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Sample records for dynamic probe selection

  1. Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays

    Directory of Open Access Journals (Sweden)

    Chen Tsute

    2010-02-01

    Full Text Available Abstract Background Current commercial high-density oligonucleotide microarrays can hold millions of probe spots on a single microscopic glass slide and are ideal for studying the transcriptome of microbial genomes using a tiling probe design. This paper describes a comprehensive computational pipeline implemented specifically for designing tiling probe sets to study microbial transcriptome profiles. Results The pipeline identifies every possible probe sequence from both forward and reverse-complement strands of all DNA sequences in the target genome including circular or linear chromosomes and plasmids. Final probe sequence lengths are adjusted based on the maximal oligonucleotide synthesis cycles and best isothermality allowed. Optimal probes are then selected in two stages - sequential and gap-filling. In the sequential stage, probes are selected from sequence windows tiled alongside the genome. In the gap-filling stage, additional probes are selected from the largest gaps between adjacent probes that have already been selected, until a predefined number of probes is reached. Selection of the highest quality probe within each window and gap is based on five criteria: sequence uniqueness, probe self-annealing, melting temperature, oligonucleotide length, and probe position. Conclusions The probe selection pipeline evaluates global and local probe sequence properties and selects a set of probes dynamically and evenly distributed along the target genome. Unique to other similar methods, an exact number of non-redundant probes can be designed to utilize all the available probe spots on any chosen microarray platform. The pipeline can be applied to microbial genomes when designing high-density tiling arrays for comparative genomics, ChIP chip, gene expression and comprehensive transcriptome studies.

  2. Structural Dynamics of GaN Microcrystals in Evolutionary Selection Selective Area Growth probed by X-ray Microdiffraction

    Science.gov (United States)

    Kachkanov, V.; Leung, B.; Song, J.; Zhang, Y.; Tsai, M.-C.; Yuan, G.; Han, J.; O'Donnell, K. P.

    2014-01-01

    A method to grow high quality, single crystalline semiconductor material irrespective of the substrate would allow a cost-effective improvement to functionality and performance of optoelectronic devices. Recently, a novel type of substrate-insensitive growth process called Evolutionary Selection Selective Area Growth (ES-SAG) has been proposed. Here we report the use of X-ray microdiffraction to study the structural properties of GaN microcrystals grown by ES-SAG. Utilizing high resolution in both direct and reciprocal spaces, we have unraveled structural dynamics of GaN microcrystals in growth structures of different dimensions. It has been found that the geometric proportions of the growth constrictions play an important role: 2.6 μm and 4.5 μm wide growth tunnels favor the evolutionary selection mechanism, contrary to the case of 8.6 μm growth tunnels. It was also found that GaN microcrystal ensembles are dominated by slight tensile strain irrespective of growth tunnel shape. PMID:24722064

  3. (113)Cd Nuclear Magnetic Resonance as a Probe of Structural Dynamics in a Flexible Porous Framework Showing Selective O2/N2 and CO2/N2 Adsorption.

    Science.gov (United States)

    Haldar, Ritesh; Inukai, Munehiro; Horike, Satoshi; Uemura, Kazuhiro; Kitagawa, Susumu; Maji, Tapas Kumar

    2016-05-02

    Two new isomorphous three-dimensional porous coordination polymers, {[Cd(bpe)0.5(bdc)(H2O)]·EtOH}n (1) and {[Cd(bpe)0.5(bdc)(H2O)]·2H2O}n (2) [bpe = 1,2-bis(4-pyridyl)ethane, and H2bdc = 1,4-benzenedicarboxylic acid], have been synthesized by altering the solvent media. Both structures contain one-dimensional channels filled with metal-bound water and guest solvent molecules, and desolvated frameworks show significant changes in structure. However, exposure to the solvent vapors (water and methanol) reverts the structure back to the as-synthesized structure, and thus, the reversible flexible nature of the structure was elucidated. The flexibility and permanent porosity were further reinforced from the CO2 adsorption profiles (195 and 273 K) that show stepwise uptake. Moreover, a high selectivity for O2 over N2 at 77 K was realized. The framework exhibits interesting solvent vapor adsorption behavior with dynamic structural transformation depending upon the size, polarity, and coordination ability of the solvent molecules. Further investigation was conducted by solid state (113)Cd nuclear magnetic resonance (NMR) spectroscopy that unambiguously advocates the reversible transformation "pentagonal-bipyramidal CdO6N → octahedral CdO5N" geometry in the desolvated state. For the first time, (113)Cd NMR has been used as a probe of structural flexibility in a porous coordination polymer system.

  4. Probing Chemical Dynamics at Surfaces

    Institute of Scientific and Technical Information of China (English)

    KLEYN, A.W.; KLEYN, A.W

    2001-01-01

    An account is given of recent progress concerning chemical reaction dynamics at surfaces. The goal is to elucidate the reaction dynamics at the molecular level, both as time and distance is concerned. The methods of study include molecular beam scattering, scanning tunnelling microscopy, and (femtosecond) laser spectroscopy. Systems studied include elementary interactions of NO, CO, and O2 at single crystal metal surfaces.

  5. Probing Cellular Dynamics with Mesoscopic Simulations

    DEFF Research Database (Denmark)

    Shillcock, Julian C.

    2010-01-01

    Cellular processes span a huge range of length and time scales from the molecular to the near-macroscopic. Understanding how effects on one scale influence, and are themselves influenced by, those on lower and higher scales is a critical issue for the construction of models in Systems Biology....... Advances in computing hardware and software now allow explicit simulation of some aspects of cellular dynamics close to the molecular scale. Vesicle fusion is one example of such a process. Experiments, however, typically probe cellular behavior from the molecular scale up to microns. Standard particle...... soon be coupled to Mass Action models allowing the parameters in such models to be continuously tuned according to the finer resolution simulation. This will help realize the goal of a computational cellular simulation that is able to capture the dynamics of membrane-associated processes...

  6. Empirical evaluation of oligonucleotide probe selection for DNA microarrays.

    Directory of Open Access Journals (Sweden)

    Jennifer G Mulle

    Full Text Available DNA-based microarrays are increasingly central to biomedical research. Selecting oligonucleotide sequences that will behave consistently across experiments is essential to the design, production and performance of DNA microarrays. Here our aim was to improve on probe design parameters by empirically and systematically evaluating probe performance in a multivariate context. We used experimental data from 19 array CGH hybridizations to assess the probe performance of 385,474 probes tiled in the Duchenne muscular dystrophy (DMD region of the X chromosome. Our results demonstrate that probe melting temperature, single nucleotide polymorphisms (SNPs, and homocytosine motifs all have a strong effect on probe behavior. These findings, when incorporated into future microarray probe selection algorithms, may improve microarray performance for a wide variety of applications.

  7. Empirical evaluation of oligonucleotide probe selection for DNA microarrays.

    Science.gov (United States)

    Mulle, Jennifer G; Patel, Viren C; Warren, Stephen T; Hegde, Madhuri R; Cutler, David J; Zwick, Michael E

    2010-03-29

    DNA-based microarrays are increasingly central to biomedical research. Selecting oligonucleotide sequences that will behave consistently across experiments is essential to the design, production and performance of DNA microarrays. Here our aim was to improve on probe design parameters by empirically and systematically evaluating probe performance in a multivariate context. We used experimental data from 19 array CGH hybridizations to assess the probe performance of 385,474 probes tiled in the Duchenne muscular dystrophy (DMD) region of the X chromosome. Our results demonstrate that probe melting temperature, single nucleotide polymorphisms (SNPs), and homocytosine motifs all have a strong effect on probe behavior. These findings, when incorporated into future microarray probe selection algorithms, may improve microarray performance for a wide variety of applications.

  8. NMR probe for dynamic-angle spinning

    Science.gov (United States)

    Mueller, K. T.; Chingas, G. C.; Pines, A.

    1991-06-01

    We describe the design of a probe for dynamic-angle spinning (DAS) NMR experiments, comprised of a spinning cylindrical sample holder whose axis may be reoriented rapidly between discrete directions within the bore of a superconducting magnet. This allows the refocusing of nuclear spin magnetization that evolves under anisotropic interactions such as chemical shift anisotropy and quadrupolar coupling, providing high resolution NMR spectra for quadrupolar nuclei in solid materials. The probe includes an axial air delivery system to bearing and drive jets which support and spin a rotor containing the sample. Axis reorientation is accomplished with a pulley attached to the probehead and coupled to a stepping motor outside of the magnet. The choice of motor and gear ratio is based on an analysis of the moments of inertia of the motor and load, the desired angular resolution, and simplicity of design. Control of angular accuracy and precision are discussed, as well as the efficiency of radiofrequency irradiation and detection. High resolution DAS spectra of oxygen-17 and aluminum-27 nuclei in polycrystalline minerals illustrate the experimental capabilities.

  9. Probing dynamical spacetimes with gravitational waves

    CERN Document Server

    Broeck, Chris Van Den

    2013-01-01

    This decade will see the first direct detections of gravitational waves by observatories such as Advanced LIGO and Virgo. Among the prime sources are coalescences of binary neutron stars and black holes, which are ideal probes of dynamical spacetime. This will herald a new era in the empirical study of gravitation. For the first time, we will have access to the genuinely strong-field dynamics, where low-energy imprints of quantum gravity may well show up. In addition, we will be able to search for effects which might only make their presence known at large distance scales, such as the ones that gravitational waves must traverse in going from source to observer. Finally, coalescing binaries can be used as cosmic distance markers, to study the large-scale structure and evolution of the Universe. With the advanced detector era fast approaching, concrete data analysis algorithms are being developed to look for deviations from general relativity in signals from coalescing binaries, taking into account the noisy de...

  10. Dynamic Probing for Intrusion Detection under Resource Constraints

    Science.gov (United States)

    2013-06-01

    performance measure of regret, defined as the performance loss compared to that of a genie who knows the entire attack processes a priori and probes...performance as that of the omniscient genie . Index Terms—Intrusion detection, dynamic probing, non- stochastic multi-armed bandit, regret. I...dynamic probing strategy under the performance measure of regret, de ned as the performance loss compared to that of a genie who knows the entire attack

  11. Probe Selection for DNA Microarrays using OligoWiz

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Juncker, Agnieszka; Nielsen, Henrik Bjørn

    2007-01-01

    Nucleotide abundance measurements using DNA microarray technology are possible only if appropriate probes complementary to the target nucleotides can be identified. Here we present a protocol for selecting DNA probes for microarrays using the OligoWiz application. OligoWiz is a client......-server application that offers a detailed graphical interface and real-time user interaction on the client side, and massive computer power and a large collection of species databases (400, summer 2007) on the server side. Probes are selected according to five weighted scores: cross-hybridization, deltaT(m), folding...... computer skills and can be executed from any Internet-connected computer. The probe selection procedure for a standard microarray design targeting all yeast transcripts can be completed in 1 h....

