space/glial segments. Each interface contains transmembrane ionic transports, such as ionic channels, cotransporters, exchangers and pumps. Neuronal interconnections are mediated by gap-junctions, electric field effects and extracellular ionic fluctuations modulated by extracellular electrodiffusion. Mechanisms investigated are those that change intracellular and extracellular ionic concentrations and are able to affect [H(+)]. Our simulations suggest that the intense fluctuations in intra and extracellular concentrations of Na(+), K(+) and Cl(-) that accompany NEA are able to affect the combined action of the Na(+)/H(+) exchanger (NHE), [HCO(-)(3)]/Cl(-) exchanger (HCE), H(+) pump and the catalytic activity of intra and extracellular carbonic anhydrase. Cellular volume changes and extracellular electrodiffusion are responsible for modulating pH.

Technical Note: Maximising accuracy and minimising cost of a potentiometrically regulated ocean acidification simulation system

NASA Astrophysics Data System (ADS)

MacLeod, C. D.; Doyle, H. L.; Currie, K. I.

2015-02-01

This article describes a potentiometric ocean acidification simulation system which automatically regulates pH through the injection of 100% CO2 gas into temperature-controlled seawater. The system is ideally suited to long-term experimental studies of the effect of acidification on biological processes involving small-bodied (10-20 mm) calcifying or non-calcifying organisms. Using hobbyist-grade equipment, the system was constructed for approximately USD 1200 per treatment unit (tank, pH regulation apparatus, chiller, pump/filter unit). An overall tolerance of ±0.05 pHT units (SD) was achieved over 90 days in two acidified treatments (7.60 and 7.40) at 12 °C using glass electrodes calibrated with synthetic seawater buffers, thereby preventing liquid junction error. The performance of the system was validated through the independent calculation of pHT (12 °C) using dissolved inorganic carbon and total alkalinity data taken from discrete acidified seawater samples. The system was used to compare the shell growth of the marine gastropod Zeacumantus subcarinatus infected with the trematode parasite Maritrema novaezealandensis with that of uninfected snails at pH levels of 7.4, 7.6, and 8.1.

Biotic Control of Surface pH and Evidence of Light-Induced H+ Pumping and Ca2+-H+ Exchange in a Tropical Crustose Coralline Alga.

PubMed

Hofmann, Laurie C; Koch, Marguerite; de Beer, Dirk

2016-01-01

Presently, an incomplete mechanistic understanding of tropical reef macroalgae photosynthesis and calcification restricts predictions of how these important autotrophs will respond to global change. Therefore, we investigated the mechanistic link between inorganic carbon uptake pathways, photosynthesis and calcification in a tropical crustose coralline alga (CCA) using microsensors. We measured pH, oxygen (O2), and calcium (Ca2+) dynamics and fluxes at the thallus surface under ambient (8.1) and low (7.8) seawater pH (pHSW) and across a range of irradiances. Acetazolamide (AZ) was used to inhibit extracellular carbonic anhydrase (CAext), which mediates hydrolysis of HCO3-, and 4,4' diisothiocyanatostilbene-2,2'-disulphonate (DIDS) that blocks direct HCO3- uptake by anion exchange transport. Both inhibited photosynthesis, suggesting both diffusive uptake of CO2 via HCO3- hydrolysis to CO2 and direct HCO3- ion transport are important in this CCA. Surface pH was raised approximately 0.3 units at saturating irradiance, but less when CAext was inhibited. Surface pH was lower at pHSW 7.8 than pHSW 8.1 in the dark, but not in the light. The Ca2+ fluxes were large, complex and temporally variable, but revealed net Ca2+ uptake under all conditions. The temporal variability in Ca2+ dynamics was potentially related to localized dissolution during epithallial cell sloughing, a strategy of CCA to remove epiphytes. Simultaneous Ca2+ and pH dynamics suggest the presence of Ca2+/H+ exchange. Rapid light-induced H+ surface dynamics that continued after inhibition of photosynthesis revealed the presence of a light-mediated, but photosynthesis-independent, proton pump. Thus, the study indicates metabolic control of surface pH can occur in CCA through photosynthesis and light-inducible H+ pumps. Our results suggest that complex light-induced ion pumps play an important role in biological processes related to inorganic carbon uptake and calcification in CCA.

Biotic Control of Surface pH and Evidence of Light-Induced H+ Pumping and Ca2+-H+ Exchange in a Tropical Crustose Coralline Alga

PubMed Central

Hofmann, Laurie C.; Koch, Marguerite; de Beer, Dirk

2016-01-01

Presently, an incomplete mechanistic understanding of tropical reef macroalgae photosynthesis and calcification restricts predictions of how these important autotrophs will respond to global change. Therefore, we investigated the mechanistic link between inorganic carbon uptake pathways, photosynthesis and calcification in a tropical crustose coralline alga (CCA) using microsensors. We measured pH, oxygen (O2), and calcium (Ca2+) dynamics and fluxes at the thallus surface under ambient (8.1) and low (7.8) seawater pH (pHSW) and across a range of irradiances. Acetazolamide (AZ) was used to inhibit extracellular carbonic anhydrase (CAext), which mediates hydrolysis of HCO3-, and 4,4′ diisothiocyanatostilbene-2,2′-disulphonate (DIDS) that blocks direct HCO3- uptake by anion exchange transport. Both inhibited photosynthesis, suggesting both diffusive uptake of CO2 via HCO3- hydrolysis to CO2 and direct HCO3- ion transport are important in this CCA. Surface pH was raised approximately 0.3 units at saturating irradiance, but less when CAext was inhibited. Surface pH was lower at pHSW 7.8 than pHSW 8.1 in the dark, but not in the light. The Ca2+ fluxes were large, complex and temporally variable, but revealed net Ca2+ uptake under all conditions. The temporal variability in Ca2+ dynamics was potentially related to localized dissolution during epithallial cell sloughing, a strategy of CCA to remove epiphytes. Simultaneous Ca2+ and pH dynamics suggest the presence of Ca2+/H+ exchange. Rapid light-induced H+ surface dynamics that continued after inhibition of photosynthesis revealed the presence of a light-mediated, but photosynthesis-independent, proton pump. Thus, the study indicates metabolic control of surface pH can occur in CCA through photosynthesis and light-inducible H+ pumps. Our results suggest that complex light-induced ion pumps play an important role in biological processes related to inorganic carbon uptake and calcification in CCA. PMID:27459463

Dynamic cervicomedullary cord compression and alterations in cerebrospinal fluid dynamics in children with achondroplasia: review of an 11-year surgical case series.

PubMed

Mukherjee, Debraj; Pressman, Barry D; Krakow, Deborah; Rimoin, David L; Danielpour, Moise

2014-09-01

Achondroplasia may be associated with compression at the cervicomedullary junction. Determining which patients are at greatest risk for neurological complications of cervicomedullary compression can be difficult. In the current study the authors reviewed their records to determine the incidence and clinical significance of dynamic cervicomedullary stenosis and obstruction of CSF flow along with surgical outcomes following posterior fossa decompression. The authors reviewed 34 consecutive cases involving symptomatic children with achondroplasia undergoing cervicomedullary decompression performed by a single surgeon over 11 years. Of these patients, 29 had undergone preoperative dynamic MRI of the cervicomedullary junction with cine (cinema) CSF flow studies; 13 of these patients underwent postoperative dynamic MRI studies. Clinical outcomes included changes in polysomnography, head circumference percentile, and fontanel characteristics. Radiographic outcomes included changes in dynamic spinal cord diameter, improvement in CSF flow at the foramen magnum, and change in the Evans ratio. Patients were predominantly female, with a mean age at presentation of 6.6 years and mean follow-up of 3.7 years (range 1-10 years). All patients had moderate to excellent improvement in postoperative polysomnography, slight decrease in average head circumference percentile (from 46.9th percentile to 45.7th percentile), and no subjective worsening of fontanel characteristics. The Evans ratio decreased by 2%, spinal cord diameter increased an average of 3.1 mm, 5.2 mm, and 0.2 mm in the neutral, flexed, and extended positions, respectively, and CSF flow improved qualitatively in all 3 positions. There were no postoperative infections, CSF leaks, or other major complications. None of the patients undergoing initial foramen magnum decompression performed at our medical center required reoperation. Patients with achondroplasia and symptomatic cervicomedullary compression have increased risk of dynamic stenosis at the foramen magnum evident upon dynamic cine MRI. Operative decompression may be offered with low risk of complications or need for reoperation.

Communication: Quantum molecular dynamics simulation of liquid para-hydrogen by nuclear and electron wave packet approach.

PubMed

Hyeon-Deuk, Kim; Ando, Koji

2014-05-07

Liquid para-hydrogen (p-H2) is a typical quantum liquid which exhibits strong nuclear quantum effects (NQEs) and thus anomalous static and dynamic properties. We propose a real-time simulation method of wave packet (WP) molecular dynamics (MD) based on non-empirical intra- and inter-molecular interactions of non-spherical hydrogen molecules, and apply it to condensed-phase p-H2. The NQEs, such as WP delocalization and zero-point energy, are taken into account without perturbative expansion of prepared model potential functions but with explicit interactions between nuclear and electron WPs. The developed MD simulation for 100 ps with 1200 hydrogen molecules is realized at feasible computational cost, by which basic experimental properties of p-H2 liquid such as radial distribution functions, self-diffusion coefficients, and shear viscosities are all well reproduced.

A high-grain diet alters the omasal epithelial structure and expression of tight junction proteins in a goat model.

PubMed

Liu, Jun-Hua; Xu, Ting-Ting; Zhu, Wei-Yun; Mao, Sheng-Yong

2014-07-01

The omasal epithelial barrier plays important roles in maintaining nutrient absorption and immune homeostasis in ruminants. However, little information is currently available about the changes in omasal epithelial barrier function at the structural and molecular levels during feeding of a high-grain (HG) diet. Ten male goats were randomly assigned to two groups, fed either a hay diet (0% grain; n = 5) or HG diet (65% grain; n = 5). Changes in omasal epithelial structure and expression of tight junction (TJ) proteins were determined via electron microscopy and Western blot analysis. After 7 weeks on each diet, omasal contents in the HG group showed significantly lower pH (P <0.001) and significantly higher concentrations of free lipopolysaccharides (LPS; P = 0.001) than the hay group. The goats fed a HG diet showed profound alterations in omasal epithelial structure and TJ proteins, corresponding to depression of thickness of total epithelia, stratum granulosum, and the sum of the stratum spinosum and stratum basale, marked epithelial cellular damage, erosion of intercellular junctions and down-regulation in expression of the TJ proteins, claudin-4 and occludin. The study demonstrates that feeding a HG diet is associated with omasal epithelial cellular damage and changes in expression of TJ proteins. These research findings provide an insight into the possible significance of diet on the omasal epithelial barrier in ruminants. Copyright © 2014 Elsevier Ltd. All rights reserved.

Barrett’s esophagus and its correlation with gastroesophageal reflux in Chinese

PubMed Central

Zhang, Jun; Chen, Xiao-Li; Wang, Kang-Min; Guo, Xiao-Dan; Zuo, Ai-Li; Gong, Jun

2004-01-01

AIM: To study the prevalence of Barrett’s esophagus in Chinese and its correlation with gastroesophageal reflux. METHODS: This study was carried out in a large prospective series of 391 patients who had undergone upper endoscopy. The patients were divided into 3 groups according to the position of squamocolumnar junction (SCJ). Reflux esophagitis (RE) and its degree were recorded. Intestinal metaplasia (IM) in biopsy specimen was typed according to histochemistry and HE and alcian blue (pH2.5) staining separately. Results correlating with clinical, endoscopic, and pathological data were analysed. RESULTS: The prevalence of IM endoscopically appearing Long-segment Barrett’s Esophagus (LSBE) was 26.53%, Short-segment Barrett’s Esophagus (SSBE) was 33.85% and gastroesophageal junction (GEJ) was 34.00%. IM increased with age of above 40 years old and no difference was found between male and female. Twelve were diagnosed as dysplasia (7 low -grade, 5 high-grade), 16 were diagnosed as cardiac adenocarcinoma and 1 as esophageal adenocarcinoma. The more far away the SCJ moved upward above GEJ, the higher the prevalence and the more severe the RE were. CONCLUSION: There was no difference of the prevalence of IM in different places of SCJ, and IM increased with age of above 40 years old. It is important to pay attention to dysplasia in the distal esophagus and gastro-esophageal junction, and adenocarcinoma is more common in cardia than in esophagus. BE is a consequence of gastroesophageal reflux disease. PMID:15052695

Direct single-molecule dynamic detection of chemical reactions.

PubMed

Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N; Zhang, Deqing; Guo, Xuefeng

2018-02-01

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

Twist1-positive epithelial cells retain adhesive and proliferative capacity throughout dissemination

PubMed Central

Shamir, Eliah R.; Coutinho, Kester; Georgess, Dan; Auer, Manfred

2016-01-01

ABSTRACT Dissemination is the process by which cells detach and migrate away from a multicellular tissue. The epithelial-to-mesenchymal transition (EMT) conceptualizes dissemination in a stepwise fashion, with downregulation of E-cadherin leading to loss of intercellular junctions, induction of motility, and then escape from the epithelium. This gain of migratory activity is proposed to be mutually exclusive with proliferation. We previously developed a dissemination assay based on inducible expression of the transcription factor Twist1 and here utilize it to characterize the timing and dynamics of intercellular adhesion, proliferation and migration during dissemination. Surprisingly, Twist1+ epithelium displayed extensive intercellular junctions, and Twist1– luminal epithelial cells could still adhere to disseminating Twist1+ cells. Although proteolysis and proliferation were both observed throughout dissemination, neither was absolutely required. Finally, Twist1+ cells exhibited a hybrid migration mode; their morphology and nuclear deformation were characteristic of amoeboid cells, whereas their dynamic protrusive activity, pericellular proteolysis and migration speeds were more typical of mesenchymal cells. Our data reveal that epithelial cells can disseminate while retaining competence to adhere and proliferate. PMID:27402962

Boattail juncture shaping for spin-stabilized rounds in supersonic flight

NASA Astrophysics Data System (ADS)

Jiajan, W.; Chue, R. S. M.; Nguyen, T.; Yu, S. C. M.

2015-03-01

In this paper, the effects of boattail junction shaping on aerodynamic drag and stability of supersonic spin-stabilized rounds are investigated using computational fluid dynamics. For a generic round body comprising of a secant-ogive nose, a cylindrical body and a conical boattail, the shaping technique was achieved by adding a convex surface of varying degrees of radius of curvature to the junction between the cylindrical body and the boattail. It was shown through numerical simulations that this shaping technique can provide a reduction in aerodynamic drag of up to 5.4 % without destabilizing the round bodies when the radius of curvature is less than 8.8 times the diameter of the cylindrical body. The more gradual change of the flow characteristics, e.g., the pressure over the convex surface, was identified as the main reason for the drag reduction. A unique aspect of the current work is that stability is treated as an integral part of the performance assessment. It was also found that the dynamic instability encountered at large radii of curvature is due to the Magnus effects.

Dynamics of Bloch oscillating transistor near bifurcation threshold and its applicability for common mode rejection capability of a differential pair BOT

NASA Astrophysics Data System (ADS)

Sarkar, Jayanta; Puska, Antti; Hassel, Juha; Hakonen, Pertti

2014-03-01

Bloch oscillating transistor (BOT) is mesoscopic current amplier based on a combination of a Josephson junction or a squid connected with a large resistor and a NIS junction. We have studied the dynamics of BOT near the bifurcation threshold. This is an important feature for an amplifier as this can be utilized to improve its performance characteristics. We have measured the I - V characteristics of the BOT with different base currents (IB) over a wide range of Josephson coupling energies (EJ) . The current gain (β) is found to be increasing with increasing IB and eventually diverging. We have found a record large β = 50 in our experiment. In order to determine the common mode rejection ratio (CMRR) of a differential pair BOT we have used two BOTs fabricated on the same chip. The common mode port is connected to the bases of the two BOTs and fed with varying voltages; simultaneously emitter currents of the two BOTs are recorded. In our experiment we found a 20dB of CMRR.

Bistable front dynamics in a contractile medium: travelling wave and cortical advection define stable zones of RhoA signaling at epithelial adherens junctions

NASA Astrophysics Data System (ADS)

Neufeld, Zoltan

Recent studies have demonstrated that mechanical forces can lead to novel mechanisms of pattern formation such as clustering and oscillations in contractile systems. We investigate how contractile forces in mechanically active media can affect bistable front propagation. We found that contraction regulates the front speed or can fully suppress its propagation in space to create a static localized zone. We demonstrate how the interplay between biochemical signaling through positive feedback, combined with diffusion on the cell membrane and mechanical forces generated in the actomyosin cortex, can determine the spatial distribution of RhoA signaling at cell-cell junctions. The dynamical mechanism relies on the balance between a propagating bistable signal that is opposed by an advective flow generated by an actomyosin stress gradient. Experimental observations on the behaviour of the system when contractility is inhibited are in qualitative agreement with the predictions of the model. In collaboration with: Zoltan Neufeld, Guillermo A. Gomez, and Alpha S. Yap, University of Queensland, Brisbane, Australia

Direct single-molecule dynamic detection of chemical reactions

PubMed Central

Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N.; Zhang, Deqing; Guo, Xuefeng

2018-01-01

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry. PMID:29487914

Fast Low-Current Spin-Orbit-Torque Switching of Magnetic Tunnel Junctions through Atomic Modifications of the Free-Layer Interfaces

NASA Astrophysics Data System (ADS)

Shi, Shengjie; Ou, Yongxi; Aradhya, S. V.; Ralph, D. C.; Buhrman, R. A.

2018-01-01

Future applications of spin-orbit torque will require new mechanisms to improve the efficiency of switching nanoscale magnetic tunnel junctions (MTJs), while also controlling the magnetic dynamics to achieve fast nanosecond-scale performance with low-write-error rates. Here, we demonstrate a strategy to simultaneously enhance the interfacial magnetic anisotropy energy and suppress interfacial spin-memory loss by introducing subatomic and monatomic layers of Hf at the top and bottom interfaces of the ferromagnetic free layer of an in-plane magnetized three-terminal MTJ device. When combined with a β -W spin Hall channel that generates spin-orbit torque, the cumulative effect is a switching current density of 5.4 ×106 A /cm2 .

Influence of Contact Angle Boundary Condition on CFD Simulation of T-Junction

NASA Astrophysics Data System (ADS)

Arias, S.; Montlaur, A.

2018-03-01

In this work, we study the influence of the contact angle boundary condition on 3D CFD simulations of the bubble generation process occurring in a capillary T-junction. Numerical simulations have been performed with the commercial Computational Fluid Dynamics solver ANSYS Fluent v15.0.7. Experimental results serve as a reference to validate numerical results for four independent parameters: the bubble generation frequency, volume, velocity and length. CFD simulations accurately reproduce experimental results both from qualitative and quantitative points of view. Numerical results are very sensitive to the gas-liquid-wall contact angle boundary conditions, confirming that this is a fundamental parameter to obtain accurate CFD results for simulations of this kind of problems.