  12. Efficient oligonucleotide probe selection for pan-genomic tiling arrays

    Directory of Open Access Journals (Sweden)

    Zhang Wei

    2009-09-01

    Full Text Available Abstract Background Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates. This method, as with all microarray applications, requires adequate coverage of probes targeting the regions of interest. An unbiased tiling of probes across the entire length of the genome is the most flexible design approach. However, such a whole-genome tiling requires that the genome sequence is known in advance. For the accurate analysis of uncharacterized bacteria, an array must query a fully representative set of sequences from the species' pan-genome. Prior microarrays have included only a single strain per array or the conserved sequences of gene families. These arrays omit potentially important genes and sequence variants from the pan-genome. Results This paper presents a new probe selection algorithm (PanArray that can tile multiple whole genomes using a minimal number of probes. Unlike arrays built on clustered gene families, PanArray uses an unbiased, probe-centric approach that does not rely on annotations, gene clustering, or multi-alignments. Instead, probes are evenly tiled across all sequences of the pan-genome at a consistent level of coverage. To minimize the required number of probes, probes conserved across multiple strains in the pan-genome are selected first, and additional probes are used only where necessary to span polymorphic regions of the genome. The viability of the algorithm is demonstrated by array designs for seven different bacterial pan-genomes and, in particular, the design of a 385,000 probe array that fully tiles the genomes of 20 different Listeria monocytogenes strains with overlapping probes at greater than twofold coverage. Conclusion PanArray is an oligonucleotide probe selection algorithm for tiling multiple genome sequences using a minimal number of probes. It is capable of fully tiling all genomes of a species on

  13. Spectroscopic probing of location and dynamics of an environment-sensitive intramolecular charge transfer probe within liposome membranes.

    Science.gov (United States)

    Paul, Bijan Kumar; Guchhait, Nikhil

    2011-11-15

    The present work demonstrates the interaction of an intramolecular charge transfer (ICT) probe 5-(4-dimethylamino-phenyl)-penta-2,4-dienoic acid methyl ester (DPDAME) with liposome membranes of dimyristoyl-L-α-phosphatidylcholine (DMPC) and dimyristoyl-L-α-phosphatidylglycerol (DMPG) studied by steady-state absorption, emission and time-resolved emission techniques. A huge hypsochromic shift together with remarkable enhancement of fluorescence quantum yield of the polarity sensitive ICT emission of DPDAME upon interaction with the lipids has been rationalized in terms of incorporation of the probe into hydrophobic interior of the lipids. Compelling evidences for penetration of the probe into the hydrocarbon interior of the lipids have been deduced from intertwining different experimental results e.g., micropolarity in the immediate vicinity of the probe in lipid environments, steady-state anisotropy, red-edge excitation shift (REES), fluorescence quenching experiments and time-resolved measurements. The rotational relaxation dynamics study of the membrane-bound probe unveils the impartation of high degree of motional rigidity. Wavelength-selective emission behaviour paves way for monitoring of solvent-relaxation in the membranes. Overall, the ICT probe DPDAME displays its commendable sensitivity in deciphering the microheterogeneous environments of liposomal membranes of DMPC and DMPG and promises a new membrane-polarity sensitizing probe.

  14. Journal Club: screen, select, probe & evaluate

    Directory of Open Access Journals (Sweden)

    Kanthraj G

    2005-01-01

    Full Text Available Postgraduate dermatology training programs like seminars, panel discussions, and case presentations help residents to acquire knowledge. Journal club (JC exercises help residents to update themselves with the current literature. What article a resident should choose and how a resident should evaluate and analyze an article or critically appraise a topic are issues that are most relevant for the success of a JC. Little guidance is available in the biomedical literature on how to deal with such issues. The objective of this article is to provide guidance to neophytes on dealing with JC exercises in a way that helps them in learning the critical appraisal skills. A review of the literature and of the author′s experience in JC exercises will be presented. Knowing the methodology of rapid screening of articles along with the art of evaluating them, coupled with a sound knowledge of epidemiology and bio-statistics, helps a resident to select appropriate articles and discard poorly conceived or designed topics that may not generate interest in JC attendees. Hence, such an approach helps the resident in acquiring new knowledge in the shortest time. Choosing the right topic and then applying the newly obtained information to clinical practice, participants succeed in making the JC a valuable learning experience. Further, such well-formatted JCs help residents to improve the quality of health care delivered to patients.

  15. [Development of Zn(2+) selective fluorescent probes for biological applications].

    Science.gov (United States)

    Hagimori, Masayori

    2013-01-01

    Zn(2+) is an essential element for life and is known to play important roles in biological processes including gene expression, apoptosis, enzyme regulation, immune system and neurotransmission. To investigate physiological roles of free or chelatable Zn(2+) in living cells, Zn(2+)-selective fluorescent probes are valuable tools. A variety of fluorescent probes based on quinoline, BF2 chelated dipyrromethene, fluorescein, etc. has been developed recently. In principle, such tools can provide useful information about zinc biology. However, most of the fluorescent probes presented so far possess a fluorescent core and a separate part for binding to Zn(2+) within the molecule, so that the molecular weight is usually large and the molecules are hydrophobic. As a result, the applications of such molecules in biological systems often face difficulties. Therefore, we need to develop a new class of fluorescent probes for Zn(2+) with improved molecular characteristics. If the initial core structure is small enough, the fluorescent probes may still be molecular weight below 500 with desirable physico-chemical properties, even after the modifications. In this review, we described novel low-molecular-weight fluorescent probes for Zn(2+) based on pyridine-pyridone. Small modification of pyridine-pyridone core structure brought about a marked improvement such as aqueous solubility, affinity toward Zn(2+), and fluorescence ON/OFF switching. Fluorescence images of Zn(2+) in cells showed that the pyridine-pyridone probe can be used in biological applications.

  16. Maximizing Information on the Environment by Dynamically Controlled Qubit Probes

    Science.gov (United States)

    Zwick, Analia; Álvarez, Gonzalo A.; Kurizki, Gershon

    2016-01-01

    We explore the ability of a qubit probe to characterize unknown parameters of its environment. By resorting to the quantum estimation theory, we analytically find the ultimate bound on the precision of estimating key parameters of a broad class of ubiquitous environmental noises ("baths") which the qubit may probe. These include the probe-bath coupling strength, the correlation time of generic types of bath spectra, and the power laws governing these spectra, as well as their dephasing times T2. Our central result is that by optimizing the dynamical control on the probe under realistic constraints one may attain the maximal accuracy bound on the estimation of these parameters by the least number of measurements possible. Applications of this protocol that combines dynamical control and estimation theory tools to quantum sensing are illustrated for a nitrogen-vacancy center in diamond used as a probe.

  17. Maximizing information on the environment by dynamically controlled qubit probes

    CERN Document Server

    Zwick, Analia; Kurizki, Gershon

    2015-01-01

    We explore the ability of a qubit probe to characterize unknown parameters of its environment. By resorting to quantum estimation theory, we analytically find the ultimate bound on the precision of estimating key parameters of a broad class of ubiquitous environmental noises ("baths") which the qubit may probe. These include the probe-bath coupling strength, the correlation time of generic bath spectra, the power laws governing these spectra, as well as their dephasing times T2. Our central result is that by optimizing the dynamical control on the probe under realistic constraints one may attain the maximal accuracy bound on the estimation of these parameters by the least number of measurements possible. Applications of this protocol that combines dynamical control and estimation theory tools to quantum sensing are illustrated for a nitrogen-vacancy center in diamond used as a probe.

  18. Dynamic Insurance and Adverse Selection

    NARCIS (Netherlands)

    M.C.W. Janssen (Maarten); V.A. Karamychev (Vladimir)

    2001-01-01

    textabstractWe take a dynamic perspective on insurance markets under adverse selection and study a generalized Rothschild and Stiglitz model where agents may differ with respect to the accidental probability and their expenditure levels in case an accident occurs. We investigate the nature of dynami

  19. Site-directed spectroscopic probes of actomyosin structural dynamics.

    Science.gov (United States)

    Thomas, David D; Kast, David; Korman, Vicci L

    2009-01-01

    Spectroscopy of myosin and actin has entered a golden age. High-resolution crystal structures of isolated actin and myosin have been used to construct detailed models for the dynamic actomyosin interactions that move muscle. Improved protein mutagenesis and expression technologies have facilitated site-directed labeling with fluorescent and spin probes. Spectroscopic instrumentation has achieved impressive advances in sensitivity and resolution. Here we highlight the contributions of site-directed spectroscopic probes to understanding the structural dynamics of myosin II and its actin complexes in solution and muscle fibers. We emphasize studies that probe directly the movements of structural elements within the myosin catalytic and light-chain domains, and changes in the dynamics of both actin and myosin due to their alternating strong and weak interactions in the ATPase cycle. A moving picture emerges in which single biochemical states produce multiple structural states, and transitions between states of order and dynamic disorder power the actomyosin engine.

  20. About supramolecular systems for dynamically probing cells

    NARCIS (Netherlands)

    Brinkmann, J.; Cavatorta, E.; Sankaran, S.; Schmidt, B.; van Weerd, Jasper; Jonkheijm, Pascal

    2014-01-01

    This article reviews the state of the art in the development of strategies for generating supramolecular systems for dynamic cell studies. Dynamic systems are crucial to further our understanding of cell biology and are consequently at the heart of many medical applications. Increasing interest has

  1. FIR line profiles as probes of warm gas dynamics

    Science.gov (United States)

    Betz, A. L.; Boreiko, R. T.

    1995-01-01

    Measurements of the shapes, velocities, and intensities of FIR lines all help to probe the dynamics, physical associations, and excitation conditions of warm gas in molecular clouds. With this in mind, we have observed the J=9-8, 12-11,14-13, and 16-15 lines of (12)CO and the 158 micron line of C II in a number of positions in 4 selected clouds. The data were obtained with a laser heterodyne spectrometer aboard NASA's Kuiper Airborne Observatory. Line measurements at 0.6 km/s resolution allow us to resolve the profiles completely, and thereby to distinguish between UV-and shock-heating mechanisms for the high-excitation gas. For CO, the high-J linewidths lie in the range of 4-20 km/s (FWHM), similar to those observed for low-J (J less than 4) transitions in these sources. This correspondence suggests that the hotter gas (T = 200-600 K) is dynamically linked to the quiescent gas component, perhaps by association with the UV-heated peripheries of the numerous cloud clumps. Much of the C II emission is thought to emanate from these cloud peripheries, but the line profiles generally do not match those seen in CO. None of the observed sources show any evidence in high-J (12)CO emission for shock-excitation (i.e., linewidths greater than 30 km/s).

  2. Huygens probe entry dynamic model and accelerometer data analysis

    Science.gov (United States)

    Colombatti, Giacomo; Aboudan, Alessio; Ferri, Francesca; Angrilli, Francesco

    2008-04-01

    During the first phase of Huygens arrival into Titan's atmosphere the probe is subjected to gravitational and aerodynamic forces in aerodynamic hypersonic regime. Atmospheric drag exerts a strong deceleration on the capsule measured by Huygens atmospheric structure instrument (HASI) servo accelerometer. A 6 DOF (Degree of Freedom) model of the Huygens probe entry dynamics has been developed and used for data analysis. The accelerometer data are analysed and the model allows the retrieval of dynamics information of Huygens probe from 1545 km altitude down to end of the entry phase. Probe's initial conditions (velocity and position) were refined to match the measured deceleration profile resulting in a different altitude at interface epoch with respect to those of the Cassini Navigation Team. Velocity and position of probe at interface epoch are compatible with those used by Descent Trajectory Working Group (DTWG). Measurements acquired before atmosphere detection are used to estimate probe's angular rate, bound attitude and characterise the angle of attack profile which results to be lower than 4∘ during the whole entry. Probe's spin calculated (6.98 RPM) is slightly different with respect to DTWG of 7.28 RPM but considering a 2% error in the Inertia matrix these results are inside the 1-σ error band.

  3. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT

    Science.gov (United States)

    Kirmizialtin, Serdal; Hennelly, Scott P.; Schug, Alexander; Onuchic, Jose N.; Sanbonmatsu, Karissa Y.

    2016-01-01

    Integration and calibration of molecular dynamics simulations with experimental data remains a challenging endeavor. We have developed a novel method to integrate chemical probing experiments with molecular simulations of RNA molecules by using a native structure-based model. Selective 2’-hydroxyl acylation by primer extension (SHAPE) characterizes the mobility of each residue in the RNA. Our method, SHAPE-FIT, automatically optimizes the potential parameters of the forcefield according to measured reactivities from SHAPE. The optimized parameter set allows simulations of dynamics highly consistent with SHAPE probing experiments. Such atomistic simulations, thoroughly grounded in experiment, can open a new window on RNA structure-function relations. PMID:25726467

  4. Probing neutron-proton dynamics by pions

    CERN Document Server

    Ikeno, Natsumi; Nara, Yasushi; Ohnishi, Akira

    2016-01-01

    In order to investigate the nuclear symmetry energy at high density, we study the pion production in central collisions of neutron-rich nuclei ${}^{132}\\mathrm{Sn}+{}^{124}\\mathrm{Sn}$ at 300 MeV/nucleon using a new approach by combining the antisymmetrized molecular dynamics (AMD) and a hadronic cascade model (JAM). The dynamics of neutrons and protons is solved by AMD, and then pions and $\\Delta$ resonances in the reaction process are handled by JAM. We see the mechanism how the $\\Delta$ resonance and pions are produced reflecting the dynamics of neutrons and protons. We also investigate the impacts of cluster correlations as well as of the high-density symmetry energy on the nucleon dynamics and consequently on the pion ratio. We find that the $\\Delta^-/\\Delta^{++}$ production ratio agrees very well with the neutron-proton squared ratio $(N/Z)^2$ in the high-density and high-momentum region. We show quantitatively that $\\Delta$ production ratio, and therefore $(N/Z)^2$, are directly reflected in the $\\pi^-...

  5. Probing Stellar Dynamics With Space Photometry

    Science.gov (United States)

    García, Rafael A.; Salabert, D.; Ballot, J.; Beck, P. G.; Bigot, L.; Corsaro, E.; Creevey, O.; Egeland, R.; Jiménez, A.; Mathur, S.; Metcalfe, T.; do Nascimento, J.; Pallé, P. L.; Pérez Hernández, F.; Regulo, C.

    2016-08-01

    The surface magnetic field has substantial influence on various stellar properties that can be probed through various techniques. With the advent of new space-borne facilities such as CoRoT and Kepler, uninterrupted long high-precision photometry is available for hundred of thousand of stars. This number will substantially grow through the forthcoming TESS and PLATO missions. The unique Kepler observations -covering up to 4 years with a 30-min cadence- allows studying stellar variability with different origins such as pulsations, convection, surface rotation, or magnetism at several time scales from hours to years. We study the photospheric magnetic activity of solar-like stars by means of the variability induced in the observed signal by starspots crossing the visible disk. We constructed a solar photometric magnetic activity proxy, Sph from SPM/VIRGO/SoHO, as if the Sun was a distant star and we compare it with several solar well-known magnetic proxies. The results validate this approach. Thus, we compute the Sph proxy for a set of CoRoT and Kepler solar-like stars for which pulsations were already detected. After characterizing the rotation and the magnetic properties of 300 solar-like stars, we use their seismic properties to characterize 18 solar analogs for which we study their magnetism. This allows us to put the Sun into context of its siblings.

  6. A highly selective phosphorescence probe for histidine in living bodies.

    Science.gov (United States)

    Gao, Quankun; Song, Bo; Ye, Zhiqiang; Yang, Liu; Liu, Ruoyang; Yuan, Jingli

    2015-11-14

    In this work, we designed and synthesized a heterobimetallic ruthenium(ii)-nickel(ii) complex, [Ru(bpy)2(phen-DPA)Ni](PF6)4 (Ru-Ni), as a highly selective phosphorescence probe for histidine. The probe exhibited weak emission at 603 nm because the phosphorescence of the Ru(ii) complex can be strongly quenched by the paramagnetic Ni(2+) ion. In the presence of histidine, reaction of Ru-Ni with histidine resulted in the release of nickel(ii) and an enhancement in the phosphorescence intensity at 603 nm. Ru-Ni showed high selectivity for histidine even in the presence of other amino acids and cellular abundant species. Cell imaging experimental results demonstrated that Ru-Ni is membrane permeable, and can be applied for visualizing histidine in live cells. More interestingly, Ru-Ni also can act as a novel reaction-based nuclear staining agent for visualizing exclusively the nuclei of living cells with a significant phosphorescence enhancement. In addition, the potential of the probe for biological applications was confirmed by employing it for phosphorescence imaging of histidine in larval zebrafish and Daphnia magna. These results demonstrated that Ru-Ni would be a useful tool for physiological and pathological studies involving histidine.

  7. Superconducting detector dynamics studied by quantum pump-probe spectroscopy

    NARCIS (Netherlands)

    Heeres, R.W.; Zwiller, V.

    2012-01-01

    We explore the dynamics of superconducting single-photon detectors (SSPDs) on the picosecond time-scale using a correlated photon-pair source based on spontaneous parametric downconversion (SPDC), corresponding to a pump-probe experiment at the single-photon level. We show that the detector can oper

  8. Probing Stellar Dynamics in Galactic Nuclei

    CERN Document Server

    Miller, M Coleman; Amaro-Seoane, Pau; Barth, Aaron J; Cutler, Curt; Gair, Jonathan R; Hopman, Clovis; Merritt, David; Phinney, E Sterl; Richstone, Douglas O

    2009-01-01

    Electromagnetic observations over the last 15 years have yielded a growing appreciation for the importance of supermassive black holes (SMBH) to the evolution of galaxies, and for the intricacies of dynamical interactions in our own Galactic center. Here we show that future low-frequency gravitational wave observations, alone or in combination with electromagnetic data, will open up unique windows to these processes. In particular, gravitational wave detections in the 10^{-5}-10^{-1} Hz range will yield SMBH masses and spins to unprecedented precision and will provide clues to the properties of the otherwise undetectable stellar remnants expected to populate the centers of galaxies. Such observations are therefore keys to understanding the interplay between SMBHs and their environments.

  9. Ultrasonic Periodontal Probing Based on the Dynamic Wavelet Fingerprint

    Directory of Open Access Journals (Sweden)

    Rose S Timothy

    2005-01-01

    Full Text Available Manual pocket depth probing has been widely used as a retrospective diagnosis method in periodontics. However, numerous studies have questioned its ability to accurately measure the anatomic pocket depth. In this paper, an ultrasonic periodontal probing method is described, which involves using a hollow water-filled probe to focus a narrow beam of ultrasound energy into and out of the periodontal pocket, followed by automatic processing of pulse-echo signals to obtain the periodontal pocket depth. The signal processing algorithm consists of three steps: peak detection/characterization, peak classification, and peak identification. A dynamic wavelet fingerprint (DWFP technique is first applied to detect suspected scatterers in the A-scan signal and generate a two-dimensional black and white pattern to characterize the local transient signal corresponding to each scatterer. These DWFP patterns are then classified by a two-dimensional FFT procedure and mapped to an inclination index curve. The location of the pocket bottom was identified as the third broad peak in the inclination index curve. The algorithm is tested on full-mouth probing data from two sequential visits of 14 patients. Its performance is evaluated by comparing ultrasonic probing results with that of full-mouth manual probing at the same sites, which is taken as the "gold standard."

  10. Ultrasonic slow dynamics to probe concrete aging and damage

    Science.gov (United States)

    Larose, E.; Tremblay, N.; Payan, C.; Garnier, V.; Rossetto, V.

    2013-01-01

    The stiffness of concrete experiences a drop immediately after a moderate mechanical solicitation. Then the stiffness rises back logarithmically toward its initial value. This Slow Dynamics behavior has been probed by macroscopic quantities averaged over the sample volume, including resonant frequency. This article presents a different approach based on diffuse acoustic wave spectroscopy, a technique that is directly sensitive to the details of the sample structure. The parameters of the dynamics are found to depend on mechanical and thermal damage of the medium. Results confirm that slow dynamics can be used onsite to assess the level of damage of a given structure.

  11. Effect of solvent model when probing protein dynamics with molecular dynamics.

    Science.gov (United States)

    Genheden, Samuel

    2017-01-01

    We probe the dynamics of the Bpti and Galectin-3 proteins using molecular dynamics simulations employing three water models at different levels of resolution, viz. the atomistic TIP4P-Ewald, the coarse-grained Elba and an implicit generalised Born model. The dynamics are quantified indirectly by model-free order parameters, S(2) of the backbone NH and selected side-chain bond vectors, which also have been determined experimentally through NMR relaxation measurements. For the backbone, the order parameters produced with the three solvent models agree to a large extent with experiments, giving average unsigned deviations between 0.03 and 0.06. For the side-chains, for which the experimental data is incomplete, the deviations are considerably larger with mean deviations between 0.13 and 0.17. However, for both backbone and side-chains, it is difficult to pick a winner, as all models perform equally well overall. For a more complete set of side-chain vectors, we resort to analysing the variation among the estimates from different solvent models. Unfortunately, the variations are found to be sizeable with mean deviations between 0.11 and 0.15. Implications for computational assessment of protein dynamics are discussed.

  12. Probing electron correlation and nuclear dynamics in Momentum Space

    Energy Technology Data Exchange (ETDEWEB)

    Deleuze, M S; Hajgato, B; Morini, F; Knippenberg, S, E-mail: michael.deleuze@uhasselt.b [Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan, Gebouw D, B3590 Diepenbeek (Belgium)

    2010-02-01

    Orbital imaging experiments employing Electron Momentum Spectroscopy are subject to many complications, such as distorted wave effects, conformational mobility in the electronic ground state, ultra-fast nuclear dynamics in the final state, or a dispersion of the ionization intensity over electronically excited (shake-up) configurations of the cation. The purpose of the present contribution is to illustrate how a proper treatment of these complications enables us to probe in momentum space the consequences of electron correlation and nuclear dynamics in neutral and cationic states.

  13. Adhesion Dynamics in Probing Micro- and Nanoscale Thin Solid Films

    Directory of Open Access Journals (Sweden)

    Xiaoling He

    2008-01-01

    Full Text Available This study focuses on modeling the probe dynamics in scratching and indenting thin solid films at micro- and nanoscales. The model identifies bifurcation conditions that define the stick-slip oscillation patterns of the tip. It is found that the local energy fluctuations as a function of the inelastic deformation, defect formation, material properties, and contact parameters determine the oscillation behavior. The transient variation of the localized function makes the response nonlinear at the adhesion junction. By quantifying the relation between the bifurcation parameters and the oscillation behavior, this model gives a realistic representation of the complex adhesion dynamics. Specifically, the model establishes the link between the stick-slip behavior and the inelastic deformation and the local potentials. This model justifies the experimental observations and the molecular dynamics simulation of the adhesion and friction dynamics in both the micro- and nanoscale contact.

  14. Dynamical Dipole as a Probe of Isospin Dynamics

    Science.gov (United States)

    Corsi, A.; Wieland, O.; Bracco, A.; Camera, F.; Benzoni, G.; Blasi, N.; Brambilla, S.; Crespi, F. C. L.; Giussani, A.; Leoni, S.; Million, B.; Montanari, D.; Moroni, A.; Kravchuk, V. L.; Gramegna, F.; Lanchais, A.; Mastinu, P.; Brekiesz, M.; Kmiecik, M.; Maj, A.; Bruno, M.; Geraci, E.; Vannini, G.; Barlini, S.; Casini, G.; Chiari, M.; Nannini, A.; Ordine, A.; di Toro, M.; Rizzo, C.; Colonna, M.