Phase-locking transition in a chirped superconducting Josephson resonator.

PubMed

Naaman, O; Aumentado, J; Friedland, L; Wurtele, J S; Siddiqi, I

2008-09-12

We observe a sharp threshold for dynamic phase locking in a high-Q transmission line resonator embedded with a Josephson tunnel junction, and driven with a purely ac, chirped microwave signal. When the drive amplitude is below a critical value, which depends on the chirp rate and is sensitive to the junction critical current I0, the resonator is only excited near its linear resonance frequency. For a larger amplitude, the resonator phase locks to the chirped drive and its amplitude grows until a deterministic maximum is reached. Near threshold, the oscillator evolves smoothly in one of two diverging trajectories, providing a way to discriminate small changes in I0 with a nonswitching detector, with potential applications in quantum state measurement.

Mechanism for Si–Si Bond Rupture in Single Molecule Junctions

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

Li, Haixing; Kim, Nathaniel T.; Su, Timothy A.

The stability of chemical bonds can be studied experimentally by rupturing single molecule junctions under applied voltage. Here, we compare voltage-induced bond rupture in two Si–Si backbones: one has no alternate conductive pathway whereas the other contains an additional naphthyl pathway in parallel to the Si–Si bond. We show that in contrast to the first system, the second can conduct through the naphthyl group when the Si–Si bond is ruptured using an applied voltage. We investigate this voltage induced Si–Si bond rupture by ab initio density functional theory calculations and molecular dynamics simulations that ultimately demonstrate that the excitation ofmore » molecular vibrational modes by tunneling electrons leads to homolytic Si–Si bond rupture.« less

Mechanism for Si-Si Bond Rupture in Single Molecule Junctions.

PubMed

Li, Haixing; Kim, Nathaniel T; Su, Timothy A; Steigerwald, Michael L; Nuckolls, Colin; Darancet, Pierre; Leighton, James L; Venkataraman, Latha

2016-12-14

The stability of chemical bonds can be studied experimentally by rupturing single molecule junctions under applied voltage. Here, we compare voltage-induced bond rupture in two Si-Si backbones: one has no alternate conductive pathway whereas the other contains an additional naphthyl pathway in parallel to the Si-Si bond. We show that in contrast to the first system, the second can conduct through the naphthyl group when the Si-Si bond is ruptured using an applied voltage. We investigate this voltage induced Si-Si bond rupture by ab initio density functional theory calculations and molecular dynamics simulations that ultimately demonstrate that the excitation of molecular vibrational modes by tunneling electrons leads to homolytic Si-Si bond rupture.

Network Characteristics of Collective Chemosensing

NASA Astrophysics Data System (ADS)

Sun, Bo; Duclos, Guillaume; Stone, Howard A.

2013-04-01

The collective chemosensing of nonexcitable mammalian cells involves a biochemical network that features gap junction communications and heterogeneous single cell activities. To understand the integrated multicellular chemosensing, we study the calcium dynamics of micropatterned fibroblast cell colonies in response to adenosine triphosphate (ATP) stimulation. We find that the cross-correlation function between the responses of individual cells decays with topological distance as a power law for large colonies and much faster for smaller colonies. Furthermore, the strongly correlated cell pairs tend to form clusters and are more likely to exceed the percolation threshold. At a given topological distance, the cross-correlations exhibit characteristics of Poisson distributions, which allows us to estimate the unitary conductance of a single gap junction which is in good agreement with direct experimental measurements.

Ion bipolar junction transistors

PubMed Central

Tybrandt, Klas; Larsson, Karin C.; Richter-Dahlfors, Agneta; Berggren, Magnus

2010-01-01

Dynamic control of chemical microenvironments is essential for continued development in numerous fields of life sciences. Such control could be achieved with active chemical circuits for delivery of ions and biomolecules. As the basis for such circuitry, we report a solid-state ion bipolar junction transistor (IBJT) based on conducting polymers and thin films of anion- and cation-selective membranes. The IBJT is the ionic analogue to the conventional semiconductor BJT and is manufactured using standard microfabrication techniques. Transistor characteristics along with a model describing the principle of operation, in which an anionic base current amplifies a cationic collector current, are presented. By employing the IBJT as a bioelectronic circuit element for delivery of the neurotransmitter acetylcholine, its efficacy in modulating neuronal cell signaling is demonstrated. PMID:20479274

The Effect of Mixing Events on the Dynamics of pH1N1 Outbreaks at Small Residential Colleges

ERIC Educational Resources Information Center

Palin, Karen; Greer, Meredith L.

2012-01-01

Objective: The authors examine the dynamics and the impact of all-campus events on pH1N1 spread at Bates College in fall 2009, with comparisons to 3 other campuses. Participants: Students (N = 285) presented or called in to the Bates Health Center with symptoms consistent with influenza-like illness. Methods: Health Center staff at Bates collected…

Effect of pH on the hinge region of influenza viral protein: a combined constant pH and well-tempered molecular dynamics study

NASA Astrophysics Data System (ADS)

Pathak, Arup Kumar

2018-05-01

Despite the knowledge that the influenza protein, hemagglutinin, undergoes a large conformational change at low pH during the process of fusion with the host cell, its molecular mechanism remains elusive. The present constant pH molecular dynamics (CpHMD) study identifies the residues responsible for large conformational change in acidic condition. Based on the pKa calculations, it is predicted that His-106 is much more responsible for the large conformational change than any other residues in the hinge region of hemagglutinin protein. Potential of mean force profile from well-tempered meta-dynamics (WT-MtD) simulation is also generated along the folding pathway by considering radius of gyration (R gyr) as a collective variable (CV). It is very clear from the present WT-MtD study, that the initial bending starts at that hinge region, which may trigger other conformational changes. Both the protein–protein and protein–water HB time correlation functions are monitored along the folding pathway. The protein–protein (full or hinge region) HB time correlation functions are always found to be stronger than those of the protein–water time correlation functions. The dynamical balance between protein–protein and protein–water HB interactions favors the stabilization of the folded state.

Fermentation pH influences the physiological-state dynamics of Lactobacillus bulgaricus CFL1 during pH-controlled culture.

PubMed

Rault, Aline; Bouix, Marielle; Béal, Catherine

2009-07-01

This study aims at better understanding the effects of fermentation pH and harvesting time on Lactobacillus bulgaricus CFL1 cellular state in order to improve knowledge of the dynamics of the physiological state and to better manage starter production. The Cinac system and multiparametric flow cytometry were used to characterize and compare the progress of the physiological events that occurred during pH 6 and pH 5 controlled cultures. Acidification activity, membrane damage, enzymatic activity, cellular depolarization, intracellular pH, and pH gradient were determined and compared during growing conditions. Strong differences in the time course of viability, membrane integrity, and acidification activity were displayed between pH 6 and pH 5 cultures. As a main result, the pH 5 control during fermentation allowed the cells to maintain a more robust physiological state, with high viability and stable acidification activity throughout growth, in opposition to a viability decrease and fluctuation of activity at pH 6. This result was mainly explained by differences in lactate concentration in the culture medium and in pH gradient value. The elevated content of the ionic lactate form at high pH values damaged membrane integrity that led to a viability decrease. In contrast, the high pH gradient observed throughout pH 5 cultures was associated with an increased energetic level that helped the cells maintain their physiological state. Such results may benefit industrial starter producers and fermented-product manufacturers by allowing them to better control the quality of their starters, before freezing or before using them for food fermentation.

Bacterial community dynamics and product distribution during pH-adjusted fermentation of vegetable wastes.

PubMed

Ye, N-F; Lü, F; Shao, L-M; Godon, J-J; He, P-J

2007-10-01

To estimate the effect of pH on the structures of bacterial community during fermentation of vegetable wastes and to investigate the relationship between bacterial community dynamics and product distribution. The bacterial communities in five batch tests controlled at different pH values [uncontrolled (about pH 4), 5, 6, 7 and 8] were monitored by denaturing gradient gel electrophoresis (DGGE) and single-strand conformation polymorphism (SSCP). The two fingerprinting methods provided consistent results and principal component analysis indicated a close similarity of bacterial community at pH 7 and 8 in addition to those at pH 4-6. This clustering also corresponded to dominant metabolic pathway. Thus, pH 7-8 shifted from alcohol-forming to acid-forming, especially butyric acid, whereas both alcohol-forming and acid-forming dominated at pH 5-6, and at pH 4, fermentation was inhibited. Shannon-weaver index was calculated to analyse the DGGE profiles, which revealed that the bacterial diversities at pH 7 and 8 were the highest while those at pH 5 and 4 (uncontrolled) were the lowest. According to sequencing results of the bands excised from DGGE gels, lactic acid bacteria and Clostridium sp. were predominant at all pH values, but varieties in species were observed as pH changed and time prolonged. The bacterial community during fermentation was materially influenced by pH and the diverse product distribution was related to the shift of different bacterial population. The study reveals that the impact of pH on fermentation product distribution is implemented primarily by changes of bacterial community. It also provides information about the comparison of two fingerprinting methods, DGGE and SSCP.

Nuclear Dynamics at Molecule–Metal Interfaces: A Pseudoparticle Perspective

DOE PAGES

Galperin, Michael; Nitzan, Abraham

2015-11-20

We discuss nuclear dynamics at molecule-metal interfaces including nonequilibrium molecular junctions. Starting from the many-body states (pseudoparticle) formulation of the molecule-metal system in the molecular vibronic basis, we introduce gradient expansion to reduce the adiabatic nuclear dynamics (that is, nuclear dynamics on a single molecular potential surface) into its semiclassical form while maintaining the effect of the nonadiabatic electronic transitions between different molecular charge states. Finally, this yields a set of equations for the nuclear dynamics in the presence of these nonadiabatic transitions, which reproduce the surface-hopping formulation in the limit of small metal-molecule coupling (where broadening of the molecularmore » energy levels can be disregarded) and Ehrenfest dynamics (motion on the potential of mean force) when information on the different charging states is traced out.« less

Electrostatics Control Actin Filament Nucleation and Elongation Kinetics*

PubMed Central

Crevenna, Alvaro H.; Naredi-Rainer, Nikolaus; Schönichen, André; Dzubiella, Joachim; Barber, Diane L.; Lamb, Don C.; Wedlich-Söldner, Roland

2013-01-01

The actin cytoskeleton is a central mediator of cellular morphogenesis, and rapid actin reorganization drives essential processes such as cell migration and cell division. Whereas several actin-binding proteins are known to be regulated by changes in intracellular pH, detailed information regarding the effect of pH on the actin dynamics itself is still lacking. Here, we combine bulk assays, total internal reflection fluorescence microscopy, fluorescence fluctuation spectroscopy techniques, and theory to comprehensively characterize the effect of pH on actin polymerization. We show that both nucleation and elongation are strongly enhanced at acidic pH, with a maximum close to the pI of actin. Monomer association rates are similarly affected by pH at both ends, although dissociation rates are differentially affected. This indicates that electrostatics control the diffusional encounter but not the dissociation rate, which is critical for the establishment of actin filament asymmetry. A generic model of protein-protein interaction, including electrostatics, explains the observed pH sensitivity as a consequence of charge repulsion. The observed pH effect on actin in vitro agrees with measurements of Listeria propulsion in pH-controlled cells. pH regulation should therefore be considered as a modulator of actin dynamics in a cellular environment. PMID:23486468

Assessment of polyelectrolyte coating stability under dynamic buffer conditions in CE.

PubMed

Swords, Kyleen E; Bartline, Peter B; Roguski, Katherine M; Bashaw, Sarah A; Frederick, Kimberley A

2011-09-01

Dynamic buffer conditions are present in many electrophoretically driven separations. Polyelectrolyte multilayer coatings have been employed in CE because of their chemical and physical stability as well as their ease of application. The goal of this study is to measure the effect of dynamic changes in buffer pH on flow using a real-time method for measuring EOF. Polyelectrolyte multilayers (PEMs) were composed of pairs of strong or completely ionized polyelectrolytes including poly(diallyldimethylammonium) chloride and poly(styrene sulfonate) and weak or ionizable polyelectrolytes including poly(allylamine) and poly(methacrylic acid). Polyelectrolyte multilayers of varying thicknesses (3, 4, 7, 8, 15, or 16 layers) were also studied. While the magnitude of the EOF was monitored every 2 s, the buffer pH was exchanged from a relatively basic pH (7.1) to increasingly acidic pHs (6.6, 6.1, 5.5, and 5.1). Strong polyelectrolytes responded minimally to changes in buffer pH (<1%), whereas substantial (>10%) and sometimes irreversible changes were measured with weak polyelectrolytes. Thicker coatings resulted in a similar magnitude of response but were more likely to degrade in response to buffer pH changes. The most stable coatings were formed from thinner layers of strong polyelectrolytes. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modeling the dynamic volatile fatty acids profiles with pH and hydraulic retention time in an anaerobic baffled reactor during the startup period.

PubMed

Shi, En; Li, Jianzheng; Leu, Shao-Yuan; Antwi, Philip

2016-12-01

To predict the dynamic profiles in volatile fatty acids (VFAs) with pH and hydraulic retention time (HRT) during the startup of a 4-compartment ABR, a mathematical model was constructed by introducing pH and thermodynamic inhibition functions into the biochemical processes derived from the ADM1. The calibration of inhibition parameter for propionate uptake effectively improved the prediction accuracy of VFAs. The developed model could simulate the VFAs profiles very well no matter the observable change of pH or/and HRT. The simulation results indicated that both H 2 -producing acetogenesis and methanogenesis in the ABR would be inhibited with a pH less than 4.61, and the propionate oxidation could be thermodynamically restricted even with a neutral pH. A decreased HRT would enhanced the acidogenesis and H 2 -producing acetogenesis in the first 3 compartments, but no observable increase in effluent VFAs could be found due to the synchronously enhanced methanogenesis in the last compartment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Regulation of blood-testis barrier dynamics by desmosome, gap junction, hemidesmosome and polarity proteins

PubMed Central

Wong, Elissa WP; Lie, Pearl PY; Li, Michelle WM; Mruk, Dolores D; Yan, Helen HN; Mok, Ka-Wai; Mannu, Jayakanthan; Mathur, Premendu P; Lui, Wing-yee; Lee, Will M; Bonanomi, Michele; Silvestrini, Bruno

2011-01-01

The blood-testis barrier (BTB) is a unique ultrastructure in the mammalian testis. Unlike other blood-tissue barriers, such as the blood-brain barrier and the blood-ocular (or blood-retina) barrier which formed by tight junctions (TJ) between endothelial cells of the microvessels, the BTB is constituted by coexisting TJ, basal ectoplasmic specialization (basal ES), desmosomes and gap junctions between adjacent Sertoli cells near the basement membrane of the seminiferous tubule. The BTB also divides the seminiferous epithelium into the apical (or adluminal) and basal compartments so that meiosis I and II and post-meiotic germ cell development can all take place in a specialized microenvironment in the apical compartment behind the BTB. While the unusual anatomical features of the BTB have been known for decades, the physiological function of the coexisting junctions, in particular the desmosome and gap junction, that constitute the BTB was unknown until recently. Based on recently published findings, we critically evaluate the role of the desmosome and gap junction that serve as a signaling platform to coordinate the “opening” and “closing” of the TJ-permeability barrier conferred by TJ and basal ES during the seminiferous epithelial cycle of spermatogenesis. This is made possible by polarity proteins working in concert with nonreceptor protein tyrosine kinases, such as focal adhesion kinase (FAK) and c-Src, at the site to regulate endosome-mediated protein trafficking events (e.g., endocytosis, transcytosis, recycling or protein degradation). These events not only serve to destabilize the existing “old” BTB above preleptotene spermatocytes in transit in “clones” at the BTB, but also contribute to the assembly of “new” BTB below the transiting spermatocytes. Furthermore, hemidesmosomes at the Sertoli cell-basement membrane interface also contribute to the BTB restructuring events at stage VIII of the epithelial cycle. Additionally, the findings that a gap junction at the BTB provides a possible route for the passage of toxicants [e.g., bisphenol A (BPA)] and potential male contraceptives (e.g., adjudin) across the BTB also illustrate that these coexisting junctions, while helpful to maintain the immunological barrier integrity during the transit of spermatocytes, can be the “gateway” to making the BTB so vulnerable to toxicants and/or chemicals, causing male reproductive dysfunction. PMID:22319658

Connexin Communication Compartments and Wound Repair in Epithelial Tissue.

PubMed

Chanson, Marc; Watanabe, Masakatsu; O'Shaughnessy, Erin M; Zoso, Alice; Martin, Patricia E

2018-05-03

Epithelial tissues line the lumen of tracts and ducts connecting to the external environment. They are critical in forming an interface between the internal and external environment and, following assault from environmental factors and pathogens, they must rapidly repair to maintain cellular homeostasis. These tissue networks, that range from a single cell layer, such as in airway epithelium, to highly stratified and differentiated epithelial surfaces, such as the epidermis, are held together by a junctional nexus of proteins including adherens, tight and gap junctions, often forming unique and localised communication compartments activated for localised tissue repair. This review focuses on the dynamic changes that occur in connexins, the constituent proteins of the intercellular gap junction channel, during wound-healing processes and in localised inflammation, with an emphasis on the lung and skin. Current developments in targeting connexins as corrective therapies to improve wound closure and resolve localised inflammation are also discussed. Finally, we consider the emergence of the zebrafish as a concerted whole-animal model to study, visualise and track the events of wound repair and regeneration in real-time living model systems.

Strong ferromagnetic proximity polarization in ferromagnetic metal MnGa/n-type GaAs quantum well junction

NASA Astrophysics Data System (ADS)

Ji, Xiaochen; Shen, Chao; Wu, Yuanjun; Lu, Jun; Zhao, Jianhua; Zheng, Houzhi

2017-11-01

By biasing a ferromagnetic metal MnGa/10 nm-thick, n-type GaAs quantum well (QW) junction from negative to positive, it is found that its spin dynamics at zero magnetic field is composed of two components with opposite signs. One is excited by a circularly polarized pump beam. The other is induced by ferromagnetic proximity polarization (FPP), which is continuously enhanced as the bias increases towards the positive direction. The time-resolved Kerr rotations have also been measured at a magnetic field of 0.9 Tesla. A phase reversion of Larmor precession is observed as the bias passes through  +0.5 V. Following simple quantum mechanics, we become aware of the fact that the transmission and reflection rates of electrons at the interface of MnGa/n-type GaAs QW are enhanced by a factor of ν , which is the attempting frequency of electron onto a ferromagnet/semiconductor interface. That gives a reasonable explanation why the FPP effect in our MnGa/n-type GaAs QW junction is greatly enhanced as biasing it into forward direction.

Proximity coupling in superconductor-graphene heterostructures.

PubMed

Lee, Gil-Ho; Lee, Hu-Jong

2018-05-01

This review discusses the electronic properties and the prospective research directions of superconductor-graphene heterostructures. The basic electronic properties of graphene are introduced to highlight the unique possibility of combining two seemingly unrelated physics, superconductivity and relativity. We then focus on graphene-based Josephson junctions, one of the most versatile superconducting quantum devices. The various theoretical methods that have been developed to describe graphene Josephson junctions are examined, together with their advantages and limitations, followed by a discussion on the advances in device fabrication and the relevant length scales. The phase-sensitive properties and phase-particle dynamics of graphene Josephson junctions are examined to provide an understanding of the underlying mechanisms of Josephson coupling via graphene. Thereafter, microscopic transport of correlated quasiparticles produced by Andreev reflections at superconducting interfaces and their phase-coherent behaviors are discussed. Quantum phase transitions studied with graphene as an electrostatically tunable 2D platform are reviewed. The interplay between proximity-induced superconductivity and the quantum-Hall phase is discussed as a possible route to study topological superconductivity and non-Abelian physics. Finally, a brief summary on the prospective future research directions is given.

Proximity coupling in superconductor-graphene heterostructures

NASA Astrophysics Data System (ADS)

Lee, Gil-Ho; Lee, Hu-Jong

2018-05-01

This review discusses the electronic properties and the prospective research directions of superconductor-graphene heterostructures. The basic electronic properties of graphene are introduced to highlight the unique possibility of combining two seemingly unrelated physics, superconductivity and relativity. We then focus on graphene-based Josephson junctions, one of the most versatile superconducting quantum devices. The various theoretical methods that have been developed to describe graphene Josephson junctions are examined, together with their advantages and limitations, followed by a discussion on the advances in device fabrication and the relevant length scales. The phase-sensitive properties and phase-particle dynamics of graphene Josephson junctions are examined to provide an understanding of the underlying mechanisms of Josephson coupling via graphene. Thereafter, microscopic transport of correlated quasiparticles produced by Andreev reflections at superconducting interfaces and their phase-coherent behaviors are discussed. Quantum phase transitions studied with graphene as an electrostatically tunable 2D platform are reviewed. The interplay between proximity-induced superconductivity and the quantum-Hall phase is discussed as a possible route to study topological superconductivity and non-Abelian physics. Finally, a brief summary on the prospective future research directions is given.

Remodeling the zonula adherens in response to tension and the role of afadin in this response

PubMed Central

Acharya, Bipul R.; Peyret, Grégoire; Fardin, Marc-Antoine; Mège, René-Marc; Ladoux, Benoit; Yap, Alpha S.; Fanning, Alan S.

2016-01-01

Morphogenesis requires dynamic coordination between cell–cell adhesion and the cytoskeleton to allow cells to change shape and move without losing tissue integrity. We used genetic tools and superresolution microscopy in a simple model epithelial cell line to define how the molecular architecture of cell–cell zonula adherens (ZA) is modified in response to elevated contractility, and how these cells maintain tissue integrity. We previously found that depleting zonula occludens 1 (ZO-1) family proteins in MDCK cells induces a highly organized contractile actomyosin array at the ZA. We find that ZO knockdown elevates contractility via a Shroom3/Rho-associated, coiled-coil containing protein kinase (ROCK) pathway. Our data suggest that each bicellular border is an independent contractile unit, with actin cables anchored end-on to cadherin complexes at tricellular junctions. Cells respond to elevated contractility by increasing junctional afadin. Although ZO/afadin knockdown did not prevent contractile array assembly, it dramatically altered cell shape and barrier function in response to elevated contractility. We propose that afadin acts as a robust protein scaffold that maintains ZA architecture at tricellular junctions. PMID:27114502

Kinetic Measurements Reveal Enhanced Protein-Protein Interactions at Intercellular Junctions

PubMed Central

Shashikanth, Nitesh; Kisting, Meridith A.; Leckband, Deborah E.

2016-01-01

The binding properties of adhesion proteins are typically quantified from measurements with soluble fragments, under conditions that differ radically from the confined microenvironment of membrane bound proteins in adhesion zones. Using classical cadherin as a model adhesion protein, we tested the postulate that confinement within quasi two-dimensional intercellular gaps exposes weak protein interactions that are not detected in solution binding assays. Micropipette-based measurements of cadherin-mediated, cell-cell binding kinetics identified a unique kinetic signature that reflects both adhesive (trans) bonds between cadherins on opposing cells and lateral (cis) interactions between cadherins on the same cell. In solution, proposed lateral interactions were not detected, even at high cadherin concentrations. Mutations postulated to disrupt lateral cadherin association altered the kinetic signatures, but did not affect the adhesive (trans) binding affinity. Perturbed kinetics further coincided with altered cadherin distributions at junctions, wound healing dynamics, and paracellular permeability. Intercellular binding kinetics thus revealed cadherin interactions that occur within confined, intermembrane gaps but not in solution. Findings further demonstrate the impact of these revealed interactions on the organization and function of intercellular junctions. PMID:27009566

Jochem Weber | NREL

Science.gov Websites

mechanical engineering (design) and physical engineering (fluid and system dynamics), and a Ph.D. in modeling Ph.D. in Engineering, University College Cork (Ireland); M.S. and B.S. in Physical Engineering

A dynamic system for the simulation of fasting luminal pH-gradients using hydrogen carbonate buffers for dissolution testing of ionisable compounds.

PubMed

Garbacz, Grzegorz; Kołodziej, Bartosz; Koziolek, Mirko; Weitschies, Werner; Klein, Sandra

2014-01-23

The hydrogen carbonate buffer is considered as the most biorelevant buffer system for the simulation of intestinal conditions and covers the physiological pH range of the luminal fluids from pH 5.5 to about pH 8.4. The pH value of a hydrogen carbonate buffer is the result of a complex and dynamic interplay of the concentration of hydrogen carbonate ions, carbonic acid, the concentration of dissolved and solvated carbon dioxide and its partial pressure above the solution. The complex equilibrium between the different ions results in a thermodynamic instability of hydrogen carbonate solutions. In order to use hydrogen carbonate buffers with pH gradients in the physiological range and with the dynamics observed in vivo without changing the ionic strength of the solution, we developed a device (pHysio-grad®) that provides both acidification of the dissolution medium by microcomputer controlled carbon dioxide influx and alkalisation by degassing. This enables a continuous pH control and adjustment during dissolution of ionisable compounds. The results of the pH adjustment indicate that the system can compensate even rapid pH changes after addition of a basic or acidic moiety in amounts corresponding up to 90% of the overall buffer capacity. The results of the dissolution tests performed for a model formulation containing ionizable compounds (Nexium 20mg mups) indicate that both the simulated fasting intraluminal pH-profiles and the buffer species can significantly affect the dissolution process by changing the lag time prior to initial drug release and the release rate of the model compound. A prediction of the in vivo release behaviour of this formulation is thus most likely strongly related to the test conditions such as pH and buffer species. Copyright © 2013 Elsevier B.V. All rights reserved.

An epidermal plakin that integrates actin and microtubule networks at cellular junctions.

PubMed

Karakesisoglou, I; Yang, Y; Fuchs, E

2000-04-03

Plakins are cytoskeletal linker proteins initially thought to interact exclusively with intermediate filaments (IFs), but recently were found to associate additionally with actin and microtubule networks. Here, we report on ACF7, a mammalian orthologue of the Drosophila kakapo plakin genetically involved in epidermal-muscle adhesion and neuromuscular junctions. While ACF7/kakapo is divergent from other plakins in its IF-binding domain, it has at least one actin (K(d) = 0.35 microM) and one microtubule (K(d) approximately 6 microM) binding domain. Similar to its fly counterpart, ACF7 is expressed in the epidermis. In well spread epidermal keratinocytes, ACF7 discontinuously decorates the cytoskeleton at the cell periphery, including microtubules (MTs) and actin filaments (AFs) that are aligned in parallel converging at focal contacts. Upon calcium induction of intercellular adhesion, ACF7 and the cytoskeleton reorganize at cell-cell borders but with different kinetics from adherens junctions and desmosomes. Treatments with cytoskeletal depolymerizing drugs reveal that ACF7's cytoskeletal association is dependent upon the microtubule network, but ACF7 also appears to stabilize actin at sites where microtubules and microfilaments meet. We posit that ACF7 may function in microtubule dynamics to facilitate actin-microtubule interactions at the cell periphery and to couple the microtubule network to cellular junctions. These attributes provide a clear explanation for the kakapo mutant phenotype in flies.

Performance analysis of nanodisk and core/shell/shell-nanowire type III-Nitride heterojunction solar cell for efficient energy harvesting

NASA Astrophysics Data System (ADS)

Routray, S. R.; Lenka, T. R.

2017-11-01

Now-a-days III-Nitride nanowires with axial (nanodisk) and radial (core/shell/shell-nanowire) junctions are two unique and potential methods for solar energy harvesting adopted by worldwide researchers. In this paper, polarization behavior of GaN/InGaN/GaN junction and its effect on carrier dynamics of nanodisk and CSS-nanowire type solar cells are intensively studied and compared with its planar counterpart by numerical simulations using commercially available Victory TCAD. It is observed that CSS-NW with hexagonal geometrical shapes are robust to detrimental impact of polarization charges and could be good enough to accelerate carrier collection efficiency as compared to nanodisk and planar solar cells. This numerical study provides an innovative aspect of fundamental device physics with respect to polarization charges in CSS-NW and nanodisk type junction towards photovoltaic applications. The internal quantum efficiencies (IQE) are also discussed to evaluate carrier collection mechanisms and recombination losses in each type of junctions of solar cell. Finally, it is interesting to observe a maximum conversion efficiency of 6.46% with 91.6% fill factor from n-GaN/i-In0.1Ga0.9N/p-GaN CSS-nanowire solar cell with an optimized thickness of 180 nm InGaN layer under one Sun AM1.5 illumination.

Tricellulin, occludin and claudin-3 expression in salmon intestine and kidney during salinity adaptation.

PubMed

Tipsmark, C K; Madsen, S S

2012-08-01

Molecular regulation of tight junctions in osmoregulatory epithelia of euryhaline fishes must be extensive during ontogeny and acclimation to salinity changes. In this study, five tight junction proteins were examined in Atlantic salmon (Salmo salar): tight junction associated tricellulin, occludin and claudin-3 isoforms (a, b, c). A survey of tissue distribution in freshwater (FW) salmon showed that tricellulin expression was highest in the intestine. Occludin was detected in tissues with importance for epithelial transport and the order of expression was gill>intestine>kidney. The three claudin-3 isoforms were expressed at highest level in kidney tissue. Transfer of juvenile FW salmon to seawater (SW) elevated intestinal tricellulin and occludin mRNA, and these transcripts were also elevated at the time of best SW-tolerance during the course of smoltification. In the kidney, expression of tricellulin and claudin-3 isoforms was elevated after SW-transfer and tricellulin, occludin, claudin-3a and -3b increased in March before the peak smolt stage. In the gill, none of the examined tight junction proteins were impacted by SW-transfer. The data suggest that expression of tricellulin and occludin is dynamically involved in reorganization of intestinal epithelium and possibly changed paracellular permeability during SW-acclimation. The increased renal tricellulin and claudin-3 expression in SW suggests a role in remodeling of the kidney during SW-acclimation. Copyright © 2012 Elsevier Inc. All rights reserved.

Intrinsic line shape of electromagnetic radiation from a stack of intrinsic Josephson junctions synchronized by an internal cavity resonance

NASA Astrophysics Data System (ADS)

Koshelev, Alexei

2013-03-01

Stacks of intrinsic Josephson-junctions are realized in mesas fabricated out of layered superconducting single crystals, such as Bi2Sr2CaCu2O8 (BSCCO). Synchronization of phase oscillations in different junctions can be facilitated by the coupling to the internal cavity mode leading to powerful and coherent electromagnetic radiation in the terahertz frequency range. An important characteristic of this radiation is the shape of the emission line. A finite line width appears due to different noise sources leading to phase diffusion. We investigated the intrinsic line shape caused by the thermal noise for a mesa fabricated on the top of a BSCCO single crystal. In the ideal case of fully synchronized stack the finite line width is coming from two main contributions, the quasiparticle-current noise inside the mesa and the fluctuating radiation in the base crystal. We compute both contributions and conclude that for realistic mesa's parameters the second mechanism typically dominates. The role of the cavity quality factor in the emission line spectrum is clarified. Analytical results were verified by numerical simulations. In real mesa structures part of the stack may not be synchronized and chaotic dynamics of unsynchronized junctions may determine the real line width. Work supported by UChicago Argonne, LLC, under contract No. DE-AC02-06CH11357.

Magnetic field oscillations of the critical current in long ballistic graphene Josephson junctions

NASA Astrophysics Data System (ADS)

Rakyta, Péter; Kormányos, Andor; Cserti, József

2016-06-01

We study the Josephson current in long ballistic superconductor-monolayer graphene-superconductor junctions. As a first step, we have developed an efficient computational approach to calculate the Josephson current in tight-binding systems. This approach can be particularly useful in the long-junction limit, which has hitherto attracted less theoretical interest but has recently become experimentally relevant. We use this computational approach to study the dependence of the critical current on the junction geometry, doping level, and an applied perpendicular magnetic field B . In zero magnetic field we find a good qualitative agreement with the recent experiment of M. Ben Shalom et al. [Nat. Phys. 12, 318 (2016), 10.1038/nphys3592] for the length dependence of the critical current. For highly doped samples our numerical calculations show a broad agreement with the results of the quasiclassical formalism. In this case the critical current exhibits Fraunhofer-like oscillations as a function of B . However, for lower doping levels, where the cyclotron orbit becomes comparable to the characteristic geometrical length scales of the system, deviations from the results of the quasiclassical formalism appear. We argue that due to the exceptional tunability and long mean free path of graphene systems a new regime can be explored where geometrical and dynamical effects are equally important to understand the magnetic field dependence of the critical current.

Silicon Carbide Diodes Characterization at High Temperature and Comparison With Silicon Devices

NASA Technical Reports Server (NTRS)

Lebron-Velilla, Ramon C.; Schwarze, Gene E.; Gardner, Brent G.; Adams, Jerry D., Jr.

2004-01-01

Commercially available silicon carbide (SiC) Schottky diodes from different manufacturers rated at 200, 300, 600, and 1200 V, were electrically tested and characterized as a function of temperature up to 300 C. Electrical tests included both steady state and dynamic tests. Steady state tests produced forward and reverse I-V characteristic curves. Transient tests evaluated the switching performance of the diodes in either a hard-switched DC to DC buck converter or a half-bridge boost converter. For evaluation and comparison purposes, the same tests were performed with current state-of-the-art ultra fast silicon (Si) pn-junction diodes of similar ratings and also a Si Schottky diode. The comparisons made were forward voltage drop at rated current, reverse current at rated voltage, and turn-off peak reverse recovery current and reverse recovery time. In addition, efficiency measurements were taken for the buck DC to DC converter using both the SiC Schottky diodes and the Si pn-junction diodes at different temperatures and frequencies. The test results showed that at high temperature, the forward voltage drop for SiC Schottky diodes is higher than the forward drop of the ultra fast Si pn-junction diodes. As the temperature increased, the forward voltage drop of the SiC Schottky increased while for the ultra fast Si pn-junction diodes, the forward voltage drop decreased as temperature increased. For the elevated temperature steady state reverse voltage tests, the SiC Schottky diodes showed low leakage current at their rated voltage. Likewise, for the transient tests, the SiC Schottky diodes displayed low reverse recovery currents over the range of temperatures tested. Conversely, the Si pn-junction diodes showed increasing peak reverse current values and reverse recovery times with increasing temperature. Efficiency measurements in the DC to DC buck converter showed the advantage of the SiC Schottky diodes over the ultra fast Si pn-junction diodes, especially at the higher temperatures and higher frequencies.

Measurement of esophago-gastric junction cross-sectional area and distensibility by an endolumenal functional lumen imaging probe for the diagnosis of gastro-esophageal reflux disease.

PubMed

Tucker, E; Sweis, R; Anggiansah, A; Wong, T; Telakis, E; Knowles, K; Wright, J; Fox, M

2013-11-01

Measurement of esophago-gastric junction (EGJ) cross-sectional area (CSA) and distensibility by an Endolumenal Functional Lumen Imaging Probe (EndoFLIP®) may distinguish between gastro-esophageal reflux disease (GERD) patients and healthy volunteers (HV). We aimed to assess the agreement of EndoFLIP® measurements with clinical and physiologic diagnosis of GERD. Twenty-one HV and 18 patients with typical GERD symptoms were studied. After gastroscopy, EGJ CSA, and distensibility were measured by EndoFLIP®. Forty-eight hour esophageal pH monitoring was then performed by a wireless system. The ability of EndoFLIP® to discriminate GERD patient and HVs was assessed. Planned secondary analysis then assessed whether EGJ CSA and distensibility were increased in individuals with pathologic acid exposure. Healthy volunteers were younger and had lower body mass index (BMI; both p < 0.001). Pathologic acid exposure was present in 3/21 (14%) HVs and 9/18 (50%) patients (p = 0.126). At 30 mL EndoFLIP® bag volume, EGJ CSA was higher (p = 0.058) and EGJ distensibility was lower (p = 0.020) in HVs than patients. Secondary analysis showed that EGJ measurements were similar in participants with and without pathologic acid exposure (CSA 98 mm² vs 107 mm²; p = 0.789, distensibility; p = 0.704). An inverse association between BMI and CSA (R² = 0.2758, p = 0.001) and distensibility (R² = 0.2005, p = 0.005) was present. Endolumenal Functional Lumen Imaging Probe is not useful for GERD diagnosis because EGJ CSA and distensibility do not distinguish between HVs and GERD patients defined by clinical presentation or pH measurement. This unexpected result may be due to an important, confounding interaction of obesity. © 2013 John Wiley & Sons Ltd.

Mammalian target of rapamycin complex (mTOR) pathway modulates blood-testis barrier (BTB) function through F-actin organization and gap junction

PubMed Central

Li, Nan; Cheng, C. Yan

2016-01-01

mTOR (mammalian target of rapamycin) is one of the most important signaling molecules in mammalian cells which regulates an array of cellular events, ranging from cell metabolism to cell proliferation. Based on the association of mTOR with the core component proteins, such as Raptor or Rictor, mTOR can become the mTORC1 (mammalian target of rapamycin complex 1) or mTORC2, respectively. Studies have shown that during the epithelial cycle of spermatogenesis, mTORC1 promotes remodeling and restructuring of the blood-testis barrier (BTB) in vitro and in vivo, making the Sertoli cell tight junction (TJ)-permeability barrier “leaky”; whereas mTORC2 promotes BTB integrity, making the Sertoli cell TJ-barrier “tighter”. These contrasting effects, coupled with the spatiotemporal expression of the core signaling proteins at the BTB that confer the respective functions of mTORC1 vs. mTORC2 thus provide a unique mechanism to modulate BTB dynamics, allowing or disallowing the transport of biomolecules and also preleptotene spermatocytes across the immunological barrier. More importantly, studies have shown that these changes to BTB dynamics conferred by mTORC1 and mTORC2 are mediated by changes in the organization of the actin microfilament networks at the BTB, and involve gap junction (GJ) intercellular communication. Since GJ has recently been shown to be crucial to reboot spermatogenesis and meiosis following toxicant-induced aspermatogenesis, these findings thus provide new insightful information regarding the integration of mTOR and GJ to regulate spermatogenesis. PMID:26957088

pH responsiveness of dendrimer-like poly(ethylene oxide)s.