    2009-03-01

    The gamma -ray emission due to dynamical dipole oscillations during fusion process was measured for the N/Z asymmetric reaction 16O + 116Sn at 8.1 and 15.6 MeV/u. High-energy gamma -rays and light charged particles were measured in coincidence with the recoiling residual nuclei. The measured yield of the high-energy gamma -rays exceeds that of the thermalized compound nucleus and this extra-yield increases with beam energy. Data are compared with theoretical predictions of a dynamical calculation based on Boltzmann-Nordheim-Vlasov (BNV) model.

  15. Quantum Dynamics Simulations for Modeling Experimental Pump-Probe Measurements

    Science.gov (United States)

    Pearson, Brett; Nayyar, Sahil; Liss, Kyle; Weinacht, Thomas

    2016-05-01

    Time-resolved studies of quantum dynamics have benefited greatly from developments in ultrafast table-top and free electron lasers. Advances in computer software and hardware have lowered the barrier for performing calculations such that relatively simple simulations allow for direct comparison with experimental results. We describe here a set of quantum dynamics calculations in low-dimensional molecular systems. The calculations incorporate coupled electronic-nuclear dynamics, including two interactions with an applied field and nuclear wave packet propagation. The simulations were written and carried out by undergraduates as part of a senior research project, with the specific goal of allowing for detailed interpretation of experimental pump-probe data (in additional to the pedagogical value).

  16. Homology modeling, docking studies and molecular dynamic simulations using graphical processing unit architecture to probe the type-11 phosphodiesterase catalytic site: a computational approach for the rational design of selective inhibitors.

    Science.gov (United States)

    Cichero, Elena; D'Ursi, Pasqualina; Moscatelli, Marco; Bruno, Olga; Orro, Alessandro; Rotolo, Chiara; Milanesi, Luciano; Fossa, Paola

    2013-12-01

    Phosphodiesterase 11 (PDE11) is the latest isoform of the PDEs family to be identified, acting on both cyclic adenosine monophosphate and cyclic guanosine monophosphate. The initial reports of PDE11 found evidence for PDE11 expression in skeletal muscle, prostate, testis, and salivary glands; however, the tissue distribution of PDE11 still remains a topic of active study and some controversy. Given the sequence similarity between PDE11 and PDE5, several PDE5 inhibitors have been shown to cross-react with PDE11. Accordingly, many non-selective inhibitors, such as IBMX, zaprinast, sildenafil, and dipyridamole, have been documented to inhibit PDE11. Only recently, a series of dihydrothieno[3,2-d]pyrimidin-4(3H)-one derivatives proved to be selective toward the PDE11 isoform. In the absence of experimental data about PDE11 X-ray structures, we found interesting to gain a better understanding of the enzyme-inhibitor interactions using in silico simulations. In this work, we describe a computational approach based on homology modeling, docking, and molecular dynamics simulation to derive a predictive 3D model of PDE11. Using a Graphical Processing Unit architecture, it is possible to perform long simulations, find stable interactions involved in the complex, and finally to suggest guideline for the identification and synthesis of potent and selective inhibitors.

  17. Probing Protein Channel Dynamics At The Single Molecule Level.

    Science.gov (United States)

    Lee, M. Ann; Dunn, Robert C.

    1997-03-01

    It would be difficult to overstate the importance played by protein ion channels in cellular function. These macromolecular pores allow the passage of ions across the cellular membrane and play indispensable roles in all aspects of neurophysiology. While the patch-clamp technique continues to provide elegant descriptions of the kinetic processes involved in ion channel gating, the associated conformational changes remain a mystery. We are using the spectroscopic capabilities and single molecule fluorescence sensitivity of near-field scanning optical microscopy (NSOM) to probe these dynamics at the single channel level. Using a newly developed cantilevered NSOM probe capable of probing soft biological samples with single molecule fluorescence sensitivity, we have begun mapping the location of single NMDA receptors in intact rat cortical neurons with <100 nm spatial resolution. We will also present recent results exploring the conformational changes accompanying activation of nuclear pore channels located in the nuclear membrane of Xenopus oocytes. Our recent NSOM and AFM measurements on single nuclear pore complexes reveal large conformational changes taking place upon activation, providing rich, new molecular level details of channel function.

  18. Real-time probing of structural dynamics in perovskite materials

    Energy Technology Data Exchange (ETDEWEB)

    Elsaesser, Thomas [Max-Born-Institut fuer Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin (Germany)

    2009-07-01

    Femtosecond x-ray diffraction probes structural dynamics of solids in real-time and gives insight into reversible geometry changes on atomic length and time scales. After a brief introduction into this field, recent results on the lattice dynamics of ferroelectric SrRuO{sub 3}/PbZr{sub 0.2}Ti{sub 0.8}O{sub 3} superlattice structures and their interplay with the electric polarization of the material are presented. Ultrafast optical generation of mechanical stress allows for switching-off the polarization on a time scale of a few picoseconds. As a second example, magnetostriction in a ferromagnetic SrRuO{sub 3}/SrTiO{sub 3} superlattice structure is analyzed in real time.

  19. In-vitro accuracy and reproducibility evaluation of probing depth measurements of selected periodontal probes

    Directory of Open Access Journals (Sweden)

    K.N. Al Shayeb

    2014-01-01

    Conclusion: Depth measurements with the Chapple UB-CF-15 probe were more accurate and reproducible compared to measurements with the Vivacare TPS and Williams 14 W probes. This in vitro model may be useful for intra-examiner calibration or clinician training prior to the clinical evaluation of patients or in longitudinal studies involving periodontal evaluation.

  20. Positron emission tomography probe to monitor selected sugar metabolism in vivo

    Energy Technology Data Exchange (ETDEWEB)

    Witte, Owen; Clark, Peter M.; Castillo, Blanca Graciela Flores; Jung, Michael E.; Evdokimov, Nikolai M.

    2017-03-14

    The invention disclosed herein discloses selected ribose isomers that are useful as PET probes (e.g. [18F]-2-fluoro-2-deoxy-arabinose). These PET probes are useful, for example, in methods designed to monitor physiological processes including ribose metabolism and/or to selectively observe certain tissue/organs in vivo. The invention disclosed herein further provides methods for making and using such probes.

  1. Positron emission tomography probe to monitor selected sugar metabolism in vivo

    Science.gov (United States)

    Witte, Owen; Clark, Peter M.; Castillo, Blanca Graciela Flores; Jung, Michael E.; Evdokimov, Nikolai M.

    2017-03-14

    The invention disclosed herein discloses selected ribose isomers that are useful as PET probes (e.g. [18F]-2-fluoro-2-deoxy-arabinose). These PET probes are useful, for example, in methods designed to monitor physiological processes including ribose metabolism and/or to selectively observe certain tissue/organs in vivo. The invention disclosed herein further provides methods for making and using such probes.

  2. Proceedings of "Optical Probes of Dynamics in Complex Environments"

    Energy Technology Data Exchange (ETDEWEB)

    Sension, R; Tokmakoff, A

    2008-04-01

    This document contains the proceedings from the symposium on Optical Probes of Dynamics in Complex Environments, which organized as part of the 235th National Meeting of the American Chemical Society in New Orleans, LA from April 6 to 10, 2008. The study of molecular dynamics in chemical reaction and biological processes using time ƒresolved spectroscopy plays an important role in our understanding of energy conversion, storage, and utilization problems. Fundamental studies of chemical reactivity, molecular rearrangements, and charge transport are broadly supported by the DOE Office of Science because of their role in the development of alternative energy sources, the understanding of biological energy conversion processes, the efficient utilization of existing energy resources, and the mitigation of reactive intermediates in radiation chemistry. In addition, time resolved spectroscopy is central to all of DOEs grand challenges for fundamental energy science. This symposium brought together leaders in the field of ultrafast spectroscopy, including experimentalists, theoretical chemists, and simulators, to discuss the most recent scientific and technological advances. DOE support for this conference was used to help young US and international scientists travel to the meeting. The latest technology in ultrafast infrared, optical, and xray spectroscopy and the scientific advances that these methods enable were covered. Particular emphasis was placed on new experimental methods used to probe molecular dynamics in liquids, solids, interfaces, nanostructured materials, and biomolecules.

  3. Spin probe dynamics of n-hexadecane in confined geometry

    Science.gov (United States)

    Lukešová, Miroslava; Švajdlenková, Helena; Sippel, Pit; Macová, Eva; Berek, Dušan; Loidl, Alois; Bartoš, Josef

    2015-02-01

    A combined study of the rotational dynamics of the stable free radical 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) and the phase behavior of n-hexadecane (n-HXD) in the bulk and the confined states in a series of silica gels (SG) by means of ESR and DSC is presented. A slow to fast motion transition of the spin probe TEMPO in the bulk n-HXD occurs at T50 G,bulk ≪ Tm,bulk, i.e., well below the melting temperature due to its trapping and localized mobility in the interlamellar gap of the crystallites [J. Bartoš, H. Švajdlenková, M. Zaleski, M. Edelmann, M. Lukešová, Physica B 430, 99 (2013)]. On the other hand, the dynamics of the TEMPO in the confined systems is strongly slowing down with T50 G (Dpore) >Tm(Dpore) and slightly increases with the pore size Dpore = 60, 100 and 300 Å of the SG's. At the same time, both the corresponding melting temperature, Tm (Dpore), and melting enthalpy, ΔHm (Dpore), decrease with Dpore together with the mutual anti-correlation between T50 G and Tm as a function of the inverse of pore diameter, 1/Dpore. Moreover, the dynamic heterogeneity of the TEMPO in the confined state below T50 G (Dpore) is closely related to the phase transformation. The strong slowing down of the spin probe motion likely results from its preferential localization at the interface layer of the matrix pore due to specific interaction of TEMPO molecules with the polar silanol groups of the SG matrix. This is supported by special study on a series of the variously filled n-HXD/SG systems, other similar experimental findings as well as by theoretical spectral argument.

  4. Probing protein flexibility reveals a mechanism for selective promiscuity

    Science.gov (United States)

    Pabon, Nicolas A; Camacho, Carlos J

    2017-01-01

    Many eukaryotic regulatory proteins adopt distinct bound and unbound conformations, and use this structural flexibility to bind specifically to multiple partners. However, we lack an understanding of how an interface can select some ligands, but not others. Here, we present a molecular dynamics approach to identify and quantitatively evaluate the interactions responsible for this selective promiscuity. We apply this approach to the anticancer target PD-1 and its ligands PD-L1 and PD-L2. We discover that while unbound PD-1 exhibits a hard-to-drug hydrophilic interface, conserved specific triggers encoded in the cognate ligands activate a promiscuous binding pathway that reveals a flexible hydrophobic binding cavity. Specificity is then established by additional contacts that stabilize the PD-1 cavity into distinct bound-like modes. Collectively, our studies provide insight into the structural basis and evolution of multiple binding partners, and also suggest a biophysical approach to exploit innate binding pathways to drug seemingly undruggable targets. DOI: http://dx.doi.org/10.7554/eLife.22889.001 PMID:28432789

  5. The geometry of the Fisher selection dynamics

    CERN Document Server

    Shapovalov, A V

    1998-01-01

    We study the Fisher model describing natural selection in a population with a diploid structure of a genome by differential- geometric methods. For the selection dynamics we introduce an affine connection which is shown to be the projectively Euclidean and the equiaffine one. The selection dynamics is reformulated similar to the motion of an effective particle moving along the geodesic lines in an 'effective external field' of a tensor type. An exact solution is found to the Fisher equations for the special case of fitness matrix associated to the effect of chromosomal imprinting of mammals. Biological sense of the differential- geometric constructions is discussed. The affine curvature is considered as a direct consequence of an allele coupling in the system. This curving of the selection dynamics geometry is related to an inhomogenity of the time flow in the course of the selection.