PubMed

Feng, Xiaoshuang; Taton, Daniel; Borsali, Redouane; Chaikof, Elliot L; Gnanou, Yves

2006-09-06

Poly(ethylene oxide) (PEO) and poly(acrylic acid) (PAA), two polymers known to form pH-sensitive aggregates through noncovalent interactions, were assembled in purposely designed architecture -a dendrimer-like PEO scaffold carrying short inner PAA chains-to produce unimolecular systems that exhibit pH responsiveness. Because of the particular placement of the PAA chains within the dendrimer-like structure, intermolecular complexation between acrylic acid (AA) and ethylene oxide (EO) units-and thus macroscopic aggregation or even mesoscopic micellization-could be avoided in favor of the sole intramolecular complexation. The sensitivity of such interactions to pH was exploited to generate dendrimer-like PEOs that reversibly shrink and expand with the pH. Such PAA-carrying dendrimer-like PEOs were synthesized in two main steps. First, a fifth-generation dendrimer-like PEO was obtained by combining anionic ring-opening polymerization (AROP) of ethylene oxide from a tris-hydroxylated core and selective branching reactions of PEO chain ends. To this end, an AB(2)C-type branching agent was designed: the latter includes a chloromethyl (A) group for its covalent attachment to the arm ends, two geminal hydroxyls (B(2)) protected in the form of a ketal ring for the growth of subsequent PEO generations by AROP, and a vinylic (C) double bonds for further functionalization of the interior of dendrimer-like PEOs. Reiteration of AROP and derivatization of PEO branches allowed us to prepare a dendrimer-like PEO of fourth generation with a total molar mass of 52,000 g x mol(-1), containing 24 external hydroxyl functions and 21 inner vinylic groups in the interior. A fifth generation of PEO chains was generated from this parent dendrimer-like PEO of fourth generation using a "conventional" AB(2)-type branching agent, and 48 PEO branches could be grown by AROP. The 48 outer hydroxy-end groups of the fifth-generation dendrimer-like PEO obtained were subsequently quantitatively converted into inert benzylic groups using benzyl bromide. The 21 internal vinylic groups carried by the PEO scaffold were then chemically modified in a two-step sequence into bromoester groups. The latter which are atom transfer radical polymerization (ATRP) initiating sites thus served to grow poly(tert-butylacrylate) chains. After a final step of hydrolysis of the tert-butyl ester groups, double, hydrophilic, dendrimer-like PEOs comprising 21 internal junction-attached poly(acrylic acid) (PAA) blocks could be obtained. Dynamic light scattering was used to determine the size of these dendrimer-like species in water and to investigate their response to pH variation: in particular, how the pH-sensitive complexation of EO and AA units affects their overall behavior.

Real-Time and High-Fidelity Simulation Environment for Autonomous Ground Vehicle Dynamics

DTIC Science & Technology

2013-08-01

Propulsion Laboratory California Institute of Technology Paramsothy Jayakumar , Ph.D. U.S. Army TARDEC Jim Overholt, Ph.D. U.S. Air Force...NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Paramsothy Jayakumar ; Jim Overholt; Calvin Kuo; Abhi Jain; Havard Grip 5d. PROJECT...Dynamics, Cameron, et al. UNCLASSIFIED Page 10 of 11 REFERENCES [1] P. Jayakumar , W. Smith, B. A. Ross, R. Jategoankar and K. Konarzewski

pH-Driven Reversible Self-Assembly of Micron-Scale DNA Scaffolds.

PubMed

Green, Leopold N; Amodio, Alessia; Subramanian, Hari K K; Ricci, Francesco; Franco, Elisa

2017-12-13

Inspired by cytoskeletal scaffolds that sense and respond dynamically to environmental changes and chemical inputs with a unique capacity for reconfiguration, we propose a strategy that allows the dynamic and reversible control of the growth and breakage of micron-scale synthetic DNA structures upon pH changes. We do so by rationally designing a pH-responsive system composed of synthetic DNA strands that act as pH sensors, regulators, and structural elements. Sensor strands can dynamically respond to pH changes and route regulatory strands to direct the self-assembly of structural elements into tubular structures. This example represents the first demonstration of the reversible assembly and disassembly of micron-scale DNA scaffolds using an external chemical input other than DNA. The capacity to reversibly modulate nanostructure size may promote the development of smart devices for catalysis or drug-delivery applications.

The pH-sensing receptor OGR1 improves barrier function of epithelial cells and inhibits migration in an acidic environment.

PubMed

de Vallière, Cheryl; Vidal, Solange; Clay, Ieuan; Jurisic, Giorgia; Tcymbarevich, Irina; Lang, Silvia; Ludwig, Marie-Gabrielle; Okoniewski, Michal; Eloranta, Jyrki J; Kullak-Ublick, Gerd A; Wagner, Carsten A; Rogler, Gerhard; Seuwen, Klaus

2015-09-15

The pH-sensing receptor ovarian cancer G protein-coupled receptor 1 (OGR1; GPR68) is expressed in the gut. Inflammatory bowel disease is typically associated with a decrease in local pH, which may lead to altered epithelial barrier function and subsequent gastrointestinal repair involving epithelial cell adhesion and migration. As the mechanisms underlying the response to pH changes are not well understood, we have investigated OGR1-mediated, pH-dependent signaling pathways in intestinal epithelial cells. Caco-2 cells stably overexpressing OGR1 were created and validated as tools to study OGR1 signaling. Barrier function, migration, and proliferation were measured using electric cell-substrate impedance-sensing technology. Localization of the tight junction proteins zonula occludens protein 1 and occludin and the rearrangement of cytoskeletal actin were examined by confocal microscopy. Paracellular permeability and protein and gene expression analysis using DNA microarrays were performed on filter-grown Caco-2 monolayers. We report that an acidic pH shift from pH 7.8 to 6.6 improved barrier function and stimulated reorganization of filamentous actin with prominent basal stress fiber formation. Cell migration and proliferation during in vitro wound healing were inhibited. Gene expression analysis revealed significant upregulation of genes related to cytoskeleton remodeling, cell adhesion, and growth factor signaling. We conclude that acidic extracellular pH can have a signaling function and impact the physiology of intestinal epithelial cells. The deconstruction of OGR1-dependent signaling may aid our understanding of mucosal inflammation mechanisms. Copyright © 2015 the American Physiological Society.

Fretting-corrosion behavior in hip implant modular junctions: The influence of friction energy and pH variation.

PubMed

Royhman, Dmitry; Patel, Megha; Runa, Maria J; Wimmer, Markus A; Jacobs, Joshua J; Hallab, Nadim J; Mathew, Mathew T

2016-09-01

Recently, there has been increasing concern in the orthopedic community over the use of hip implant modular devices due to an increasing number of reports of early failure, failure that has been attributed to fretting-corrosion at modular interfaces. Much is still unknown about the electrochemical and mechanical degradation mechanisms associated with the use of such devices. Accordingly, the purpose of our study was to develop a methodology for testing the fretting-corrosion behavior of modular junctions. A fretting-corrosion apparatus was used to simulate the fretting-corrosion conditions of a CoCrMo hip implant head on a Ti6Al4V hip implant stem. The device features two perpendicularly-loaded CoCrMo pins that articulated against a Ti6Al4V rod. A sinusoidal fretting motion was applied to the rod at various displacement amplitudes (25, 50, 100, 150 and 200μm) at a constant load of 200N. Bovine calf serum at two different pH levels (3.0 and 7.6) was used to simulate the fluid environment around the joint. Experiments were conducted in two modes of electrochemical control - free-potential and potentiostatic. Electrochemical impedance spectroscopy tests were done before and after the fretting motion to assess changes in corrosion kinetics. In free potential mode, differences were seen in change in potential as a function of displacement amplitude. In general, VDrop (the drop in potential at the onset of fretting), VFretting, (the average potential during fretting), ΔVFretting (the change in potential from the onset of fretting to its termination) and VRecovery (the change in potential from the termination of fretting until stabilization) appeared linear at both pH levels, but showed drastic deviation from linearity at 100μm displacement amplitude. Subsequent EDS analysis revealed a large number of Ti deposits on the CoCrMo pin surfaces. Potentiostatic tests at both pH levels generally showed increasing current with increasing displacement amplitude. Electrochemical impedance spectroscopy measurements from free potential and potentiostatic tests indicated increased levels of resistance of the system after induction of the fretting motion. In free potential tests, the largest increase in impedance was found for the 100μm group. We conclude that the 100µm group exhibits deviations from linearity for several parameters, and this was most likely due to adhesive wear between Ti6Al4V and CoCrMo surfaces. Overall, the degradation of the system was dominated by wear at all pH levels, and displacement amplitudes. Copyright © 2016. Published by Elsevier Ltd.

Pgas, a Low-pH-Induced Promoter, as a Tool for Dynamic Control of Gene Expression for Metabolic Engineering of Aspergillus niger.

PubMed

Yin, Xian; Shin, Hyun-Dong; Li, Jianghua; Du, Guocheng; Liu, Long; Chen, Jian

2017-03-15

The dynamic control of gene expression is important for adjusting fluxes in order to obtain desired products and achieve appropriate cell growth, particularly when the synthesis of a desired product drains metabolites required for cell growth. For dynamic gene expression, a promoter responsive to a particular environmental stressor is vital. Here, we report a low-pH-inducible promoter, P gas , which promotes minimal gene expression at pH values above 5.0 but functions efficiently at low pHs, such as pH 2.0. First, we performed a transcriptional analysis of Aspergillus niger , an excellent platform for the production of organic acids, and we found that the promoter P gas may act efficiently at low pH. Then, a gene for synthetic green fluorescent protein ( sGFP ) was successfully expressed by P gas at pH 2.0, verifying the results of the transcriptional analysis. Next, P gas was used to express the cis -aconitate decarboxylase ( cad ) gene of Aspergillus terreus in A. niger , allowing the production of itaconic acid at a titer of 4.92 g/liter. Finally, we found that P gas strength was independent of acid type and acid ion concentration, showing dependence on pH only. IMPORTANCE The promoter P gas can be used for the dynamic control of gene expression in A. niger for metabolic engineering to produce organic acids. This promoter may also be a candidate tool for genetic engineering. Copyright © 2017 American Society for Microbiology.

Computational Nanotechnology of Materials, Devices, and Machines: Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Kwak, Dolhan (Technical Monitor)

2000-01-01

The mechanics and chemistry of carbon nanotubes have relevance for their numerous electronic applications. Mechanical deformations such as bending and twisting affect the nanotube's conductive properties, and at the same time they possess high strength and elasticity. Two principal techniques were utilized including the analysis of large scale classical molecular dynamics on a shared memory architecture machine and a quantum molecular dynamics methodology. In carbon based electronics, nanotubes are used as molecular wires with topological defects which are mediated through various means. Nanotubes can be connected to form junctions.

Computational Nanotechnology of Materials, Electronics and Machines: Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Srivastava, Deepak

2001-01-01

This report presents the goals and research of the Integrated Product Team (IPT) on Devices and Nanotechnology. NASA's needs for this technology are discussed and then related to the research focus of the team. The two areas of focus for technique development are: 1) large scale classical molecular dynamics on a shared memory architecture machine; and 2) quantum molecular dynamics methodology. The areas of focus for research are: 1) nanomechanics/materials; 2) carbon based electronics; 3) BxCyNz composite nanotubes and junctions; 4) nano mechano-electronics; and 5) nano mechano-chemistry.

Non-Abelian holonomies, charge pumping, and quantum computation with Josephson junctions.

PubMed

Faoro, Lara; Siewert, Jens; Fazio, Rosario

2003-01-17

Non-Abelian holonomies can be generated and detected in certain superconducting nanocircuits. Here we consider an example where the non-Abelian operations are related to the adiabatic charge dynamics of the Josephson network. We demonstrate that such a device can be applied both for adiabatic charge pumping and as an implementation of a quantum computer.

Layered transition metal thiophosphates /MPX3/ as photoelectrodes in photoelectrochemical cells

NASA Technical Reports Server (NTRS)

Byvik, C. E.; Smith, B. T.; Reichman, B.

1982-01-01

Layered crystals of the transition metal thiophosphates were synthesized and characterized for use as photoelectrodes in photoelectrochemical cells. Crystals incorporating tin and manganese show n-type response while those with iron and nickel show p-type response. These materials have a measured indirect bandgap of about 2.1 eV. They show ability to photoelectrolyze water in acid solutions with onset potentials which change in a Nernstian way as the PH of the solution changes. The onset potential is near zero volts versus a saturated calomel electrode at pH 2. At n-type crystals, oxygen could be evolved upon irradiation at underpotentials of 850 mV and at p-type crystals, hydrogen could be evolved at underpotentials of 400 mV, indicating a net gain in energy conversion. All crystals were unstable in basic solution. Liquid junction photovoltaic cells in iodide-triiodide acid solution using these layered materials were also constructed and found to have low efficiences.

Capillary zone electrophoresis-tandem mass spectrometry detects low concentration host cell impurities in monoclonal antibodies

PubMed Central

Zhu, Guijie; Sun, Liangliang; Heidbrink-Thompson, Jennifer; Kuntumalla, Srilatha; Lin, Hung-yu; Larkin, Christopher J.; McGivney, James B.; Dovichi, Norman J.

2016-01-01

We have evaluated capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) for detection of trace amounts of host cell protein impurities in recombinant therapeutics. Compared to previously published procedures, we have optimized the buffer pH used in the formation of a pH junction to increase injection volume. We also prepared a five-point calibration curve by spiking twelve standard proteins into a solution of a human monoclonal antibody. A custom CZE-MS/MS system was used to analyze the tryptic digest of this mixture without depletion of the antibody. CZE generated a ~70 min separation window (~90 min total analysis duration) and ~300 peak capacity. We also analyzed the sample using ultra-performance liquid chromatography (UPLC)-MS/MS. CZE-MS/MS generated ~five times higher base peak intensity and more peptide identifications for low-level spiked proteins. Both methods detected all proteins spiked at the ~100 ppm level with respect to the antibody. PMID:26530276

Synergistic effects of arsenic trioxide combined with ascorbic acid in human osteosarcoma MG-63 cells: a systems biology analysis.

PubMed

Huang, X C; Maimaiti, X Y M; Huang, C W; Zhang, L; Li, Z B; Chen, Z G; Gao, X; Chen, T Y

2014-01-01

To further understand the synergistic mechanism of As2O3 and asscorbic acid (AA) in human osteosarcoma MG-63 cells by systems biology analysis. Human osteosarcoma MG-63 cells were treated by As2O3 (1 µmol/L), AA (62.5 µmol/L) and combined drugs (1 µmol/L As2O3 plus 62.5 µmol/L AA). Dynamic morphological characteristics were recorded by Cell-IQ system, and growth rate was calculated. Illumina beadchip assay was used to analyze the differential expression genes in different groups. Synergic effects on differential expression genes (DEGs) were analyzed by mixture linear model and singular value decomposition model. KEGG pathway annotations and GO enrichment analysis were performed to figure out the pathways involved in the synergic effects. We captured 1987 differential expression genes in combined therapy MG-63 cells. FAT1 gene was significantly upregulated in all three groups, which is a promising drug target as an important tumor suppressor analogue; meanwhile, HIST1H2BD gene was markedly downregulated in the As2O3 monotherapy group and the combined therapy group, which was found to be upregulated in prostatic cancer. These two genes might play critical roles in synergetic effects of AA and As2O3, although the exact mechanism needs further investigation. KEGG pathway analysis showed many DEGs were related with tight junction, and GO analysis also indicated that DEGs in the combined therapy cells gathered in occluding junction, apical junction complex, cell junction, and tight junction. AA potentiates the efficacy of As2O3 in MG-63 cells. Systems biology analysis showed the synergic effect on the DEGs.

Dynamic light-scattering study of gelatin and aggregation of gastric mucin

NASA Astrophysics Data System (ADS)

Bansil, Rama; Cao, Xingxiang; Bhaskar, K. Ramakrishnan; LaMont, Jeffrey T.

1997-05-01

Dynamic light scattering studies show that concentration and pH play important roles in determining pig gastric mucin's (PGM) ability to aggregate and gel. At low concentrations, PGM macromolecules exist in solution predominantly in the form of monomers. At high concentrations, PGM macromolecules aggregate to form supra-macromolecular clusters. When the pH of the high concentration PGM solution is changed from 7.0 to 2.0, the system undergoes a sol-gel transition: from a solution of polydisperse aggregates to a gel. This pH and concentration dependent sol-gel transition of PGM solution may provide a mechanism for the mammalian stomach to protect itself against being digested by the gastric juice.

The effect of motion and signalling on drivers' ability to predict intentions of other road users.

PubMed

Lee, Yee Mun; Sheppard, Elizabeth

2016-10-01

Failure in making the correct judgment about the intention of an approaching vehicle at a junction could lead to a collision. This paper investigated the impact of dynamic information on drivers' judgments about the intentions of approaching cars and motorcycles, and whether a valid or invalid signal was provided was also manipulated. Participants were presented with videoclips of vehicles approaching a junction which terminated immediately before the vehicle made any manoeuvre, or images of the final frame of each video. They were asked to judge whether or not the vehicle would turn. Drivers were better in judging the manoeuvre of approaching vehicles in dynamic than static stimuli, for both vehicle types. Drivers were better in judging the manoeuvre of cars than motorcycles for videos, but not for photographs. Drivers were also better in judging the manoeuvre of approaching vehicles when a valid signal was provided than an invalid signal, demonstrating the importance of providing a valid signal while driving. However, drivers were still somewhat successful in their judgments in most of the conditions with an invalid signal, suggesting that drivers were able to focus on other cues to intention. Finally, given that dynamic stimuli more closely reflect the demands of real-life driving there may be a need for drivers to adopt a more cautious approach while inferring a motorcyclist's intentions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Fabrication of magnetic tunnel junctions connected through a continuous free layer to enable spin logic devices

NASA Astrophysics Data System (ADS)

Wan, Danny; Manfrini, Mauricio; Vaysset, Adrien; Souriau, Laurent; Wouters, Lennaert; Thiam, Arame; Raymenants, Eline; Sayan, Safak; Jussot, Julien; Swerts, Johan; Couet, Sebastien; Rassoul, Nouredine; Babaei Gavan, Khashayar; Paredis, Kristof; Huyghebaert, Cedric; Ercken, Monique; Wilson, Christopher J.; Mocuta, Dan; Radu, Iuliana P.

2018-04-01

Magnetic tunnel junctions (MTJs) interconnected via a continuous ferromagnetic free layer were fabricated for spin torque majority gate (STMG) logic. The MTJs are biased independently and show magnetoelectric response under spin transfer torque. The electrical control of these devices paves the way to future spin logic devices based on domain wall (DW) motion. In particular, it is a significant step towards the realization of a majority gate. To our knowledge, this is the first fabrication of a cross-shaped free layer shared by several perpendicular MTJs. The fabrication process can be generalized to any geometry and any number of MTJs. Thus, this framework can be applied to other spin logic concepts based on magnetic interconnect. Moreover, it allows exploration of spin dynamics for logic applications.

Temperature dependence of spin-torque driven ferromagnetic resonance in MgO-based magnetic tunnel junction with a perpendicularly free layer

NASA Astrophysics Data System (ADS)

Wang, Xiao; Feng, Jiafeng; Guo, Peng; Wei, H. X.; Han, X. F.; Fang, B.; Zeng, Z. M.

2017-12-01

We report the temperature dependence of the spin-torque (ST) driven ferromagnetic resonance in MgO-based magnetic tunnel junction (MTJ) nanopillars with a perpendicularly free layer and an in-plane reference layer. From the evolution of the resonance frequency with magnetic field, we clearly identify the free-layer resonance mode and reference-layer mode. For the reference layer, we demonstrate a monotonic increase in resonance frequency and the effective damping with decreasing temperature, which suggests the saturated magnetization of the reference layer is dominant. However, for the free layer, the frequency and damping exhibit almost no change with temperature, indicating that the perpendicular magnetic anisotropy plays an important role in magnetization dynamics of the free layer.

Solitonic Josephson Thermal Transport

NASA Astrophysics Data System (ADS)

Guarcello, Claudio; Solinas, Paolo; Braggio, Alessandro; Giazotto, Francesco

2018-03-01

We explore the coherent thermal transport sustained by solitons through a long Josephson junction as a thermal gradient across the system is established. We observe that a soliton causes the heat current through the system to increase. Correspondingly, the junction warms up in conjunction with the soliton, with temperature peaks up to, e.g., approximately 56 mK for a realistic Nb-based proposed setup at a bath temperature Tbath=4.2 K . The thermal effects on the dynamics of the soliton are also discussed. Markedly, this system inherits the topological robustness of the solitons. In view of these results, the proposed device can effectively find an application as a superconducting thermal router in which the thermal transport can be locally mastered through solitonic excitations, whose positions can be externally controlled through a magnetic field and a bias current.

Influence of voids distribution on the deformation behavior of nanocrystalline palladium

NASA Astrophysics Data System (ADS)

Bachurin, D. V.

2018-07-01

Uniaxial deformation of three-dimensional nanocrystalline palladium containing porosity in the form of voids was investigated by means of molecular dynamics method. Simulations were performed at temperature of 300 K and at a constant strain rate of 108s-1. Two cases of voids distribution were considered: random and at triple or quadrupole junctions. It has been revealed that both the voids distribution and subsequent annealing at elevated temperature influence the deformation behavior of nanocrystalline palladium. In particular, the presence of voids at grain junctions results in a reduction of the Young's modulus and more pronounced softening effect during plastic deformation. The subsequent annealing evokes shrinkage of voids and strengthening effect. Contribution of grain boundary accommodation processes into both elastic and plastic deformation of nanocrystalline materials is discussed.

Evolution of nano-rheological properties of Nafion¯ thin films during pH modification by strong base treatment: A static and dynamic force spectroscopy study

NASA Astrophysics Data System (ADS)

Eslami, Babak; López-Guerra, Enrique A.; Raftari, Maryam; Solares, Santiago D.

2016-04-01

Addition of a strong base to Nafion® proton exchange membranes is a common practice in industry to increase their overall performance in fuel cells. Here, we investigate the evolution of the nano-rheological properties of Nafion thin films as a function of the casting pH, via characterization with static and dynamic, contact and intermittent-contact atomic force microscopy (AFM) techniques. The addition of KOH causes non-monotonic changes in the viscoelastic properties of the films, which behave as highly dissipative, softer materials near neutral pH values, and as harder, more elastic materials at extreme pH values. We quantify this behavior through calculation of the temporal evolution of the compliance and the glassy compliance under static AFM measurements. We complement these observations with dynamic AFM metrics, including dissipated power and virial (for intermittent-contact-mode measurements), and contact resonance frequency and quality factor (for dynamic contact-mode measurements). We explain the non-monotonic material property behavior in terms of the degree of ionic crosslinking and moisture content of the films, which vary with the addition of KOH. This work focuses on the special case study of the addition of strong bases, but the observed mechanical property changes are broadly related to water plasticizing effects and ionic crosslinking, which are also important in other types of films.

Ligand Accessibility and Bioactivity of a Hormone-Dendrimer Conjugate Depend on pH and pH History

PubMed Central

Kim, Sung Hoon; Madak-Erdogan, Zeynep; Bae, Sung Chul; Carlson, Kathryn E.; Mayne, Christopher G.; Granick, Steve; Katzenellenbogen, Benita S.; Katzenellenbogen, John A.

2016-01-01

Estrogen conjugates with a polyamidoamine (PAMAM) dendrimer have shown remarkably selective regulation of the non-genomic actions of estrogens in target cells. In response to pH changes, however, these estrogen-dendrimer conjugates (EDCs) display a major morphological transition that alters the accessibility of the estrogen ligands that compromises the bioactivity of the EDC. A sharp break in dynamic behavior near pH 7 occurs for three different ligands on the surface of a PAMAM-G6 dendrimer: a fluorophore (tetramethylrhodamine, TMR) and two estrogens (17α-ethynylestradiol and diphenolic acid). Collisional quenching and time-resolved fluorescence anisotropy experiments with TMR-PAMAM reveal high ligand shielding above pH 7 and low shielding below pH 7. Furthermore, when pH was cycled from 8.5 (conditions of ligand-PAMAM conjugation) to 4.5 (e.g., endosome/lysosome) and through 6.5 (e.g., hypoxic environment) back to pH 8.5, the 17α-ethynylestradiol and diphenolic acid PAMAM conjugates experience a dramatic, irreversible loss in cell stimulatory activity; dynamic NMR studies indicate that the hormonal ligands had become occluded within the more hydrophobic core of the PAMAM dendrimer. Thus, the active state of these estrogen-dendrimer conjugates appears to be metastable. This pH-dependent irreversible masking of activity is of considerable relevance to the design of drug conjugates with amine-bearing PAMAM dendrimers. PMID:26186415

Fluorescent Silicon Nanorods-Based Ratiometric Sensors for Long-Term and Real-Time Measurements of Intracellular pH in Live Cells.

PubMed

Chu, Binbin; Song, Bin; Ji, Xiaoyuan; Su, Yuanyuan; Wang, Houyu; He, Yao

2017-11-21

Long-term and real-time investigation of the dynamic process of pH i changes is critically significant for understanding the related pathogenesis of diseases and the design of intracellular drug delivery systems. Herein, we present a one-step synthetic strategy to construct ratiometric pH sensors, which are made of europium (Eu)-doped one-dimensional silicon nanorods (Eu@SiNRs). The as-prepared Eu@SiNRs have distinct emission maxima peaks at 470 and 620 nm under 405 nm excitation. Of particular note, the fluorescence emission intensity at 470 nm decreases along with the increase of pH, while the one at 620 nm is nearly unaffected by pH changes, making Eu@SiNRs a feasible probe for pH sensing ratiometrically. Moreover, Eu@SiNRs are found to be responsive to a broad pH range (ca. 3-9), biocompatible (e.g., ∼100% of cell viability during 24 h treatment) and photostable (e.g., ∼10% loss of intensity after 40 min continuous UV irradiation). Taking advantages of these merits, we employ Eu@SiNRs for the visualization of the cytoplasmic alkalization process mediated by nigericin in living cells, for around 30 min without interruption, revealing important information for understanding the dynamic process of pH i fluctuations.

Estimation of pH effect on the structure and stability of kinase domain of human integrin-linked kinase.

PubMed

Syed, Sunayana Begum; Shahbaaz, Mohd; Khan, Sabab Hassan; Srivastava, Saurabha; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

2018-01-07

Integrin-linked kinase (ILK) is an evolutionarily conserved Ser/Thr protein kinase, involved in many physiological functions such as signal transduction, actin rearrangement, cell proliferation, migration, polarisation, angiogenesis and apoptosis. An increased expression of ILK is associated with different cancers and thus considered as an attractive target for cancer therapy. We have successfully cloned, expressed and purified the kinase domain (193-446 residues) of ILK. To see the effect of pH on the structure and conformation, we performed circular diachroism, fluorescence and absorbance measurements in a wide range of pH conditions. We observed that within the range of pH 7.5-11.0, ILK 193-446 maintains its both secondary and tertiary structures. While visible aggregates were observed under the acidic pH 2.0-5.5 conditions, in order to complement these observations, we have performed molecular dynamics simulations of this kinase domain by mimicking diverse pH conditions which enabled us to see conformational preferences of the protein under such conditions. A significant correlation between the spectroscopic and molecular dynamics simulation was observed. These findings are useful to understand the conformation of ILK protein under certain pH condition which may be further implicated in the drug design and discovery.

Aggregation behaviors of PEO-PPO-ph-PPO-PEO and PPO-PEO-ph-PEO-PPO at an air/water interface: experimental study and molecular dynamics simulation.

PubMed

Gong, Houjian; Xu, Guiying; Liu, Teng; Xu, Long; Zhai, Xueru; Zhang, Jian; Lv, Xin

2012-09-25

The block polyethers PEO-PPO-ph-PPO-PEO (BPE) and PPO-PEO-ph-PEO-PPO (BEP) are synthesized by anionic polymerization using bisphenol A as initiator. Compared with Pluronic P123, the aggregation behaviors of BPE and BEP at an air/water interface are investigated by the surface tension and dilational viscoelasticity. The molecular construction can influence the efficiency and effectiveness of block polyethers in decreasing surface tension. BPE has the most efficient ability to decrease surface tension of water among the three block polyethers. The maximum surface excess concentration (Γ(max)) of BPE is larger than that of BEP or P123. Moreover, the dilational modulus of BPE is almost the same as that of P123, but much larger than that of BEP. The molecular dynamics simulation provides the conformational variations of block polyethers at the air/water interface.

Effect of pH and Ibuprofen on Phopholipid Bilayer Bending Modulus

NASA Astrophysics Data System (ADS)

Boggara, Mohan; Faraone, Antonio; Krishnamoorti, Ramanan

2010-03-01

Non-steroidal anti-inflammatory drugs (NSAIDs) e.g. Aspirin and Ibuprofen, are known to cause gastrointestinal (GI) toxicity with chronic usage. However, NSAIDs pre-associated with phospholipids has been experimentally shown to reduce the GI toxicity and increase the therapeutic efficacy. In this study, using neutron spin-echo the effect of ibuprofen on the phospholipid membrane bending modulus is studied as a function of pH and temperature. Ibuprofen was found to lower the bending modulus at all pH values. We further present molecular insights into the observed effect on membrane dynamics based on structural studies using molecular dynamics simulations and small angle neutron scattering data as well as changes in zwitterionic headgroup electrostatics due to pH and addition of ibuprofen. This study is expected to help towards effective design of drug delivery nanoparticles based on variety of soft condensed matter such as lipids or polymers.

Nanoparticle-based measurements of pH and O2 dynamics in the rhizosphere of Zostera marina L.: effects of temperature elevation and light-dark transitions.

PubMed

Elgetti Brodersen, Kasper; Koren, Klaus; Lichtenberg, Mads; Kühl, Michael

2016-07-01

Seagrasses can modulate the geochemical conditions in their immediate rhizosphere through the release of chemical compounds from their below-ground tissue. This is a vital chemical defence mechanism, whereby the plants detoxify the surrounding sediment. Using novel nanoparticle-based optical O2 and pH sensors incorporated in reduced and transparent artificial sediment, we investigated the spatio-temporal dynamics of pH and O2 within the entire rhizosphere of Zostera marina L. during experimental manipulations of light and temperature. We combined such measurements with O2 microsensor measurements of the photosynthetic productivity and respiration of seagrass leaves. We found pronounced pH and O2 microheterogeneity within the immediate rhizosphere of Z. marina, with higher below-ground tissue oxidation capability and rhizoplane pH levels during both light exposure of the leaf canopy and elevated temperature, where the temperature-mediated stimuli of biogeochemical processes seemed to predominate. Low rhizosphere pH microenvironments appeared to correlate with plant-derived oxic microzones stimulating local sulphide oxidation and thus driving local proton generation, although the rhizoplane pH levels generally where much higher than the bulk sediment pH. Our data show that Z. marina can actively alter its rhizosphere pH microenvironment alleviating the local H2 S toxicity and enhancing nutrient availability in the adjacent sediment via geochemical speciation shift. © 2016 John Wiley & Sons Ltd.

Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor.

PubMed

Mora, Thierry; Yu, Howard; Wingreen, Ned S

2009-12-11

We present a minimal physical model for the flagellar motor that enables bacteria to swim. Our model explains the experimentally measured torque-speed relationship of the proton-driven E. coli motor at various pH and temperature conditions. In particular, the dramatic drop of torque at high rotation speeds (the "knee") is shown to arise from saturation of the proton flux. Moreover, we show that shot noise in the proton current dominates the diffusion of motor rotation at low loads. This suggests a new way to probe the discreteness of the energy source, analogous to measurements of charge quantization in superconducting tunnel junctions.

Role of direct electron-phonon coupling across metal-semiconductor interfaces in thermal transport via molecular dynamics.

PubMed

Lin, Keng-Hua; Strachan, Alejandro

2015-07-21

Motivated by significant interest in metal-semiconductor and metal-insulator interfaces and superlattices for energy conversion applications, we developed a molecular dynamics-based model that captures the thermal transport role of conduction electrons in metals and heat transport across these types of interface. Key features of our model, denoted eleDID (electronic version of dynamics with implicit degrees of freedom), are the natural description of interfaces and free surfaces and the ability to control the spatial extent of electron-phonon (e-ph) coupling. Non-local e-ph coupling enables the energy of conduction electrons to be transferred directly to the semiconductor/insulator phonons (as opposed to having to first couple to the phonons in the metal). We characterize the effect of the spatial e-ph coupling range on interface resistance by simulating heat transport through a metal-semiconductor interface to mimic the conditions of ultrafast laser heating experiments. Direct energy transfer from the conduction electrons to the semiconductor phonons not only decreases interfacial resistance but also increases the ballistic transport behavior in the semiconductor layer. These results provide new insight for experiments designed to characterize e-ph coupling and thermal transport at the metal-semiconductor/insulator interfaces.

Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer.

PubMed

Donnini, Serena; Ullmann, R Thomas; Groenhof, Gerrit; Grubmüller, Helmut

2016-03-08

In constant pH molecular dynamics simulations, the protonation states of titratable sites can respond to changes of the pH and of their electrostatic environment. Consequently, the number of protons bound to the biomolecule, and therefore the overall charge of the system, fluctuates during the simulation. To avoid artifacts associated with a non-neutral simulation system, we introduce an approach to maintain neutrality of the simulation box in constant pH molecular dynamics simulations, while maintaining an accurate description of all protonation fluctuations. Specifically, we introduce a proton buffer that, like a buffer in experiment, can exchange protons with the biomolecule enabling its charge to fluctuate. To keep the total charge of the system constant, the uptake and release of protons by the buffer are coupled to the titration of the biomolecule with a constraint. We find that, because the fluctuation of the total charge (number of protons) of a typical biomolecule is much smaller than the number of titratable sites of the biomolecule, the number of buffer sites required to maintain overall charge neutrality without compromising the charge fluctuations of the biomolecule, is typically much smaller than the number of titratable sites, implying markedly enhanced simulation and sampling efficiency.

Novel self-powered pH indicator using ionic polymeric gel muscles

NASA Astrophysics Data System (ADS)

Shahinpoor, Mohsen

1994-05-01

A novel design for a torsional spring-loaded pH indicator using ionic polymeric gel fibrous muscles is presented. The essential parts of the proposed self-powered pH indicator are a pair of co-axial and concentric cylinders, an assembly of fibrous polyacrylonitrile (PAN) muscles, a torsional spring, and a dial indicator. The two co-axial cylinders are such that the inner cylinder may pivotally rotate about the central rotation axis that is fixed to the inner bottom or side of the outer cylinder. The outer cylinder also serves as a reservoir for any liquid whose pH is to be determined either statically or dynamically. The internal cylindrical drum is further equipped with a dial indicator on one of its outer end caps such that when a pH environment is present the contraction or expansion of the PAN fibers cause the inner drum to rotate and thus give a reading of the dial indicator. The motion of the dial indicator may also be converted to an electrical signal (voltage) for digital electronics display and computer control. A mathematical model is also presented for the dynamic response of the self-powered pH indicator made with contractile PAN fiber bundle assemblies.

Constant pH Molecular Dynamics of Proteins in Explicit Solvent with Proton Tautomerism

PubMed Central

Goh, Garrett B.; Hulbert, Benjamin S.; Zhou, Huiqing; Brooks, Charles L.

2015-01-01

pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMDMSλD). In the CPHMDMSλD framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMDMSλD simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMDMSλD framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules – proteins and nucleic acids is now possible. PMID:24375620

Poromechanics of stick-slip frictional sliding and strength recovery on tectonic faults

DOE PAGES

Scuderi, Marco M.; Carpenter, Brett M.; Johnson, Paul A.; ...

2015-10-22

Pore fluids influence many aspects of tectonic faulting including frictional strength aseismic creep and effective stress during the seismic cycle. But, the role of pore fluid pressure during earthquake nucleation and dynamic rupture remains poorly understood. Here we report on the evolution of pore fluid pressure and porosity during laboratory stick-slip events as an analog for the seismic cycle. We sheared layers of simulated fault gouge consisting of glass beads in a double-direct shear configuration under true triaxial stresses using drained and undrained fluid conditions and effective normal stress of 5–10 MPa. Shear stress was applied via a constant displacementmore » rate, which we varied in velocity step tests from 0.1 to 30 µm/s. Here, we observe net pore pressure increases, or compaction, during dynamic failure and pore pressure decreases, or dilation, during the interseismic period, depending on fluid boundary conditions. In some cases, a brief period of dilation is attendant with the onset of dynamic stick slip. Our data show that time-dependent strengthening and dynamic stress drop increase with effective normal stress and vary with fluid conditions. For undrained conditions, dilation and preseismic slip are directly related to pore fluid depressurization; they increase with effective normal stress and recurrence time. Microstructural observations confirm the role of water-activated contact growth and shear-driven elastoplastic processes at grain junctions. These results indicate that physicochemical processes acting at grain junctions together with fluid pressure changes dictate stick-slip stress drop and interseismic creep rates and thus play a key role in earthquake nucleation and rupture propagation.« less

NMR studies of the dynamics of high-spin nitrophorins: comparative studies of NP4 and NP2 at close to physiological pH.