  6. Testing consistency of general relativity with kinematic and dynamical probes

    CERN Document Server

    Duan, Xiao-Wei; Zhang, Tong-Jie

    2016-01-01

    In this work, we test consistency relations between a kinematic probe, the observational Hubble data, and a dynamical probe, the growth rates for cosmic large scale structure, which should hold if general relativity is the correct theory of gravity on cosmological scales. Moreover, we summarize the development history of parametrization in testings and make an improvement of it. Taking advantage of the Hubble parameter given from both parametric and non-parametric methods, we propose three equations and test two of them performed by means of two-dimensional parameterizations, including one using trigonometric functions we propose. As a result, it is found that the consistency relations satisfies well at $1\\sigma$ CL and trigonometric functions turn out to be efficient tools in parameterizations. Furthermore, in order to confirm the validity of our test, we introduce a model of modified gravity, DGP model and compare the testing results in the cases of $\\Lambda$CDM, "DGP in GR" and DGP model with mock data. It...

  7. The Cell Probe Complexity of Dynamic Range Counting

    DEFF Research Database (Denmark)

    Larsen, Kasper Green

    2012-01-01

    In this paper we develop a new technique for proving lower bounds on the update time and query time of dynamic data structures in the cell probe model. With this technique, we prove the highest lower bound to date for any explicit problem, namely a lower bound of tq = ((lg n/ lg(wtu))2). Here n...... is the number of update operations, w the cell size, tq the query time and tu the update time. In the most natural setting of cell size w = (lg n), this gives a lower bound of tq = ((lg n/ lg lg n)2) for any polylogarithmic update time. This bound is almost a quadratic improvement over the highest previous...... is specified by a point q = (x, y), and the goal is to report the sum of the weights assigned to the points dominated by q, where a point (x0, y0) is dominated by q if x0 x and y0 y. In addition to being the highest cell probe lower bound to date, our lower bound is also tight for data struc- tures with update...

  8. The Cell Probe Complexity of Dynamic Range Counting

    DEFF Research Database (Denmark)

    Larsen, Kasper Green

    2012-01-01

    In this paper we develop a new technique for proving lower bounds on the update time and query time of dynamic data structures in the cell probe model. With this technique, we prove the highest lower bound to date for any explicit problem, namely a lower bound of tq = ((lg n/ lg(wtu))2). Here n...... is the number of update operations, w the cell size, tq the query time and tu the update time. In the most natural setting of cell size w = (lg n), this gives a lower bound of tq = ((lg n/ lg lg n)2) for any polylogarithmic update time. This bound is almost a quadratic improvement over the highest previous...... is specified by a point q = (x, y), and the goal is to report the sum of the weights assigned to the points dominated by q, where a point (x0, y0) is dominated by q if x0 x and y0 y. In addition to being the highest cell probe lower bound to date, our lower bound is also tight for data struc- tures with update...

  9. Sugar transport across lactose permease probed by steered molecular dynamics

    DEFF Research Database (Denmark)

    Jensen, Morten Østergaard; Yin, Ying; Tajkhorshid, Emad

    2007-01-01

    Escherichia coli lactose permease (LacY) transports sugar across the inner membrane of the bacterium using the proton motive force to accumulate sugar in the cytosol. We have probed lactose conduction across LacY using steered molecular dynamics, permitting us to follow molecular and energetic......, forcing it to interact with channel lining residues. Lactose forms a multitude of direct sugar-channel hydrogen bonds, predominantly with residues of the flexible N-domain, which is known to contribute a major part of LacY's affinity for lactose. In the periplasmic half-channel lactose predominantly...... interacts with hydrophobic channel lining residues, whereas in the cytoplasmic half-channel key protein-substrate interactions are mediated by ionic residues. A major energy barrier against transport is found within a tight segment of the periplasmic half-channel where sugar hydration is minimal and protein-sugar...

  10. β-Isocyanoalanine as an IR probe: comparison of vibrational dynamics between isonitrile and nitrile-derivatized IR probes.

    Science.gov (United States)

    Maj, Michał; Ahn, Changwoo; Kossowska, Dorota; Park, Kwanghee; Kwak, Kyungwon; Han, Hogyu; Cho, Minhaeng

    2015-05-07

    An infrared (IR) probe based on isonitrile (NC)-derivatized alanine 1 was synthesized and the vibrational properties of its NC stretching mode were investigated using FTIR and femtosecond IR pump-probe spectroscopy. It is found that the NC stretching mode is very sensitive to the hydrogen-bonding ability of solvent molecules. Moreover, its transition dipole strength is larger than that of nitrile (CN) in nitrile-derivatized IR probe 2. The vibrational lifetime of the NC stretching mode is found to be 5.5 ± 0.2 ps in both D2O and DMF solvents, which is several times longer than that of the azido (N3) stretching mode in azido-derivatized IR probe 3. Altogether these properties suggest that the NC group can be a very promising sensing moiety of IR probes for studying the solvation structure and dynamics of biomolecules.

  11. Probing ultrafast carrier tunneling dynamics in individual quantum dots and molecules

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Kai; Bechtold, Alexander; Kaldewey, Timo; Zecherle, Markus; Wildmann, Johannes S.; Bichler, Max; Abstreiter, Gerhard; Finley, Jonathan J. [Walter Schottky Institut and Physik-Department, Technische Universitaet Muenchen, Am Coulombwall 4, 85748, Garching (Germany); Ruppert, Claudia; Betz, Markus [Experimentelle Physik 2, TU Dortmund, 44221, Dortmund (Germany); Krenner, Hubert J. [Lehrstuhl fuer Experimentalphysik 1 and Augsburg Centre for Innovative Technologies (ACIT), Universitaet Augsburg, Universitaetsstr 1, 86159, Augsburg (Germany); Villas-Boas, Jose M. [Instituto de Fisica, Universidade Federal de Uberlandia, 38400-902, Uberlandia, MG (Brazil)

    2013-02-15

    Ultrafast pump-probe spectroscopy is employed to directly monitor the tunneling of charge carriers from single and vertically coupled quantum dots and probe intra-molecular dynamics. Immediately after resonant optical excitation, several peaks are observed in the pump-probe spectrum arising from Coulomb interactions between the photogenerated charge carriers. The influence of few-Fermion interactions in the photoexcited system and the temporal evolution of the optical response is directly probed in the time domain. In addition, the tunneling times for electrons and holes from the QD nanostructure are independently determined. In polarization resolved measurements, near perfect Pauli-spin blockade is observed in the spin-selective absorption spectrum as well as stimulated emission. While electron and hole tunneling from single quantum dots is shown to be well explained by the WKB formalism, for coupled quantum dots pronounced resonances in the electron tunneling rate are observed arising from elastic and inelastic electron tunneling between the different dots. (copyright 2012 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  12. Selection-Mutation Dynamics of Signaling Games

    Directory of Open Access Journals (Sweden)

    Josef Hofbauer

    2015-01-01

    Full Text Available We study the structure of the rest points of signaling games and their dynamic behavior under selection-mutation dynamics by taking the case of three signals as our canonical example. Many rest points of the replicator dynamics of signaling games are not isolated and, therefore, not robust under perturbations. However, some of them attract open sets of initial conditions. We prove the existence of certain rest points of the selection-mutation dynamics close to Nash equilibria of the signaling game and show that all but the perturbed rest points close to strict Nash equilibria are dynamically unstable. This is an important result for the evolution of signaling behavior, since it shows that the second-order forces that are governed by mutation can increase the chances of successful signaling.

  13. Dynamics of serial position change in probe-recognition task

    Directory of Open Access Journals (Sweden)

    Fifić Mario

    2002-01-01

    Full Text Available Relationship between practice and serial position effects was investigated, in order to obtain more evidence for underlying short-term memory processes. The investigated relationship is termed the dynamics of serial position change. To address this issue, the present study investigated mean latency, errors, and performed Ex-Gaussian convolution analysis. In six-block trials the probe-recognition task was used in the so-called fast experimental procedure. The serial position effect was significant in all six blocks. Both primacy and recency effects were detected, with primacy located in the first two blocks, producing a non-linear serial position effect. Although the serial position function became linear from the third block on, the convolution analysis revealed a non-linear change of the normal distribution parameter, suggesting special status of the last two serial positions. Further, separation of convolution parameters for serial position and practice was observed, suggesting different underlying mechanisms. In order to account for these findings, a strategy shift mechanism is suggested, rather then a mechanism based on changing the manner of memory scanning. Its influence is primarily located at the very beginning of the experimental session. The pattern of results of errors regarding the dynamics of serial position change closely paralleled those on reaction times. Several models of short-term memory were evaluated in order to account for these findings.

  14. Heavy atom quenched coumarin probes for sensitive and selective detection of biothiols in living cells.

    Science.gov (United States)

    Ji, Wengang; Ji, Yuzhuo; Jin, Qingqing; Tong, Qingxiao; Tang, Xinjing

    2015-07-07

    A series of turn-on fluorescent probes with halogen acetyl amide at the 3-position of coumarin derivatives were synthesized. Fluorescence of these probes was efficiently quenched by heavy halogen atoms (Br and I, not Cl), which could be successfully used for selective detection of biothiols with the sensitivity of Cys > GSH > Hcy and much higher than thiol containing proteins. These represent the smallest fluorescence quenchers in designing fluorescent probes for detecting both endogenous and exogenous biothiols in living cells.

  15. Optimal Relay Selection with Channel Probing in Wireless Sensor Networks

    CERN Document Server

    Naveen, K P

    2011-01-01

    Motivated by the problem of distributed geographical packet forwarding in a wireless sensor network with sleep-wake cycling nodes, we propose a local forwarding model comprising a node that wishes to forward a packet towards a destination, and a set of next-hop relay nodes, each of which is associated with a reward that summarises the cost/benefit of forwarding the packet through that relay. The relays wake up at random times, at which instants they reveal only the probability distributions of their rewards (e.g., by revealing their locations). To determine a relay's exact reward, the forwarding node has to further probe the relay, incurring a probing cost. Thus, at each relay wake-up instant, the source, given a set of relay reward distributions, has to decide whether to stop (and forward the packet to an already probed relay), continue waiting for further relays to wake-up, or probe an unprobed relay. We formulate the problem as a Markov decision process, with the objective being to minimize the packet forw...

  16. Selective ultrafast probing of transient hot chemisorbed and precursor states of CO on Ru(0001)

    DEFF Research Database (Denmark)

    Beye, M.; Anniyev, T.; Coffee, R.

    2013-01-01

    We have studied the femtosecond dynamics following optical laser excitation of CO adsorbed on a Ru surface by monitoring changes in the occupied and unoccupied electronic structure using ultrafast soft x-ray absorption and emission. We recently reported [M. Dell'Angela et al. Science 339, 1302...... (2013)SCIEAS0036-8075] a phonon-mediated transition into a weakly adsorbed precursor state occurring on a time scale of >2 ps prior to desorption. Here we focus on processes within the first picosecond after laser excitation and show that the metal-adsorbate coordination is initially increased due...... to hot-electron-driven vibrational excitations. This process is faster than, but occurs in parallel with, the transition into the precursor state. With resonant x-ray emission spectroscopy, we probe each of these states selectively and determine the respective transient populations depending on optical...