PubMed

Berry, Robert E; Muthu, Dhanasekaran; Yang, Fei; Walker, F Ann

2015-01-20

The β-barrel nitrophorin (NP) heme proteins are found in the saliva of the blood-sucking insect Rhodnius prolixus, which synthesizes and stores nitric oxide (NO) in the salivary glands. NO is bound to iron of the NPs and is released by dilution and an increase in pH when the insect spits its saliva into the tissues of a victim, to aid in obtaining a blood meal. In the adult insect, there are four nitrophorins, NP1-NP4, which have sequence similarities in two pairs, NP1 and NP4 (90% identical) and NP2 and NP3 (80% identical). The available crystal structures of NP4 have been used to propose that pH-dependent changes in the conformation of two loops between adjacent β-strands at the front opening of the protein, the A-B and G-H loops, determine the rate of NO release. At pH 7.3, NP4 releases NO 17 times faster than NP2 does. In this work, the aqua complexes of NP4 and NP2 have been investigated by nuclear magnetic resonance (NMR) relaxation measurements to probe the pico- to nanosecond and micro- to millisecond time scale motions at two pH values, 6.5 and 7.3. It is found that NP4-OH2 is fairly rigid and only residues in the loop regions show dynamics at pH 6.5; at pH 7.3, much more dynamics of the loops and most of the β-strands are observed while the α-helices remain fairly rigid. In comparison, NP2-OH2 shows much less dynamics, albeit somewhat more than that of the previously reported NP2-NO complex [Muthu, D., Berry, R. E., Zhang, H., and Walker, F. A. (2013) Biochemistry 52, 7910-7925]. The reasons for this major difference between NP4 and NP2 are discussed.

NMR Studies of the Dynamics of High-Spin Nitrophorins: Comparative Studies of NP4 and NP2 at Close to Physiological pH

PubMed Central

2015-01-01

The β-barrel nitrophorin (NP) heme proteins are found in the saliva of the blood-sucking insect Rhodnius prolixus, which synthesizes and stores nitric oxide (NO) in the salivary glands. NO is bound to iron of the NPs and is released by dilution and an increase in pH when the insect spits its saliva into the tissues of a victim, to aid in obtaining a blood meal. In the adult insect, there are four nitrophorins, NP1–NP4, which have sequence similarities in two pairs, NP1 and NP4 (90% identical) and NP2 and NP3 (80% identical). The available crystal structures of NP4 have been used to propose that pH-dependent changes in the conformation of two loops between adjacent β-strands at the front opening of the protein, the A–B and G–H loops, determine the rate of NO release. At pH 7.3, NP4 releases NO 17 times faster than NP2 does. In this work, the aqua complexes of NP4 and NP2 have been investigated by nuclear magnetic resonance (NMR) relaxation measurements to probe the pico- to nanosecond and micro- to millisecond time scale motions at two pH values, 6.5 and 7.3. It is found that NP4-OH2 is fairly rigid and only residues in the loop regions show dynamics at pH 6.5; at pH 7.3, much more dynamics of the loops and most of the β-strands are observed while the α-helices remain fairly rigid. In comparison, NP2-OH2 shows much less dynamics, albeit somewhat more than that of the previously reported NP2-NO complex [Muthu, D., Berry, R. E., Zhang, H., and Walker, F. A. (2013) Biochemistry 52, 7910–7925]. The reasons for this major difference between NP4 and NP2 are discussed. PMID:25486224

Dynamic reservoir-condition microtomography of reactive transport in complex carbonates: Effect of initial pore structure and initial brine pH

NASA Astrophysics Data System (ADS)

Menke, H. P.; Bijeljic, B.; Blunt, M. J.

2017-05-01

We study the impact of brine acidity and initial pore structure on the dynamics of fluid/solid reaction at high Péclet numbers and low Damköhler numbers. A laboratory μ-CT scanner was used to image the dissolution of Ketton, Estaillades, and Portland limestones in the presence of CO2-acidified brine at reservoir conditions (10 MPa and 50 °C) at two injected acid strengths for a period of 4 h. Each sample was scanned between 6 and 10 times at ∼4 μm resolution and multiple effluent samples were extracted. The images were used as inputs into flow simulations, and analysed for dynamic changes in porosity, permeability, and reaction rate. Additionally, the effluent samples were used to verify the image-measured porosity changes. We find that initial brine acidity and pore structure determine the type of dissolution. Dissolution is either uniform where the porosity increases evenly both spatially and temporally, or occurs as channelling where the porosity increase is concentrated in preferential flow paths. Ketton, which has a relatively homogeneous pore structure, dissolved uniformly at pH = 3.6 but showed more channelized flow at pH = 3.1. In Estaillades and Portland, increasingly complex carbonates, channelized flow was observed at both acidities with the channel forming faster at lower pH. It was found that the effluent pH, which is higher than that injected, is a reasonably good indicator of effective reaction rate during uniform dissolution, but a poor indicator during channelling. The overall effective reaction rate was up to 18 times lower than the batch reaction rate measured on a flat surface at the effluent pH, with the lowest reaction rates in the samples with the most channelized flow, confirming that transport limitations are the dominant mechanism in determining reaction dynamics at the fluid/solid boundary.

Intracellular delivery and trafficking dynamics of a lymphoma-targeting antibody-polymer conjugate

PubMed Central

Berguig, Geoffrey Y.; Convertine, Anthony J.; Shi, Julie; Palanca-Wessels, Maria Corinna; Duvall, Craig L.; Pun, Suzie H.; Press, Oliver W.; Stayton, Patrick S.

2012-01-01

Ratiometric fluorescence and cellular fractionation studies were employed to characterize the intracellular trafficking dynamics of antibody-poly(propylacrylic acid) (PPAA) conjugates in CD22+ RAMOS-AW cells. The HD39 monoclonal antibody (mAb) directs CD22-dependent, receptor-mediated uptake in human B-cell lymphoma cells where it is rapidly trafficked to the lysosomal compartment. To characterize the intracellular-releasing dynamics of the polymer-mAb conjugates, HD39-streptavidin (HD39/SA) was dual-labeled with pH-insensitive Alex Fluor 488 and pH-sensitive pHrodo fluorophores. The subcellular pH-distribution of the HD39/SA-polymer conjugates were quantified as a function of time by live-cell fluorescence microscopy, and the average intracellular pH values experienced by the conjugates were also characterized as a function of time by flow cytometry. PPAA was shown to strongly alter the intracellular trafficking kinetics compared to HD39/SA alone or HD39/SA conjugates with a control polymer, poly(methacryclic acid) (PMAA). Subcellular trafficking studies revealed that after 6 hours only 11% of the HD39/SA-PPAA conjugates had been trafficked to acidic lysosomal compartments with values at or below pH 5.6. In contrast the average intracellular pH of HD39/SA alone dropped from pH 6.7 ± 0.2 at 1 hour to pH 5.6 ± 0.5 after 3 hours and pH 4.7 ± 0.6 after 6 hours. Conjugation of the control PMAA to HD39/SA showed an average pH drop similar to HD39/SA. Subcellular fractionation studies with tritium-labeled HD39/SA demonstrated that after 6 hours, 89% of HD39/SA was associated with endosomes (Rab5+) and lysosomes (Lamp2+), while 45% of HD39/SA-PPAA was translocated to the cytosol (lactate dehydrogenase+). These results demonstrate the endosomal-releasing properties of PPAA with antibody-polymer conjugates and detail their intracellular trafficking dynamics and subcellular compartmental distributions over time. PMID:23075320

NMR Studies of the Dynamics of Nitrophorin 2 Bound to Nitric Oxide†

PubMed Central

Muthu, Dhanasekaran; Berry, Robert E.; Zhang, Hongjun; Walker, F. Ann

2013-01-01

The Rhodnius nitrophorins are β-barrel proteins of the lipocalin fold with a heme protruding from the open end of the barrel. They are found in the saliva of the blood-sucking insect Rhodnius prolixus, which synthesizes and stores nitric oxide (NO) in the salivary glands, where NO is bound to iron. NO is released by dilution and pH rise when the insect spits its saliva into the tissues of a victim, to aid in obtaining a blood meal. In the adult insect there are four nitrophorins, NP1, NP2, NP3 and NP4. At pH 7.3, NP4 releases NO 17 times faster than does NP2, as measured by stopped-flow kinetics. A number of crystal structures of the least abundant protein, NP4, are available. These structures have been used to propose that two loops between adjacent β-strands at the front opening of the protein, the A-B and G-H loops, determine the rate of NO release. In order to learn how the protein loops contribute to release of NO for each of the nitrophorins, the dynamics of these proteins are being studied in our laboratory. In this work, the NP2-NO complex has been investigated by NMR relaxation measurements to probe the pico- to nanosecond and micro- to millisecond time scale motions at three pH values, 5.0, 6.5, and 7.3. It is found that at pH 5.0 and 6.5, NP2-NO is rigid and only a few residues in the loop regions show dynamics, while at pH 7.3 somewhat more dynamics, particularly of the A-B loop, are observed. Comparison to other lipocalins shows that all are relatively rigid, and that the dynamics of lipocalins in general are much more subtle than those of mainly α-helical proteins. PMID:24116947

Exploring the Electronic Landscape at Interfaces and Junctions in Semiconductor Nanowire Devices with Subsurface Local Probing of Carrier Dynamics

NASA Astrophysics Data System (ADS)

McGuckin, Terrence

The solid state devices that are pervasive in our society, are based on building blocks composed of interfaces between materials and junctions that manipulate how charge carriers behave in a device. As the dimensions of these devices are reduced to the nanoscale, surfaces and interfaces play a larger role in the behavior of carriers in devices and must be thoroughly investigated to understand not only the material properties but how these materials interact. Separating the effects of these different building blocks is a challenge, as most testing methods measure the performance of the whole device. Semiconductor nanowires represent an excellent test system to explore the limits of size and novel device structures. The behavior of charge carriers in semiconductor nanowire devices under operational conditions is investigated using local probing technique electron beam induced current (EBIC). The behavior of locally excited carriers are driven by the forces of drift, from electric fields within a device at junctions, surfaces, contacts and, applied voltage bias, and diffusion. This thesis presents the results of directly measuring these effects spatially with nanometer resolution, using EBIC in Ge, Si, and complex heterostructure GaAs/AlGaAs nanowire devices. Advancements to the EBIC technique, have pushed the resolution from tens of nanometers down to 1 to 2 nanometers. Depth profiling and tuning of the interaction volume allows for the separating the signal originating from the surface and the interior of the nanowire. Radial junctions and variations in bands can now be analyzed including core/shell hetero-structures. This local carrier probing reveals a number of surprising behaviors; Most notably, directly imaging the evolution of surface traps filling with electrons causing bandbending at the surface of Ge nanowires that leads to an enhancement in the charge separation of electrons and holes, and extracting different characteristic lengths from GaAs and AlGaAs in core/shell nanowires. For new and emerging solid state materials, understanding charge carrier dynamics is crucial to designing functional devices. Presented here are examples of the wide application of EBIC, and its variants, through imaging domains in ferroelectric materials, local electric fields and defects in 2D semiconductor material MoS2, and gradients in doping profiles of solar cells. Measuring the local behavior of carrier dynamics, EBIC has the potential to be a key metrology technique in correlative microscopy, enabling a deeper understanding of materials and how they interact within devices.

Structural and photodynamic properties of the anti-cancer drug irinotecan in aqueous solutions of different pHs.

PubMed

di Nunzio, Maria Rosaria; Douhal, Yasmin; Organero, Juan Angel; Douhal, Abderrazzak

2018-05-23

This work reports on photophysical studies of the irinotecan (IRT) anti-cancer drug in water solutions of different acidities (pH = 1.11-9.46). We found that IRT co-exists as mono-cationic (C1), di-cationic (C2), or neutral (N) forms. The population of each prototropic species depends on the pH of the solution. At pH = 1.11-3.01, the C1 and C2 structures are stabilized. At pH = 7.00, the most populated species is C1, while at pH values larger than 9.46 the N form is the most stable species. In the 1.11-2.61 pH range, the C1* emission is efficiently quenched by protons to give rise to the emission from C2*. The dynamic quenching constant, KD, is ∼32 M-1. While the diffusion governs the rate of excited-state proton-transfer (ESPT) under these conditions, the reaction rate increases with the proton concentration. A two-step diffusive Debye-Smoluchowski model was applied at pH = 1.11-2.61 to describe the protonation of C1*. The ESPT time constants derived for C1* are 382 and 1720 ps at pH = 1.11 and 1.95, respectively. We found that one proton species is involved in the protonation of C1* to give C2*, in the analyzed acidic pH range. Under alkaline conditions (pH = 9.46), the N form is the most stable structure of IRT. These results indicate the influence of the pH of the medium on the structural and dynamical properties of IRT in water solution. They may help to provide a better understanding on the relationship between the structure and biological activity of IRT.

Fabrication of a Miniature Multi-Parameter Sensor Chip for Water Quality Assessment.

PubMed

Zhou, Bo; Bian, Chao; Tong, Jianhua; Xia, Shanhong

2017-01-14

Water contamination is a main inducement of human diseases. It is an important step to monitor the water quality in the water distribution system. Due to the features of large size, high cost, and complicated structure of traditional water determination sensors and devices, it is difficult to realize real-time water monitoring on a large scale. In this paper, we present a multi-parameter sensor chip, which is miniature, low-cost, and robust, to detect the pH, conductivity, and temperature of water simultaneously. The sensor chip was fabricated using micro-electro-mechanical system (MEMS) techniques. Iridium oxide film was electrodeposited as the pH-sensing material. The atomic ratio of Ir(III) to Ir(IV) is about 1.38 according to the X-ray photoelectron spectroscopy (XPS) analysis. The pH sensing electrode showed super-Nernstian response (-67.60 mV/pH) and good linearity (R² = 0.9997), in the range of pH 2.22 to pH 11.81. KCl-agar and epoxy were used as the electrolyte layer and liquid junction for the solid-state reference electrode, respectively, and its potential stability in deionized water was 56 h. The conductivity cell exhibited a linear determination range from 21.43 μ S / cm to 1.99 mS / cm , and the electrode constant was 1.566 cm -1 . Sensitivity of the temperature sensor was 5.46 Ω / ° C . The results indicate that the developed sensor chip has potential application in water quality measurements.

Free-Flow Zone Electrophoresis of Peptides and Proteins in PDMS Microchip for Narrow pI Range Sample Prefractionation Coupled with Mass Spectrometry

PubMed Central

Song, Yong-Ak; Chan, Michael; Celio, Chris; Tannenbaum, Steven R.; Wishnok, John S.; Han, Jongyoon

2010-01-01

In this paper, we are evaluating the strategy of sorting peptides / proteins based on the charge to mass without resorting to ampholytes and / or isoelectric focusing, using a single- and two-step free-flow zone electrophoresis. We developed a simple fabrication method to create a salt bridge for free-flow zone electrophoresis in PDMS chips by surface printing a hydrophobic layer on a glass substrate. Since the surface-printed hydrophobic layer prevents plasma bonding between the PDMS chip and the substrate, an electrical junction gap can be created for free-flow zone electrophoresis. With this device, we demonstrated a separation of positive and negative peptides and proteins at a given pH in standard buffer systems, and validated the sorting result with LC/MS. Furthermore, we coupled two sorting steps via off-chip titration, and isolated peptides within specific pI ranges from sample mixtures, where the pI range was simply set by the pH values of the buffer solutions. This free-flow zone electrophoresis sorting device, with its simplicity of fabrication, and a sorting resolution of 0.5 pH unit, can potentially be a high-throughput sample fractionation tool for targeted proteomics using LC/MS. PMID:20163146

Surface obstacles in pulsatile flow

NASA Astrophysics Data System (ADS)

Carr, Ian A.; Plesniak, Michael W.

2017-11-01

Flows past obstacles mounted on flat surfaces have been widely studied due to their ubiquity in nature and engineering. For nearly all of these studies, the freestream flow over the obstacle was steady, i.e., constant velocity, unidirectional flow. Unsteady, pulsatile flows occur frequently in biology, geophysics, biomedical engineering, etc. Our study is aimed at extending the comprehensive knowledge base that exists for steady flows to considerably more complex pulsatile flows. Characterizing the vortex and wake dynamics of flows around surface obstacles embedded in pulsatile flows can provide insights into the underlying physics in all wake and junction flows. In this study, we experimentally investigate the wake of two canonical obstacles: a cube and a circular cylinder with an aspect ratio of unity. Our previous studies of a surface-mounted hemisphere in pulsatile flow are used as a baseline for these two new, more complex geometries. Phase-averaged PIV and hot-wire anemometry are used to characterize the dynamics of coherent structures in the wake and at the windward junction of the obstacles. Complex physics occur during the deceleration phase of the pulsatile inflow. We propose a framework for understanding these physics based on self-induced vortex propagation, similar to the phenomena exhibited by vortex rings.

Revealing the distinct folding phases of an RNA three-helix junction.

PubMed

Plumridge, Alex; Katz, Andrea M; Calvey, George D; Elber, Ron; Kirmizialtin, Serdal; Pollack, Lois

2018-05-14

Remarkable new insight has emerged into the biological role of RNA in cells. RNA folding and dynamics enable many of these newly discovered functions, calling for an understanding of RNA self-assembly and conformational dynamics. Because RNAs pass through multiple structures as they fold, an ensemble perspective is required to visualize the flow through fleetingly populated sets of states. Here, we combine microfluidic mixing technology and small angle X-ray scattering (SAXS) to measure the Mg-induced folding of a small RNA domain, the tP5abc three helix junction. Our measurements are interpreted using ensemble optimization to select atomically detailed structures that recapitulate each experimental curve. Structural ensembles, derived at key stages in both time-resolved studies and equilibrium titrations, reproduce the features of known intermediates, and more importantly, offer a powerful new structural perspective on the time-progression of folding. Distinct collapse phases along the pathway appear to be orchestrated by specific interactions with Mg ions. These key interactions subsequently direct motions of the backbone that position the partners of tertiary contacts for later bonding, and demonstrate a remarkable synergy between Mg and RNA across numerous time-scales.

Macroscopic Quantum Phase-Locking Model for the Quantum Hall = Effect

NASA Astrophysics Data System (ADS)

Wang, Te-Chun; Gou, Yih-Shun

1997-08-01

A macroscopic model of nonlinear dissipative phase-locking between a Josephson-like frequency and a macroscopic electron wave frequency is proposed to explain the Quantum Hall Effect. It is well known that a r.f-biased Josephson junction displays a collective phase-locking behavior which can be described by a non-autonomous second order equation or an equivalent 2+1-dimensional dynamical system. Making a direct analogy between the QHE and the Josephson system, this report proposes a computer-solving nonlinear dynamical model for the quantization of the Hall resistance. In this model, the Hall voltage is assumed to be proportional to a Josephson-like frequency and the Hall current is assumed related to a coherent electron wave frequency. The Hall resistance is shown to be quantized in units of the fine structure constant as the ratio of these two frequencies are locked into a rational winding number. To explain the sample-width dependence of the critical current, the 2DEG under large applied current is further assumed to develop a Josephson-like junction array in which all Josephson-like frequencies are synchronized. Other remarkable features of the QHE such as the resistance fluctuation and the even-denominator states are also discussed within this picture.

New Aspects of Photocurrent Generation at Graphene pn Junctions Revealed by Ultrafast Optical Measurements

NASA Astrophysics Data System (ADS)

Aivazian, Grant; Sun, Dong; Jones, Aaron; Ross, Jason; Yao, Wang; Cobden, David; Xu, Xiaodong

2012-02-01

The remarkable electrical and optical properties of graphene make it a promising material for new optoelectronic applications. However, one important, but so far unexplored, property is the role of hot carriers in charge and energy transport at graphene interfaces. Here we investigate the photocurrent (PC) dynamics at a tunable graphene pn junction using ultrafast scanning PC microscopy. Pump-probe measurements show a temperature dependent relaxation time of photogenerated carriers that increases from 1.5ps at 290K to 4ps at 20K; while the amplitude of the PC is independent of the lattice temperature. These observations imply that it is hot carriers, not phonons, which dominate ultrafast energy transport. Gate dependent measurements show many interesting features such as pump induced saturation, enhancement, and sign reversal of probe generated PC. These observations reveal that the underlying PC mechanism is a combination of the thermoelectric and built-in electric field effects. Our results enhance the understanding of non-equilibrium electron dynamics, electron-electron interactions, and electron-phonon interactions in graphene. They also determine fundamental limits on ultrafast device operation speeds (˜500 GHz) for graphene-based photodetectors.

Dynamic formation of microenvironments at the myotendinous junction correlates with muscle fiber morphogenesis in zebrafish

PubMed Central

Snow, Chelsi J.; Henry, Clarissa A.

2009-01-01

Muscle development involves the specification and morphogenesis of muscle fibers that attach to tendons. After attachment, muscles and tendons then function as an integrated unit to transduce force to the skeletal system and stabilize joints. The attachment site is the myotendinous junction, or MTJ, and is the primary site of force transmission. We find that attachment of fast-twitch myofibers to the MTJ correlates with the formation of novel microenvironments within the MTJ. The expression or activation of two proteins involved in anchoring the intracellular cytoskeleton to the extracellular matrix, Focal adhesion kinase (Fak) and β-dystroglycan is up-regulated. Conversely, the extracellular matrix protein Fibronectin (Fn) is down-regulated. This degradation of Fn as fast-twitch fibers attach to the MTJ results in Fn protein defining a novel microenvironment within the MTJ adjacent to slow-twitch, but not fast-twitch, muscle. Interestingly, however, Fak, laminin, Fn and β-dystroglycan concentrate at the MTJ in mutants that do not have slow-twitch fibers. Taken together, these data elucidate novel and dynamic microenvironments within the MTJ and indicate that MTJ morphogenesis is spatially and temporally complex. PMID:18783736

Surgical management of Chiari I malformation based on different cerebrospinal fluid flow patterns at the cranial-vertebral junction.

PubMed

Fan, Tao; Zhao, HaiJun; Zhao, XinGang; Liang, Cong; Wang, YinQian; Gai, QiFei

2017-10-01

Chiari I malformation has been shown to present different cerebrospinal fluid (CSF) flow patterns at the cranial-vertebral junction (CVJ). Posterior fossa decompression is the first-line treatment for symptomatic Chiari I malformation. However, there is still controversy on the indication and selection of decompression procedures. This research aims to investigate the clinical indications, outcomes, and complications of the decompression procedures as alternative treatments for Chiari I malformation, based on the different CSF flow patterns at the cranial-vertebral junction. In this study, 126 Chiari I malformation patients treated with the two decompression procedures were analyzed. According to the preoperative findings obtained by using cine phase-contrast MRI (cine PC-MRI), the abnormal CSF flow dynamics at the CVJ in Chiari I malformation was classified into three patterns. After a preoperative evaluation and an intraoperative ultrasound after craniectomy, the two procedures were alternatively selected to treat the Chiari I malformation. The indication and selection of the two surgical procedures, as well as their outcomes and complications, are reported in detail in this work. Forty-eight patients underwent subdural decompression (SDD), and 78 received subarachnoid manipulation (SAM). Ninety patients were diagnosed as having Chiari I malformation with a syrinx. Two weeks after the operation, the modified Japanese Orthopedic Association (mJOA) scores increased from the preoperative value of 10.67 ± 1.61 to 12.74 ± 2.01 (P < 0.01). The mean duration of follow-up was 24.8 months; the mJOA scores increased from the postoperative value of 12.74 ± 2.01 to 12.79 ± 1.91 at the end of follow-up (P = 0.48). More complications occurred in the patients who underwent SAM than in those who received SDD (SAM 11 of 78 (9.5%) vs SDD 2 of 48 (3.5%)). The abnormal CSF flow dynamics at the CVJ in Chiari I malformation can be classified into three patterns. A SAM procedure is more feasible in Chiari I malformation (CM1) patients with pattern III CSF flow dynamics, whereas a SDD procedure is more suitable for CM1 patients with pattern I CSF flow dynamics. In CM1 patients with pattern II CSF flow dynamics, an intraoperative ultrasound after craniectomy could play an important role in the selection of an effective decompression procedure.

Broadband photodetector based on carbon nanotube thin film/single layer graphene Schottky junction

NASA Astrophysics Data System (ADS)

Zhang, Teng-Fei; Li, Zhi-Peng; Wang, Jiu-Zhen; Kong, Wei-Yu; Wu, Guo-An; Zheng, Yu-Zhen; Zhao, Yuan-Wei; Yao, En-Xu; Zhuang, Nai-Xi; Luo, Lin-Bao

2016-12-01

In this study, we present a broadband nano-photodetector based on single-layer graphene (SLG)-carbon nanotube thin film (CNTF) Schottky junction. It was found that the as-fabricated device exhibited obvious sensitivity to a wide range of illumination, with peak sensitivity at 600 and 920 nm. In addition, the SLG-CNTF device had a fast response speed (τr = 68 μs, τf = 78 μs) and good reproducibility in a wide range of switching frequencies (50-5400 Hz). The on-off ratio, responsivity, and detectivity of the device were estimated to be 1 × 102, 209 mAW-1 and 4.87 × 1010 cm Hz1/2 W-1, respectively. What is more, other device parameters including linear performance θ and linear dynamic range (LDR) were calculated to be 0.99 and 58.8 dB, respectively, which were relatively better than other carbon nanotube based devices. The totality of the above study signifies that the present SLG-CNTF Schottky junction broadband nano-photodetector may have promising application in future nano-optoelectronic devices and systems.

Investigation of dielectric pocket induced variations in tunnel field effect transistor

NASA Astrophysics Data System (ADS)

Upasana; Narang, Rakhi; Saxena, Manoj; Gupta, Mridula

2016-04-01

The performance of conventional Tunnel FETs struggling from ambipolar issues, insufficient on-current, lower transconductance value, higher delay and lower cut off frequency has been improved by introducing several material and device engineering concepts in past few years. Keeping this in view, another interesting and reliable option i.e. Dielectric Pocket TFET (featuring a dielectric pocket placement near tunneling junction) has been comprehensively and qualitatively demonstrated using ATLAS device simulator. The architecture has been explored in terms of various device electrostatic parameters such as potential, energy band profile, electron and hole concentration, electric field variation and band to band generation rate (GBTB) near the tunneling junction where the Dielectric Pocket (DP) has been introduced. Subsequently, a detailed investigation by changing the position and dielectric constant of pocket at respective junctions has been made where DP induced variations in drain current, transconductance and parasitic capacitance have been examined. The work highlights major improvements over conventional TFET in terms of lower subthreshold swing and threshold voltage, higher drain current and transconductance, improved on-to-off current ratio, suppressed ambipolar conduction and improved dynamic power dissipation issues for low voltage analog and digital applications.

Branched actin networks push against each other at adherens junctions to maintain cell-cell adhesion.

PubMed

Efimova, Nadia; Svitkina, Tatyana M

2018-05-07

Adherens junctions (AJs) are mechanosensitive cadherin-based intercellular adhesions that interact with the actin cytoskeleton and carry most of the mechanical load at cell-cell junctions. Both Arp2/3 complex-dependent actin polymerization generating pushing force and nonmuscle myosin II (NMII)-dependent contraction producing pulling force are necessary for AJ morphogenesis. Which actin system directly interacts with AJs is unknown. Using platinum replica electron microscopy of endothelial cells, we show that vascular endothelial (VE)-cadherin colocalizes with Arp2/3 complex-positive actin networks at different AJ types and is positioned at the interface between two oppositely oriented branched networks from adjacent cells. In contrast, actin-NMII bundles are located more distally from the VE-cadherin-rich zone. After Arp2/3 complex inhibition, linear AJs split, leaving gaps between cells with detergent-insoluble VE-cadherin transiently associated with the gap edges. After NMII inhibition, VE-cadherin is lost from gap edges. We propose that the actin cytoskeleton at AJs acts as a dynamic push-pull system, wherein pushing forces maintain extracellular VE-cadherin transinteraction and pulling forces stabilize intracellular adhesion complexes. © 2018 Efimova and Svitkina.

Frequency Combs in a Lumped-Element Josephson-Junction Circuit

NASA Astrophysics Data System (ADS)

Khan, Saeed; Türeci, Hakan E.

2018-04-01

We investigate the dynamics of a microwave-driven Josephson junction capacitively coupled to a lumped-element L C oscillator. In the regime of driving where the Josephson junction can be approximated as a Kerr oscillator, this minimal nonlinear system has been previously shown to exhibit a bistability in phase and amplitude. In the present study, we characterize the full phase diagram and show that besides a parameter regime exhibiting bistability, there is also a regime of self-oscillations characterized by a frequency comb in its spectrum. We discuss the mechanism of comb generation which appears to be different from those studied in microcavity frequency combs and mode-locked lasers. We then address the fate of the comblike spectrum in the regime of strong quantum fluctuations, reached when nonlinearity becomes the dominant scale with respect to dissipation. We find that the nonlinearity responsible for the emergence of the frequency combs also leads to its dephasing, leading to broadening and ultimate disappearance of sharp spectral peaks. Our study explores the fundamental question of the impact of quantum fluctuations for quantum systems which do not possess a stable fixed point in the classical limit.

Method of obtaining graphene and graphene-based electronic components and circuits with pencil directly on paper

NASA Astrophysics Data System (ADS)

Mailian, Aram; Mailian, Manvel; Shmavonyan, Gagik

2014-03-01

An easy method of obtaining graphene and graphene-based electronic components and circuits by drawing lines or repeatedly rubbing any type of graphite rod along the same path directly on paper and other insulating substrates is suggested. The structure containing rubbed-off layers behaves like a semiconducting material. The surface of the structure demonstrates ordered and oriented character containing few layer graphene. The carrier mobility is anisotropic through the thickness of the structure with the highest value of ~ 104 cm2/V .sec at the surface. Raman spectra of the structures in the near IR at excitation wavelength of 976 nm (1.27 eV) are registered. The observed phenomenon is universal, does not depend on the material of the substrate and could find a widespread application. For example, the junction between two rubbed off layers with different mobilities exhibits a non-Ohmic behavior. I-V characteristic of the junction is symmetrically curved with respect to 0 V. The greater is the difference between the carrier mobility, the higher is the curvature. The dynamic accumulation of the carriers in both sides of the junction creates a barrier responsible for non-Ohmic behavior.

Broadband photodetector based on carbon nanotube thin film/single layer graphene Schottky junction

PubMed Central

Zhang, Teng-Fei; Li, Zhi-Peng; Wang, Jiu-Zhen; Kong, Wei-Yu; Wu, Guo-An; Zheng, Yu-Zhen; Zhao, Yuan-Wei; Yao, En-Xu; Zhuang, Nai-Xi; Luo, Lin-Bao

2016-01-01

In this study, we present a broadband nano-photodetector based on single-layer graphene (SLG)-carbon nanotube thin film (CNTF) Schottky junction. It was found that the as-fabricated device exhibited obvious sensitivity to a wide range of illumination, with peak sensitivity at 600 and 920 nm. In addition, the SLG-CNTF device had a fast response speed (τr = 68 μs, τf = 78 μs) and good reproducibility in a wide range of switching frequencies (50–5400 Hz). The on-off ratio, responsivity, and detectivity of the device were estimated to be 1 × 102, 209 mAW−1 and 4.87 × 1010 cm Hz1/2 W−1, respectively. What is more, other device parameters including linear performance θ and linear dynamic range (LDR) were calculated to be 0.99 and 58.8 dB, respectively, which were relatively better than other carbon nanotube based devices. The totality of the above study signifies that the present SLG-CNTF Schottky junction broadband nano-photodetector may have promising application in future nano-optoelectronic devices and systems. PMID:27929053

Ligand accessibility and bioactivity of a hormone–dendrimer conjugate depend on pH and pH history

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

Kim, Sung Hoon; Madak-Erdogan, Zeynep; Bae, Sung Chul

Estrogen conjugates with a polyamidoamine (PAMAM) dendrimer have shown remarkably selective regulation of the nongenomic actions of estrogens in target cells in this paper. In response to pH changes, however, these estrogen–dendrimer conjugates (EDCs) display a major morphological transition that alters the accessibility of the estrogen ligands that compromises the bioactivity of the EDC. A sharp break in dynamic behavior near pH 7 occurs for three different ligands on the surface of a PAMAM-G6 dendrimer: a fluorophore (tetramethylrhodamine [TMR]) and two estrogens (17α-ethynylestradiol and diphenolic acid). Collisional quenching and time-resolved fluorescence anisotropy experiments with TMR–PAMAM revealed high ligand shielding abovemore » pH 7 and low shielding below pH 7. Furthermore, when the pH was cycled from 8.5 (conditions of ligand–PAMAM conjugation) to 4.5 (e.g., endosome/lysosome) and through 6.5 (e.g., hypoxic environment) back to pH 8.5, the 17α-ethynylestradiol– and diphenolic acid–PAMAM conjugates experienced a dramatic, irreversible loss in cell stimulatory activity; dynamic NMR studies indicated that the hormonal ligands had become occluded within the more hydrophobic core of the PAMAM dendrimer. Thus, the active state of these estrogen–dendrimer conjugates appears to be metastable. Finally, this pH-dependent irreversible masking of activity is of considerable relevance to the design of drug conjugates with amine-bearing PAMAM dendrimers.« less

Ligand accessibility and bioactivity of a hormone–dendrimer conjugate depend on pH and pH history

DOE PAGES

Kim, Sung Hoon; Madak-Erdogan, Zeynep; Bae, Sung Chul; ...

2015-07-17

Estrogen conjugates with a polyamidoamine (PAMAM) dendrimer have shown remarkably selective regulation of the nongenomic actions of estrogens in target cells in this paper. In response to pH changes, however, these estrogen–dendrimer conjugates (EDCs) display a major morphological transition that alters the accessibility of the estrogen ligands that compromises the bioactivity of the EDC. A sharp break in dynamic behavior near pH 7 occurs for three different ligands on the surface of a PAMAM-G6 dendrimer: a fluorophore (tetramethylrhodamine [TMR]) and two estrogens (17α-ethynylestradiol and diphenolic acid). Collisional quenching and time-resolved fluorescence anisotropy experiments with TMR–PAMAM revealed high ligand shielding abovemore » pH 7 and low shielding below pH 7. Furthermore, when the pH was cycled from 8.5 (conditions of ligand–PAMAM conjugation) to 4.5 (e.g., endosome/lysosome) and through 6.5 (e.g., hypoxic environment) back to pH 8.5, the 17α-ethynylestradiol– and diphenolic acid–PAMAM conjugates experienced a dramatic, irreversible loss in cell stimulatory activity; dynamic NMR studies indicated that the hormonal ligands had become occluded within the more hydrophobic core of the PAMAM dendrimer. Thus, the active state of these estrogen–dendrimer conjugates appears to be metastable. Finally, this pH-dependent irreversible masking of activity is of considerable relevance to the design of drug conjugates with amine-bearing PAMAM dendrimers.« less

Heat aggregation studies of phycobilisomes, ferritin, insulin, and immunoglobulin by dynamic light scattering.

PubMed

Singh, B P; Bohidar, H B; Chopra, S

1991-10-15

Dynamic laser light scattering studies on the heat aggregation behavior of phycobilisomes (PBS), ferritin, insulin, and immunoglobulin (IgG) in dilute aqueous solutions has been reported. Except for PBS, results are reported for heat aggregation trends in these proteins for three different pH environments (4.0, 7.5, 9.1). For PBS, studies were performed only in the neutral buffer medium (pH 7.5). The experiments were performed in the very dilute concentration regime (between 0.23 and 1.8 gL-1). For all these samples heat aggregation and dissociation trends were found to be linear with temperature. Upon temperature reversal (self-cooling), hysteresis-like behavior observed in insulin was found to be predominantly large at pH 7.5. PBS, ferritin, and IgG showed no such behavior at any of three pH values, and retraced their path of aggregation while dissociating on temperature reversal. Heat aggregation and dissociation processes in ferritin were found to be independent of pH. The IgG samples showed smooth aggregation tendency only up to 35 degrees C in the buffer media pH 4.0 and 9.1, whereas for pH 7.0 the same could be observed until 60 degrees C. Low polydispersity in the correlation spectra was observed in case of all these samples.

pH and heat-dependent behaviour of glucose oxidase down to single molecule level by combined fluorescence spectroscopy and molecular modelling.

PubMed

Dumitraşcu, Loredana; Stănciuc, Nicoleta; Bahrim, Gabriela Elena; Ciumac, Alexandrina; Aprodu, Iuliana

2016-04-01

In the food industry, glucose oxidase (GOX) is used to improve the shelf life of food materials. The pH- and heat-induced conformational changes of glucose oxidase from Aspergillus niger were quantified by means of fluorescence spectroscopy and molecular dynamics simulations. The phase diagram showed an all-or-none transition process, indicating that pH and temperature largely influence the conformational state of GOX. Shifts in maximum wavelength of Trp, Tyr were registered as the protein encounters a lower pH (pH 4.0), suggesting significant changes of the polarity around the chromophore molecule. Quenching experiments using KI showed higher quenching constants of Trp and flavin adenine dinucleotide upon heating or by changing pH value, and were mainly correlated with the conformational changes upon protein matrix. Finally, valuable insights into the thermal behaviour of GOX were obtained from molecular modelling results. The conformation and structure of GOX protein is dependent upon the pH and heat treatment applied. Molecular dynamics simulation indicated significant changes in the substrate binding region at temperatures over 60 °C that might affect enzyme activity. Moreover, an important alteration of the small pocket hosting the positively charged His(516) residue responsible for oxygen activation appears evident at high temperatures. © 2015 Society of Chemical Industry.