  17. SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

    DEFF Research Database (Denmark)

    Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R;

    2015-01-01

    Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse...

  18. Carrier dynamics in EuTiO3 films probed by femtosecond pump-probe spectroscopy

    Science.gov (United States)

    Li, Zhongguo; Zhao, Run; Li, Weiwei; Wang, Haiyan; Yang, Hao; Zhang, Xueru; Wang, Yuxiao; Wei, Tai-Huei; Song, Ying-Lin

    2015-03-01

    Recently, perovskite oxide EuTiO3 has attracted considerable attention due to its intriguing multiferroic properties. To gain a deeper understanding of its fascinating properties, it is essential to characterize the competing interactions between charge, lattice, spin, and orbital parameters. Here we present optical studies of the ultrafast carrier dynamics in EuTiO3 films grown on SrTiO3 substrates by probing photo-induced transient absorption (TA) in the weak excitation limit. All the signals were measured at room temperature. The transient curve of EuTiO3 exhibits a fast rise after photo excitation (approximately 2 ps) and a long decay component with time constant of several nanoseconds, which are attributed to carrier-phonon coupling and carrier recombination respectively. The absorption change of EuTiO3 near zero temporal delay is found to be quite different from the SrTiO3 substrates, implying carrier-phonon interactions differ distinctively between these two materials. Our results could be helpful to understand the microscopic interactions in perovskite oxide. The authors acknowledge the support of the National Natural Science Foundation of China.

  19. Probing Internal Dynamics of two SMGs with OSIRIS

    Science.gov (United States)

    Menendez-Delmestre, K.; Blain, A. W.; Chapman, S. C.; Swinbank, A. M.; Smail, I.; Ivison, R. J.; Alexander, D. M.

    2005-12-01

    We used the OH-Suppresing Infrared Imaging Spectrograph (OSIRIS) on Keck II with laser AO to investigate the internal dynamics of two of the most luminous submillimeter galaxies (SMGs) at redshifts z 2-3: SMM J030227.73+000653.5 at z=1.408 and SMM J221804.42+002154.4 at z=2.517 (Chapman et al. 2005). Recent ultradeep Chandra X-ray results indicate that the majority of SMGs contain an actively fueled AGN (Alexander et al. 2005), as their hard X-ray emission is too powerful to be explained by the high-mass X-ray binaries associated with pure star formation. This AGN contributes a minor fraction to the total luminosity, but the potential modifies the observed spectra, complicating their interpretation in terms of excitation and metallicity. We expect the restframe optical light from this nuclear emission to be centrally concentrated, surrounded by a more extended emission from star-forming regions. With AO we attempt to resolve the separation between the nuclear and extended emission, to probe the AGN and the velocity field of the wider starburst. We aimed to map the two-dimensional spatial distribution of H-alpha line emission, using the appropriate narrow band filters Hn2 and Kn5 matched to our known redshifts using the coarsest OSIRIS plate scale (0.1-arcsec) to have the largest field of view and optimize the coverage of the luminous region of the galaxies. By measuring accurately both the velocity dispersion point-by-point and the physical extent of these high redshift galaxies, we can estimate their dynamical masses. This enables us to better understand their internal astrophysics, their fate in terms of the galaxies we observe today, and the links between properties of dark matter halos and the stellar systems that form within. We thank NASA, NSF and Sloan Foundation.

  20. The Cell Probe Complexity of Dynamic Range Counting

    CERN Document Server

    Larsen, Kasper Green

    2011-01-01

    In this paper we develop a new technique for proving dynamic cell probe lower bounds. With this technique, we achieve the highest lower bound to date for any explicit problem, namely a lower bound of $t_q=\\Omega((\\lg n/\\lg(wt_u))^2)$. Here $n$ is the number of update operations, $w$ the cell size, $t_q$ the query time and $t_u$ the update time. In the most natural setting of cell size $w=\\Theta(\\lg n)$, this gives a lower bound of $t_q=\\Omega((\\lg n/\\lg \\lg n)^2)$ for any polylogarithmic update time. This bound is almost a quadratic improvement over the highest previous lower bound of $\\Omega(\\lg n)$, due to P\\v{a}tra\\c{s}cu and Demaine [SICOMP'06]. We prove our lower bound for the fundamental problem of weighted orthogonal range counting. In this problem, we are to support insertions of two-dimensional points, each assigned a $\\Theta(\\lg n)$-bit integer weight. A query to this problem is specified by a point $q=(x,y)$, and the goal is to report the sum of the weights assigned to the points dominated by $q$, ...

  1. A highly selective fluorescent probe based on Michael addition for fast detection of hydrogen sulfide

    Science.gov (United States)

    Gao, Baozhen; Cui, Lixia; Pan, Yong; Xue, Minjie; Zhu, Boyu; Zhang, Guomei; Zhang, Caihong; Shuang, Shaomin; Dong, Chuan

    2017-02-01

    A new 4-hydroxy-1,8-naphthalimide-based compound (probe 1) has been designed and synthesized. The colorimetric and fluorescent properties of probe 1 towards hydrogen sulfide (H2S) were investigated in detail. The results show that the probe 1 could selectively and sensitively recognize H2S rather than other reactive sulfur species. The reaction mechanism of this probe is an intramolecular cyclization caused by the Michael addition of H2S to give 4-hydroxy-1,8-naphthalimide. The intramolecular charge transfer of 4-hydroxy-1,8-naphthalimide is significant. Probe 1 quickly responded to H2S and showed a 75-fold fluorescence enhancement in 5 min. Moreover, probe 1 could detect H2S quantitatively with a detection limit as low as 0.23 μM.

  2. Sampling dynamics: an alternative to payoff-monotone selection dynamics

    DEFF Research Database (Denmark)

    Berkemer, Rainer

    options this result is rather counter intuitive and indeed there is experimental evidence which indicates that deviation will be likely even though the Nash equilibrium is strict. One can use the fact that strict Nash equilbria must be also sampling equilibria to test for the ``plausibility......Osborne and Rubinstein introduced sampling equilibria which are based on the concept of ``procedural rationality''. Sethi extended their idea to a dynamic framework which leads to the so called sampling dynamics. Unlike e.g the replicator dynamics this selection dynamics turns out to be neither......'' of the standard game theory result. Both, analytical tools and agent based simulation are used to investigate the dynamic stability of sampling equilibria in a generalized travelers dilemma. Two parameters are of interest: the number of strategy options (m) available to each traveler and an experience parameter...

  3. Dynamic behavior of ion-selective electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Pungor, E.; Linder, E.; Toth, K.

    1988-01-01

    This book provides a survey of the different techniques employed to study time-dependent processes of ion-selective electrodes. The fundamentals, the impedance field, the polarization field, and the activity step methods are treated in depth with emphasis on the information content of the results provided by the different techniques relevant to the dynamic characteristics of ion-selective electrodes. Within the activity step methods the different theoretical models derived to describe the potential-time function of ion-selective electrodes are critically discussed.

  4. State Feedback Control for Adjusting the Dynamic Behavior of a Piezoactuated Bimorph Atomic Force Microscopy Probe

    CERN Document Server

    Orun, Bilal; Basdogan, Cagatay; Guvenc, Levent

    2012-01-01

    We adjust the transient dynamics of a piezo-actuated bimorph Atomic Force Microscopy (AFM) probe using a state feedback controller. This approach enables us to adjust the quality factor and the resonance frequency of the probe simultaneously. First, we first investigate the effect of feedback gains on dynamic response of the probe and then show that the time constant of the probe can be reduced by reducing its quality factor and/or increasing its resonance frequency to reduce the scan error in tapping mode AFM.

  5. Dynamic Nigrostriatal Dopamine Biases Action Selection.

    Science.gov (United States)

    Howard, Christopher D; Li, Hao; Geddes, Claire E; Jin, Xin

    2017-03-22

    Dopamine is thought to play a critical role in reinforcement learning and goal-directed behavior, but its function in action selection remains largely unknown. Here we demonstrate that nigrostriatal dopamine biases ongoing action selection. When mice were trained to dynamically switch the action selected at different time points, changes in firing rate of nigrostriatal dopamine neurons, as well as dopamine signaling in the dorsal striatum, were found to be associated with action selection. This dopamine profile is specific to behavioral choice, scalable with interval duration, and doesn't reflect reward prediction error, timing, or value as single factors alone. Genetic deletion of NMDA receptors on dopamine or striatal neurons or optogenetic manipulation of dopamine concentration alters dopamine signaling and biases action selection. These results unveil a crucial role of nigrostriatal dopamine in integrating diverse information for regulating upcoming actions, and they have important implications for neurological disorders, including Parkinson's disease and substance dependence. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Imaging via complete cantilever dynamic detection: general dynamic mode imaging and spectroscopy in scanning probe microscopy

    Science.gov (United States)

    Somnath, Suhas; Collins, Liam; Matheson, Michael A.; Sukumar, Sreenivas R.; Kalinin, Sergei V.; Jesse, Stephen

    2016-10-01

    We develop and implement a multifrequency spectroscopy and spectroscopic imaging mode, referred to as general dynamic mode (GDM), that captures the complete spatially- and stimulus dependent information on nonlinear cantilever dynamics in scanning probe microscopy (SPM). GDM acquires the cantilever response including harmonics and mode mixing products across the entire broadband cantilever spectrum as a function of excitation frequency. GDM spectra substitute the classical measurements in SPM, e.g. amplitude and phase in lock-in detection. Here, GDM is used to investigate the response of a purely capacitively driven cantilever. We use information theory techniques to mine the data and verify the findings with governing equations and classical lock-in based approaches. We explore the dependence of the cantilever dynamics on the tip–sample distance, AC and DC driving bias. This approach can be applied to investigate the dynamic behavior of other systems within and beyond dynamic SPM. GDM is expected to be useful for separating the contribution of different physical phenomena in the cantilever response and understanding the role of cantilever dynamics in dynamic AFM techniques.

  7. Vibrational excitons in ionophores: Experimental probes for quantum coherence-assisted ion transport and selectivity in ion channels

    CERN Document Server

    Ganim, Ziad; Vaziri, Alipasha

    2011-01-01

    Despite a large body of work, the exact molecular details underlying ion-selectivity and transport in the potassium channel have not been fully laid to rest. One major reason has been the lack of experimental methods that can probe these mechanisms dynamically on their biologically relevant time scales. Recently it was suggested that quantum coherence and its interplay with thermal vibration might be involved in mediating ion-selectivity and transport. In this work we present an experimental strategy for using time resolved infrared spectroscopy to investigate these effects. We show the feasibility by demonstrating the IR absorption and Raman spectroscopic signatures of potassium binding model molecules that mimic the transient interactions of potassium with binding sites of the selectivity filter during ion conduction. In addition to guide our experiments on the real system we have performed molecular dynamic-based simulations of the FTIR and 2DIR spectra of the entire KcsA complex, which is the largest comp...

  8. Ad-hoc and context-dependent adjustments of selective attention in conflict control: an ERP study with visual probes.

    Science.gov (United States)

    Nigbur, R; Schneider, J; Sommer, W; Dimigen, O; Stürmer, B

    2015-02-15

    Cognitive conflict control in flanker tasks has often been described using the zoom-lens metaphor of selective attention. However, whether and how selective attention - in terms of suppression and enhancement - operates in this context has remained unclear. To examine the dynamic interplay of selective attention and cognitive control we used electrophysiological measures and presented task-irrelevant visual probe stimuli at foveal, parafoveal, and peripheral display positions. Target-flanker congruency varied either randomly from trial to trial (mixed-block) or block-wise (fixed-block) in order to induce reactive versus proactive control modes, respectively. Three EEG measures were used to capture ad-hoc adjustments within trials as well as effects of context-based predictions: the N1 component of the visual evoked potential (VEP) to probes, the VEP to targets, and the conflict-related midfrontal N2 component. Results from probe-VEPs indicate that enhanced processing of the foveal target rather than suppression of the peripheral flankers supports interference control. In incongruent mixed-block trials VEPs were larger to probes near the targets. In the fixed-blocks probe-VEPs were not modulated, but contrary to the mixed-block the preceding target-related VEP was affected by congruency. Results of the control-related N2 reveal largest amplitudes in the unpredictable context, which did not differentiate for stimulus and response incongruency. In contrast, in the predictable context, N2 amplitudes were reduced overall and differentiated between stimulus and response incongruency. Taken together these results imply that predictability alters interference control by a reconfiguration of stimulus processing. During unpredictable sequences participants adjust their attentional focus dynamically on a trial-by-trial basis as reflected in congruency-dependent probe-VEP-modulation. This reactive control mode also elicits larger N2 amplitudes. In contrast, when task demands

  9. Local collective motion analysis for multi-probe dynamic imaging and microrheology

    Science.gov (United States)

    Khan, Manas; Mason, Thomas G.

    2016-08-01

    Dynamical artifacts, such as mechanical drift, advection, and hydrodynamic flow, can adversely affect multi-probe dynamic imaging and passive particle-tracking microrheology experiments. Alternatively, active driving by molecular motors can cause interesting non-Brownian motion of probes in local regions. Existing drift-correction techniques, which require large ensembles of probes or fast temporal sampling, are inadequate for handling complex spatio-temporal drifts and non-Brownian motion of localized domains containing relatively few probes. Here, we report an analytical method based on local collective motion (LCM) analysis of as few as two probes for detecting the presence of non-Brownian motion and for accurately eliminating it to reveal the underlying Brownian motion. By calculating an ensemble-average, time-dependent, LCM mean square displacement (MSD) of two or more localized probes and comparing this MSD to constituent single-probe MSDs, we can identify temporal regimes during which either thermal or athermal motion dominates. Single-probe motion, when referenced relative to the moving frame attached to the multi-probe LCM trajectory, provides a true Brownian MSD after scaling by an appropriate correction factor that depends on the number of probes used in LCM analysis. We show that LCM analysis can be used to correct many different dynamical artifacts, including spatially varying drifts, gradient flows, cell motion, time-dependent drift, and temporally varying oscillatory advection, thereby offering a significant improvement over existing approaches.

  10. Probing of incomplete fusion dynamics by spin-distribution measurement

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Pushpendra P. [Accelerator Laboratory, Department of Physics, A.M. University, Aligarh (UP) 202002 (India); NP Group, Inter-University Accelerator Center, PO Box 10502, New Delhi 110067 (India)], E-mail: pushpendrapsingh@gmail.com; Singh, B.P. [Accelerator Laboratory, Department of Physics, A.M. University, Aligarh (UP) 202002 (India)], E-mail: bpsinghamu@gmail.com; Sharma, M.K.; Gupta, Unnati [Accelerator Laboratory, Department of Physics, A.M. University, Aligarh (UP) 202002 (India); Kumar, Rakesh [NP Group, Inter-University Accelerator Center, PO Box 10502, New Delhi 110067 (India); Singh, D. [Accelerator Laboratory, Department of Physics, A.M. University, Aligarh (UP) 202002 (India); Singh, R.P.; Murlithar, S. [NP Group, Inter-University Accelerator Center, PO Box 10502, New Delhi 110067 (India); Ansari, M.A.; Prasad, R. [Accelerator Laboratory, Department of Physics, A.M. University, Aligarh (UP) 202002 (India); Bhowmik, R.K. [NP Group, Inter-University Accelerator Center, PO Box 10502, New Delhi 110067 (India)], E-mail: ranjan@iuac.ernet.in

    2009-01-12

    Aiming to probe incomplete fusion dynamics in {sup 16}O + {sup 169}Tm system, spin-distributions of various reaction products populated via xn-, {alpha}/2{alpha}xn-channels have been measured at E{approx}5.6MeV/nucleon. Prompt {gamma}-rays in coincidence with fast charged particles (Z=1,2) have been recorded to achieve the information about involved reaction processes on the basis of their experimentally observed spin-populations during de-excitation. The experimentally observed spin-distributions for direct-{alpha}-emitting channels (associated with incomplete fusion) have been found to be distinctly different than that observed for fusion-evaporation (complete fusion) channels. The mean value of driving input angular momenta associated with various direct-{alpha}/2{alpha}xn-channels have been found to be higher than that observed for fusion-evaporation xn/{alpha}xn-channels, and increases with direct-{alpha}-multiplicity in forward cone. Experimentally measured, normalized production yields of fusion-evaporation xn/{alpha}xn-channels have been found to be in good agreement with the predictions of theoretical model code PACE4. Further, in order to understand the feeding probability in both complete and incomplete fusion reaction products, an attempt has been made to generate feeding intensity profiles from spin-distribution data. It has been observed that the complete fusion products are strongly fed over a broad spin range, while incomplete fusion products are found to be less fed and/or the population of lower spin states are strongly hindered.

  11. Numerical Investigation of Dynamic Effects on Unsteady Flow Measurements Using a Two-Dimensional Probe

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The dynamic effects in measurements of unsteady flow when using a probe with quasi-steady calibration curves has been investigated in this paper by numerical simulation of the compressible flow around a fixed two-dimensional 3-hole probe. The unsteady velocity and pressure distributions, as well as the hole-pressures, are calculated for high frequency flow variations. The measurement errors caused by the dynamic effects indicate that considerable measurement errors may occur for high frequency flow fluctuation, e.g., 2000Hz, especially, when the flow around the probe head approaches separation. This work shows how numerical simulation can be used to investigate and correct for the dynamic effects.

  12. Simple random sampling-based probe station selection for fault detection in wireless sensor networks.

    Science.gov (United States)

    Huang, Rimao; Qiu, Xuesong; Rui, Lanlan

    2011-01-01

    Fault detection for wireless sensor networks (WSNs) has been studied intensively in recent years. Most existing works statically choose the manager nodes as probe stations and probe the network at a fixed frequency. This straightforward solution leads however to several deficiencies. Firstly, by only assigning the fault detection task to the manager node the whole network is out of balance, and this quickly overloads the already heavily burdened manager node, which in turn ultimately shortens the lifetime of the whole network. Secondly, probing with a fixed frequency often generates too much useless network traffic, which results in a waste of the limited network energy. Thirdly, the traditional algorithm for choosing a probing node is too complicated to be used in energy-critical wireless sensor networks. In this paper, we study the distribution characters of the fault nodes in wireless sensor networks, validate the Pareto principle that a small number of clusters contain most of the faults. We then present a Simple Random Sampling-based algorithm to dynamic choose sensor nodes as probe stations. A dynamic adjusting rule for probing frequency is also proposed to reduce the number of useless probing packets. The simulation experiments demonstrate that the algorithm and adjusting rule we present can effectively prolong the lifetime of a wireless sensor network without decreasing the fault detected rate.

  13. PRISE2: software for designing sequence-selective PCR primers and probes.

    Science.gov (United States)

    Huang, Yu-Ting; Yang, Jiue-in; Chrobak, Marek; Borneman, James

    2014-09-25

    PRISE2 is a new software tool for designing sequence-selective PCR primers and probes. To achieve high level of selectivity, PRISE2 allows the user to specify a collection of target sequences that the primers are supposed to amplify, as well as non-target sequences that should not be amplified. The program emphasizes primer selectivity on the 3' end, which is crucial for selective amplification of conserved sequences such as rRNA genes. In PRISE2, users can specify desired properties of primers, including length, GC content, and others. They can interactively manipulate the list of candidate primers, to choose primer pairs that are best suited for their needs. A similar process is used to add probes to selected primer pairs. More advanced features include, for example, the capability to define a custom mismatch penalty function. PRISE2 is equipped with a graphical, user-friendly interface, and it runs on Windows, Macintosh or Linux machines. PRISE2 has been tested on two very similar strains of the fungus Dactylella oviparasitica, and it was able to create highly selective primers and probes for each of them, demonstrating the ability to create useful sequence-selective assays. PRISE2 is a user-friendly, interactive software package that can be used to design high-quality selective primers for PCR experiments. In addition to choosing primers, users have an option to add a probe to any selected primer pair, enabling design of Taqman and other primer-probe based assays. PRISE2 can also be used to design probes for FISH and other hybridization-based assays.

  14. Jetset: selecting the optimal microarray probe set to represent a gene

    DEFF Research Database (Denmark)

    Li, Qiyuan; Birkbak, Nicolai Juul; Gyorffy, Balazs

    2011-01-01

    Background: Interpretation of gene expression microarrays requires a mapping from probe set to gene. On many Affymetrix gene expression microarrays, a given gene may be detected by multiple probe sets, which may deliver inconsistent or even contradictory measurements. Therefore, obtaining...... an unambiguous expression estimate of a pre-specified gene can be a nontrivial but essential task. Results: We developed scoring methods to assess each probe set for specificity, splice isoform coverage, and robustness against transcript degradation. We used these scores to select a single representative probe...... set for each gene, thus creating a simple one-to-one mapping between gene and probe set. To test this method, we evaluated concordance between protein measurements and gene expression values, and between sets of genes whose expression is known to be correlated. For both test cases, we identified genes...

  15. Chemical proteomics with sulfonyl fluoride probes reveals selective labeling of functional tyrosines in glutathione transferases.

    Science.gov (United States)

    Gu, Christian; Shannon, D Alexander; Colby, Tom; Wang, Zheming; Shabab, Mohammed; Kumari, Selva; Villamor, Joji Grace; McLaughlin, Christopher J; Weerapana, Eranthie; Kaiser, Markus; Cravatt, Benjamin F; van der Hoorn, Renier A L

    2013-04-18

    Chemical probes have great potential for identifying functional residues in proteins in crude proteomes. Here we studied labeling sites of chemical probes based on sulfonyl fluorides (SFs) on plant and animal proteomes. Besides serine proteases and many other proteins, SF-based probes label Tyr residues in glutathione transferases (GSTs). The labeled GSTs represent four different GST classes that share less than 30% sequence identity. The targeted Tyr residues are located at similar positions in the promiscuous substrate binding site and are essential for GST function. The high selectivity of SF-based probes for functional Tyr residues in GSTs illustrates how these probes can be used for functional studies of GSTs and other proteins in crude proteomes.

  16. Dynamic index selection in data warehouses

    CERN Document Server

    Azefack, Stéphane; Darmont, Jérôme

    2008-01-01

    Analytical queries defined on data warehouses are complex and use several join operations that are very costly, especially when run on very large data volumes. To improve response times, data warehouse administrators casually use indexing techniques. This task is nevertheless complex and fastidious. In this paper, we present an automatic, dynamic index selection method for data warehouses that is based on incremental frequent itemset mining from a given query workload. The main advantage of this approach is that it helps update the set of selected indexes when workload evolves instead of recreating it from scratch. Preliminary experimental results illustrate the efficiency of this approach, both in terms of performance enhancement and overhead.