An investigation into the potential of phenothiazinium-based photo-sensitisers to act as PDT agents.

PubMed

Harris, F; Sayed, Z; Hussain, S; Phoenix, D A

2004-11-01

There is an urgent need for effective cancer treatments and increasingly, photo-dynamic therapy (PDT) is being used to fulfil this need as it offers a number of advantages over traditional cancer treatments. Here, the potential of a series of phenothiazinium-based photo-sensitisers (PhBPs) as PDT agents is tested. PhBPs were incubated with EMT-6 tumour cells and erythrocytes respectively under dark and light conditions (3.15Jcm(-2) over 30min). "Comet assay" and haemolytic assay were then used to assess cellular photo-damage induced by these PhBPs. Additionally, in vitro assays were used to determine light adsorption characteristics, singlet oxygen yields (ΦΔPhBP) and lipophilicity (logP) of these PhBPs. "Comet assay" showed EMT-6 incubation with PhBPs under light conditions to produce DNA "tails", which were circa 35μm long, indicating the presence of DNA photo-damage. Corresponding incubations under dark conditions led to no such damage. The majority of the PhBPs tested possessed significant singlet oxygen yields (ΦΔPhBP>0.7), suggesting the general use of type II mechanisms for photo-sensitization, and were generally lipophilic (logP>0). Incubation of erythrocytes with these PhBPs in the dark produced between 6% and 19% haemolysis. These levels were generally unaffected by illumination except in the case of DMMB, which showed haemolytic levels increasing from 11% to 61%. It is suggested that DNA may be the primary target for the photo-dynamic anti-tumour activity of the PhBPs tested with the exception of DMMB, which may potentially also target tumour cell membranes.

Contraction and elongation: Mechanics underlying cell boundary deformations in epithelial tissue.

PubMed

Hara, Yusuke

2017-06-01

The cell-cell boundaries of epithelial cells form cellular frameworks at the apical side of tissues. Deformations in these boundaries, for example, boundary contraction and elongation, and the associated forces form the mechanical basis of epithelial tissue morphogenesis. In this review, using data from recent Drosophila studies on cell boundary contraction and elongation, I provide an overview of the mechanism underlying the bi-directional deformations in the epithelial cell boundary, that are sustained by biased accumulations of junctional and apico-medial non-muscle myosin II. Moreover, how the junctional tensions exist on cell boundaries in different boundary dynamics and morphologies are discussed. Finally, some future perspectives on how recent knowledge about single cell boundary-level mechanics will contribute to our understanding of epithelial tissue morphogenesis are discussed. © 2017 Japanese Society of Developmental Biologists.

Analog Approach to Constraint Satisfaction Enabled by Spin Orbit Torque Magnetic Tunnel Junctions.

PubMed

Wijesinghe, Parami; Liyanagedera, Chamika; Roy, Kaushik

2018-05-02

Boolean satisfiability (k-SAT) is an NP-complete (k ≥ 3) problem that constitute one of the hardest classes of constraint satisfaction problems. In this work, we provide a proof of concept hardware based analog k-SAT solver, that is built using Magnetic Tunnel Junctions (MTJs). The inherent physics of MTJs, enhanced by device level modifications, is harnessed here to emulate the intricate dynamics of an analog satisfiability (SAT) solver. In the presence of thermal noise, the MTJ based system can successfully solve Boolean satisfiability problems. Most importantly, our results exhibit that, the proposed MTJ based hardware SAT solver is capable of finding a solution to a significant fraction (at least 85%) of hard 3-SAT problems, within a time that has a polynomial relationship with the number of variables(<50).

Brane junctions in the Randall-Sundrum scenario

NASA Astrophysics Data System (ADS)

Csáki, Csaba; Shirman, Yuri

2000-01-01

We present static solutions to Einstein's equations corresponding to branes at various angles intersecting in a single 3-brane. Such configurations may be useful for building models with localized gravity via the Randall-Sundrum mechanism. We find that such solutions may exist only if the mechanical forces acting on the junction exactly cancel. In addition to this constraint there are further conditions that the parameters of the theory have to satisfy. We find that at least one of these involves only the brane tensions and cosmological constants, and thus cannot have a dynamical origin. We present these conditions in detail for two simple examples. We discuss the nature of the cosmological constant problem in the framework of these scenarios, and outline the desired features of the brane configurations which may bring us closer towards a resolution of the cosmological constant problem.

Traveling wave parametric amplifier with Josephson junctions using minimal resonator phase matching

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

White, T. C.; Mutus, J. Y.; Hoi, I.-C.

Josephson parametric amplifiers have become a critical tool in superconducting device physics due to their high gain and quantum-limited noise. Traveling wave parametric amplifiers (TWPAs) promise similar noise performance, while allowing for significant increases in both bandwidth and dynamic range. We present a TWPA device based on an LC-ladder transmission line of Josephson junctions and parallel plate capacitors using low-loss amorphous silicon dielectric. Crucially, we have inserted λ/4 resonators at regular intervals along the transmission line in order to maintain the phase matching condition between pump, signal, and idler and increase gain. We achieve an average gain of 12 dB acrossmore » a 4 GHz span, along with an average saturation power of −92 dBm with noise approaching the quantum limit.« less

Measurements of quasiparticle tunneling dynamics in a band-gap-engineered transmon qubit.

PubMed

Sun, L; DiCarlo, L; Reed, M D; Catelani, G; Bishop, Lev S; Schuster, D I; Johnson, B R; Yang, Ge A; Frunzio, L; Glazman, L; Devoret, M H; Schoelkopf, R J

2012-06-08

We have engineered the band gap profile of transmon qubits by combining oxygen-doped Al for tunnel junction electrodes and clean Al as quasiparticle traps to investigate energy relaxation due to quasiparticle tunneling. The relaxation time T1 of the qubits is shown to be insensitive to this band gap engineering. Operating at relatively low-E(J)/E(C) makes the transmon transition frequency distinctly dependent on the charge parity, allowing us to detect the quasiparticles tunneling across the qubit junction. Quasiparticle kinetics have been studied by monitoring the frequency switching due to even-odd parity change in real time. It shows the switching time is faster than 10  μs, indicating quasiparticle-induced relaxation has to be reduced to achieve T1 much longer than 100  μs.

Flotillins control zebrafish epiboly through their role in cadherin-mediated cell-cell adhesion.

PubMed

Morris, Eduardo A Rios; Bodin, Stéphane; Delaval, Bénédicte; Comunale, Franck; Georget, Virginie; Costa, Manoel L; Lutfalla, Georges; Gauthier-Rouvière, Cécile

2017-05-01

Zebrafish gastrulation and particularly epiboly that involves coordinated movements of several cell layers is a dynamic process for which regulators remain to be identified. We show here that Flotillin 1 and 2, ubiquitous and highly conserved proteins, are required for epiboly. Flotillins knockdown compromised embryo survival, strongly delayed epiboly and impaired deep cell radial intercalation and directed collective migration without affecting enveloping layer cell movement. At the molecular level, we identified that Flotillins are required for the formation of E-cadherin-mediated cell-cell junctions. These results provide the first in vivo evidence that Flotillins regulate E-cadherin-mediated cell-cell junctions to allow epiboly progression. © 2017 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

Optimization of a pH-shift control strategy for producing monoclonal antibodies in Chinese hamster ovary cell cultures using a pH-dependent dynamic model.

PubMed

Hogiri, Tomoharu; Tamashima, Hiroshi; Nishizawa, Akitoshi; Okamoto, Masahiro

2018-02-01

To optimize monoclonal antibody (mAb) production in Chinese hamster ovary cell cultures, culture pH should be temporally controlled with high resolution. In this study, we propose a new pH-dependent dynamic model represented by simultaneous differential equations including a minimum of six system component, depending on pH value. All kinetic parameters in the dynamic model were estimated using an evolutionary numerical optimization (real-coded genetic algorithm) method based on experimental time-course data obtained at different pH values ranging from 6.6 to 7.2. We determined an optimal pH-shift schedule theoretically. We validated this optimal pH-shift schedule experimentally and mAb production increased by approximately 40% with this schedule. Throughout this study, it was suggested that the culture pH-shift optimization strategy using a pH-dependent dynamic model is suitable to optimize any pH-shift schedule for CHO cell lines used in mAb production projects. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Limitation of optical properties through porous silicon photonic crystals influenced by porosity and lattice dynamic

NASA Astrophysics Data System (ADS)

Amedome Min-Dianey, Kossi Aniya; Zhang, Hao-Chun; M'Bouana, Noé Landry Privace; Kougblenou, Komi; Xia, Xinlin

2018-01-01

Finite differential time domain (FDTD) tools were applied to simulate the optical properties characteristics' through square and triangular lattices of porous silicon (pSi) photonic crystals (PhCs); which consisted of periodical patterns of circular air holes built into the pSi material. This was used to investigate the influence of porosity and lattice dynamic on the reflection, transmission and absorption characteristics through unit cell pSi PhC in the visible wavelength domain (400 nm - 700 nm). The numerical simulation was achieved using FDTD Lumerical solutions with periodic boundary conditions (PBC) and perfectly matched layers (PML) as the appropriate boundary conditions. The results revealed that the limitation of optical properties is dependent on porosity and the lattice dynamic in pSi PhC. This was presented by the trend; the higher the reflection the higher the porosity and a decrease in porosity led to an increase in absorption in both lattice considerations. It was discovered that attaining optimum properties for triangular lattice will entail considering porosities less than 50% and hole radius r to the lattice constant a ratio (r / a) above 0.3 for the absorption characteristic and below 0.3 for the transmission characteristic. Triangular lattice can be adapted to improve the optical pattern through the PhC. In addition, the optimisation of these properties through pSi PhCs was achieved by controlling porosity and the ratio r / a .

PhOTO Zebrafish: A Transgenic Resource for In Vivo Lineage Tracing during Development and Regeneration

PubMed Central

Dempsey, William P.; Fraser, Scott E.; Pantazis, Periklis

2012-01-01

Background Elucidating the complex cell dynamics (divisions, movement, morphological changes, etc.) underlying embryonic development and adult tissue regeneration requires an efficient means to track cells with high fidelity in space and time. To satisfy this criterion, we developed a transgenic zebrafish line, called PhOTO, that allows photoconvertible optical tracking of nuclear and membrane dynamics in vivo. Methodology PhOTO zebrafish ubiquitously express targeted blue fluorescent protein (FP) Cerulean and photoconvertible FP Dendra2 fusions, allowing for instantaneous, precise targeting and tracking of any number of cells using Dendra2 photoconversion while simultaneously monitoring global cell behavior and morphology. Expression persists through adulthood, making the PhOTO zebrafish an excellent tool for studying tissue regeneration: after tail fin amputation and photoconversion of a ∼100µm stripe along the cut area, marked differences seen in how cells contribute to the new tissue give detailed insight into the dynamic process of regeneration. Photoconverted cells that contributed to the regenerate were separated into three distinct populations corresponding to the extent of cell division 7 days after amputation, and a subset of cells that divided the least were organized into an evenly spaced, linear orientation along the length of the newly regenerating fin. Conclusions/Significance PhOTO zebrafish have wide applicability for lineage tracing at the systems-level in the early embryo as well as in the adult, making them ideal candidate tools for future research in development, traumatic injury and regeneration, cancer progression, and stem cell behavior. PMID:22431986

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

PubMed

Goh, Garrett B; Hulbert, Benjamin S; Zhou, Huiqing; Brooks, Charles L

2014-07-01

pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible. © 2013 Wiley Periodicals, Inc.

Temperature-dependent dynamics of bovine casein micelles in the range 10-40 °C.

PubMed

Liu, Dylan Z; Weeks, Michael G; Dunstan, David E; Martin, Gregory J O

2013-12-15

Milk is a complex colloidal system that responds to changes in temperature imposed during processing. Whilst much has been learned about the effects of temperature on milk, little is known about the dynamic response of casein micelles to changes in temperature. In this study, a comprehensive physico-chemical study of casein micelles in skim milk was performed between 10 and 40 °C. When fully equilibrated, the amount of soluble casein, soluble calcium and the pH of skim milk all decreased as a function of increasing temperature, whilst the hydration and volume fraction of the casein micelles decreased. The effect of temperature on casein micelle size, as determined by dynamic light scattering and differential centrifugation, was less straightforward. Real-time measurements of turbidity and pH were used to investigate the dynamics of the system during warming and cooling of milk in the range 10-40 °C. Changes in pH are indicative of changes to the mineral system and the turbidity is a measure of alterations to the casein micelles. The pH and turbidity showed that alterations to both the casein micelles and the mineral system occurred very rapidly on warming. However, whilst mineral re-equilibration occurred very rapidly on cooling, changes to the casein micelle structure continued after 40 min of measurement, returning to equilibrium after 16 h equilibration. Casein micelle structure and the mineral system of milk were both dependent on temperature in the range 10-40 °C. The dynamic response of the mineral system to changes in temperature appeared almost instantaneous whereas equilibration of casein was considerably slower, particularly upon cooling. Copyright © 2013 Elsevier Ltd. All rights reserved.

All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.

PubMed

Huang, Yandong; Chen, Wei; Wallace, Jason A; Shen, Jana

2016-11-08

Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HEWL, and SNase. With the sampling time of 10 ns per replica, most pK a 's are converged, yielding the average absolute and root-mean-square deviations of 0.61 and 0.77, respectively, from experiment. Linear regression of the calculated vs experimental pK a shifts gives a correlation coefficient of 0.79, a slope of 1, and an intercept near 0. Analysis reveals inadequate sampling of structure relaxation accompanying a protonation-state switch as a major source of the remaining errors, which are reduced as simulation prolongs. These data suggest PME-based CpHMD can be used as a general tool for pH-controlled simulations of macromolecular systems in various environments, enabling atomic insights into pH-dependent phenomena involving not only soluble proteins but also transmembrane proteins, nucleic acids, surfactants, and polysaccharides.

Homogeneous electrochemical immunoassay of aflatoxin B1 in foodstuff using proximity-hybridization-induced omega-like DNA junctions and exonuclease III-triggered isothermal cycling signal amplification.

PubMed

Tang, Juan; Huang, Yapei; Liu, Huiqiong; Zhang, Cengceng; Tang, Dianping

2016-12-01

A new homogeneous electrochemical immunosensing platform was designed for sensitive detection of aflatoxin B 1 (AFB 1 ) in foodstuff. The system consisted of anti-AFB 1 antibody labeled DNA 1 (Ab-DNA 1 ), AFB 1 -bovine serum albumin (BSA)-conjugated DNA 2 (AFB 1 -DNA 2 ), and methylene blue functionalized hairpin DNA. Owing to a specific antigen-antibody reaction between anti-AFB 1 and AFB 1 -BSA, the immunocomplex formed assisted the proximity hybridization of DNA 1 with DNA 2 , thus resulting in the formation of an omega-like DNA junction. Thereafter, the junction opened the hairpin DNA to construct a new double-stranded DNA, which could be readily cleaved by exonuclease III to release the omega-like DNA junction and methylene blue. The dissociated DNA junction could repeatedly hybridize with residual hairpin DNA molecules with exonuclease III-based isothermal cycling amplification, thereby releasing numerous free methylene blue molecules into the detection solution. The as-produced free methylene blue molecules could be captured by a negatively charged indium tin oxide electrode, each of which could produce an electronic signal within the applied potentials. On introduction of target AFB 1 , the analyte competed with AFB 1 -DNA 2 for the conjugated anti-AFB 1 on the Ab-DNA 1 , subsequently decreasing the amount of omega-like DNA junctions formed, hence causing methylene blue labeled hairpin DNA to move far away from the electrode surface. Under optimal conditions the detectable electrochemical signal decreased with increasing amount of target AFB 1 in a dynamic working range of 0.01-30 ng mL -1 with a detection limit of 4.8 pg mL -1 . In addition, the precision and reproducibility of this system were acceptable. Finally, the method was further evaluated for analysis of naturally contaminated or AFB 1 -spiked peanut samples, giving results that matched well with those obtained with a commercial AFB 1 ELISA kit.

Computational fluid dynamics - The coming revolution

NASA Technical Reports Server (NTRS)

Graves, R. A., Jr.

1982-01-01

The development of aerodynamic theory is traced from the days of Aristotle to the present, with the next stage in computational fluid dynamics dependent on superspeed computers for flow calculations. Additional attention is given to the history of numerical methods inherent in writing computer codes applicable to viscous and inviscid analyses for complex configurations. The advent of the superconducting Josephson junction is noted to place configurational demands on computer design to avoid limitations imposed by the speed of light, and a Japanese projection of a computer capable of several hundred billion operations/sec is mentioned. The NASA Numerical Aerodynamic Simulator is described, showing capabilities of a billion operations/sec with a memory of 240 million words using existing technology. Near-term advances in fluid dynamics are discussed.

What Do I Want to Be with My PhD? The Roles of Personal Values and Structural Dynamics in Shaping the Career Interests of Recent Biomedical Science PhD Graduates

ERIC Educational Resources Information Center

Gibbs, Kenneth D., Jr.; Griffin, Kimberly A.

2013-01-01

Interest in faculty careers decreases as graduate training progresses; however, the process underlying career-interest formation remains poorly defined. To better understand this process and whether/how it differs across social identity (i.e., race/ethnicity, gender), we conducted focus groups with 38 biomedical scientists who received PhDs…

A Gold Nanoparticle Bio-Optical Transponder to Dynamically Monitor Intracellular pH.

PubMed

Carnevale, Kate J F; Riskowski, Ryan A; Strouse, Geoffrey F

2018-06-13

A pH-sensitive bio-optical transponder (pH-BOT) capable of simultaneously reporting the timing of intracellular DNA cargo release from a gold nanoparticle (AuNP) and the evolving intracellular pH (pH i) during endosomal maturation is demonstrated. The pH-BOT is designed with a triple-dye-labeled duplex DNA appended to a 6.6 nm AuNP, utilizing pH-responsive fluorescein paired with DyLight405 as a surface energy transfer (SET) coupled dye pair to ratiometrically report the pH at and after cargo release. A non-SET-coupled dye, DyLight 700, is used to provide dynamic tracking throughout the experiment. The pH-BOT beacon of the cargo uptake, release, and processing was visualized using live-cell confocal fluorescent microscopy in Chinese hamster ovary cells, and it was observed that while maturation of endosomes carrying pH-BOT is slowed significantly, the pH-BOT is distributed throughout the endolysosomal system while remaining at pH ∼6. This observed decoupling of endosomal maturation from acidification lends support to those models that propose that pH alone is not sufficient to explain endosomal maturation and may enable greater insight into our understanding of the fundamental processes of biology.