  17. Selective recoupling and stochastic dynamical decoupling

    CERN Document Server

    Kern, O

    2006-01-01

    An embedded selective recoupling method is proposed which is based on the idea of embedding the recently proposed deterministic selective recoupling scheme of Yamaguchi et al. [quant-ph/0411099] into a stochastic dynamical decoupling method, such as the recently proposed Pauli-random-error-correction-(PAREC) scheme [Eur. Phys. J. D 32, 153, quant-ph/0407262]. The recoupling scheme enables the implementation of elementary quantum gates in a quantum information processor by partial suppression of the unwanted interactions. The random dynamical decoupling method cancels a significant part of the residual interactions. Thus the time scale of reliable quantum computation is increased significantly. Numerical simulations are presented for a conditional two-qubit swap gate and for a complex iterative quantum algorithm.

  18. Sensitivity Analysis of Centralized Dynamic Cell Selection

    DEFF Research Database (Denmark)

    Lopez, Victor Fernandez; Alvarez, Beatriz Soret; Pedersen, Klaus I.;

    2016-01-01

    mechanism and solutions involving cell switching in general. Simulation results show that such solutions can greatly benefit from the use of receivers with interference suppression capabilities and a larger number of antennas, with a maximum data rate gain of 120%. High performance gains are observed...... with two different traffic models, and it is not necessary to be able to connect to a large number of cells in order to reap most of the benefits of the centralized dynamic cell selection....

  19. A Smart Near-Infrared Fluorescence Probe for Selective Detection of Tau Fibrils in Alzheimer's Disease.

    Science.gov (United States)

    Seo, Yujin; Park, Kwang-Su; Ha, Taewoong; Kim, Mi Kyoung; Hwang, Yu Jin; Lee, Junghee; Ryu, Hoon; Choo, Hyunah; Chong, Youhoon

    2016-11-16

    Development of a novel, tau-selective smart near-infrared fluorescence (NIRF) probe was attempted by combining the previously identified core scaffold 3,5-dimethoxy-N,N-dimethylaniline-4-yl moiety, with the characteristic donor-π-acceptor architecture of the smart NIRF Aβ probes DANIR-2c and MCAAD-3. A series of compounds (2 and 3) were prepared, which were identified as "turn-on" NIRF probes for the visual detection of tau aggregates and Aβ fibrils (λem = 650 nm, Stokes shifts = 70-110 nm). In particular, combination of the 3,5-dimethoxy-N,N-dimethylanilin-4-yl moiety and the donor part of MCAAD-3 endowed the resulting probes, 3g and 3h, with significant selectivity toward tau aggregates (selectivity for tau over Aβ = 5.7 and 3.8); they showed much higher fluorescence intensities upon binding to tau aggregates (FItau = 49 and 108) than when bound to Aβ fibrils (FIAβ = 9 and 28). Quantitative analysis of binding affinities and fluorescence properties of 3g and 3h revealed that microenvironment-sensitive molecular rotor-like behavior, rather than binding affinity to the target, is responsible for their selective turn-on fluorescence detection of tau fibrils. Selective fluorescent labeling of tau fibrils by 3g and 3h was further demonstrated by immunofluorescence staining of human Alzheimer's disease brain sections, which showed colocalization of the probes (3g and 3h) and phosphorylated tau antibody.

  20. Probing Advantages of Different Selectivity Strategies for Targeted Quantitative Proteomics

    Science.gov (United States)

    Merriman, M.; Hunter, C.; Mollah, Sahana

    2012-01-01

    INTRODUCTION: There has been an exponential increase in the number of ‘potential’ protein biomarkers discovered; thus requiring the need for better quantification strategies to confirm or refute their ultimate utility. Also required is increased throughput which means reduced sample preparation and/or accelerated chromatography which increases the chance of interferences that could confound robust quantification. The purpose of this study is to explore a range of new MS analysis methodologies that enable higher selectivity quantification. The different techniques rely on different properties of the molecule for specificity so their utility will depend to a large degree on the target molecules. But an exploration to determine some general guidelines will be helpful when choosing the best strategy. In this study, we compare the quantification of tryptic peptides in complex biological matrices using various strategies including combinations of sample preparation and mass spectrometric methodologies on different mass spectrometric platforms. EXPERIMENTAL METHODS: The intact or digested BNP was spiked into the crashed plasma to create calibration curves. An AB SCIEX QTRAP® 5500 system equipped with Turbo V™ source was used. Multiple reaction monitoring (MRM) transitions and MRM3 experiments for intact and digested BNP were developed and used to measure the calibration curves. For the differential mobility separations, a QTRAP 5500 system equipped with SelexION™ Technology was used. RESULTS: Three quantitative methodologies were used with the QTRAP® 5500 System: MRM provides selectivity based on the fragmentation of the peptide and monitoring of a specific product ion. When matrix interference is a problem with MRM, further selectivity can be performed using MRM3, which provides a second level of selectivity based on monitoring a secondary product ion. Alternatively, the differential mobility separation (DMS) system which provides selectivity based on the

  1. High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors.

    Science.gov (United States)

    Zhou, Ting; Caflisch, Amedeo

    2010-07-05

    A procedure based on semi-empirical quantum mechanical (QM) calculations of interaction energy is proposed for the rapid screening of compound poses generated by high-throughput docking. Small molecules (consisting of 2-10 atoms and termed "probes") are overlapped with polar groups in the binding site of the protein target. The interaction energy values between each compound pose and the probes, calculated by a semi-empirical Hamiltonian, are used as filters. The QM probe method does not require fixed partial charges and takes into account polarization and charge-transfer effects which are not captured by conventional force fields. The procedure is applied to screen approximately 100 million poses (of 2.7 million commercially available compounds) obtained by high-throughput docking in the ATP binding site of the tyrosine kinase erythropoietin-producing human hepatocellular carcinoma receptor B4 (EphB4). Three QM probes on the hinge region and one at the entrance pocket are employed to select for binding affinity, while a QM probe on the side chain of the so-called gatekeeper residue (a hypervariable residue in the kinome) is used to enforce selectivity. The poses with favorable interactions with the five QM probes are filtered further for hydrophobic matching and low ligand strain. In this way, a single-digit micromolar inhibitor of EphB4 with a relatively good selectivity profile is identified in a multimillion-compound library upon experimental tests of only 23 molecules.

  2. Temperature Relations of Selected Engine Oils Dynamic Viscosity

    Directory of Open Access Journals (Sweden)

    Hlaváč Peter

    2014-12-01

    Full Text Available This article focuses on temperature relations of dynamic viscosity for selected engine oils. The effect of temperature on new and used oil dynamic viscosity was investigated. Measurements were performed on three different motor oil samples. All the three motor oil samples were synthetic. The first oil sample was new, the second sample was used for 15,000 km, and the third sample was used for 30,000 km. There were made two measurements of samples in one week. Dynamic viscosity was measured using a digital rotational viscometer Anton Paar DV-3P. The principle of measurement is based on the dependence of sample resistance to probe rotation. The results of measurements are shown as graphical relationships between dynamic viscosity and temperature. Decreasing exponential functions in temperature relationships were used for all the samples. The highest difference between the first and second measurement was observed in the new oil, and very small differences were found in other oils. Due to different types of oils and different stage of usage, the results could not be compared.

  3. Probing the early-time dynamics of relativistic heavy-ion collisions with electromagnetic radiation

    CERN Document Server

    Vujanovic, Gojko; Denicol, Gabriel S; Luzum, Matthew; Schenke, Bjoern; Jeon, Sangyong; Gale, Charles

    2014-01-01

    Using 3+1D viscous relativistic fluid dynamics, we show that electromagnetic probes are sensitive to the initial conditions and to the out-of-equilibrium features of relativistic heavy-ion collisions. Within the same approach, we find that hadronic observables show a much lesser sensitivity to these aspects. We conclude that electromagnetic observables allow access to dynamical regions that are beyond the reach of soft hadronic probes.

  4. Probing ultrafast dynamics of condensed matter with pump and probe experiments with X-rays

    Energy Technology Data Exchange (ETDEWEB)

    Giles, Carlos; Celestre, Rafael; Tasca, Kelin R.; Vescovi, Rafael; Faria, Guilherme; Dias, Carlos S.; Tomm, Natasha; Cordeiro, Cristiano M.B. [Universidade Estadual de Campinas (IFGW/UNICAMP), SP (Brazil). Inst. de Fisica Gleb Wataghin; Silva, Rene Nome [Universidade Estadual de Campinas (IQ/UNICAMP), SP (Brazil). Inst. de Quimica

    2012-07-01

    Full text: In this presentation we will describe recent advances in the route to start ultrafast studies with X-rays in Brazil. From one side pump and probe experiments using synchrotron radiation facilities will be described, showing how the thermal expansion of an invar alloy is not occurring at the picosecond time scales after heating the sample with a femtosecond infrared laser pulse. We will also describe the experimental setup at the LNLS in Campinas were we probe the fast response of a piezoelectric material to a 1 ns electric pulse recorded by a pump and probe X-ray diffraction experiment at the XRD2 LNLS beamline. We will also present the first results of the production of sub-picosecond X-ray pulses using an amplified infrared laser at the Ultrafast Laboratory of DEQ/IFGW. The instrumentation developed at UNICAMP together with the first setup for a pump and probe experiment will be presented. Characteristic radiation of various targets (TiK{alpha}, FeK{alpha}, CuK{alpha}) have been measured at a repetition rate of 1 kHz showing unambiguously our capability of producing a pulsed X-ray source for time resolved x-ray diffraction experiments. Experiments to measure the pulse width of the X-ray radiation are under development and the latest results will be presented. All these efforts open the path to the nucleation of a research group in ultrafast studies using X-rays in Brazil. (author)

  5. Probing attosecond pulse structures by XUV-induced hole dynamics

    CERN Document Server

    You, Jhih-An; Dahlström, Jan Marcus

    2015-01-01

    We investigate a two-photon ionization process in neon by an isolated attosecond pump pulse and two coherent extreme ultraviolet probe fields. The probe fields, tuned to the 2s-2p transition in the residual ion, allow for coherent control of the photoelectron via indirect interactions with the hole. We show that the photoelectron-ion coincidence signal contains an interference pattern that can be used to reconstruct the temporal structure of attosecond pump pulses. Our results are supported by simulations based on time-dependent configuration-interaction singles and lowest-order perturbation theory within second quantization.

  6. Dynamic Range Selection in Linear Space

    CERN Document Server

    He, Meng; Nicholson, Patrick K

    2011-01-01

    Given a set $S$ of $n$ points in the plane, we consider the problem of answering range selection queries on $S$: that is, given an arbitrary $x$-range $Q$ and an integer $k > 0$, return the $k$-th smallest $y$-coordinate from the set of points that have $x$-coordinates in $Q$. We present a linear space data structure that maintains a dynamic set of $n$ points in the plane with real coordinates, and supports range selection queries in $O((\\lg n / \\lg \\lg n)^2)$ time, as well as insertions and deletions in $O((\\lg n / \\lg \\lg n)^2)$ amortized time. The space usage of this data structure is an $\\Theta(\\lg n / \\lg \\lg n)$ factor improvement over the previous best result, while maintaining asymptotically matching query and update times. We also present the first succinct data structure that supports range selection queries on a dynamic array of $n$ values drawn from a bounded universe.

  7. Hybridization probe for femtomolar quantification of selected nucleic acid sequences on a disposable electrode.

    Science.gov (United States)

    Jenkins, Daniel M; Chami, Bilal; Kreuzer, Matthias; Presting, Gernot; Alvarez, Anne M; Liaw, Bor Yann

    2006-04-01

    Mixed monolayers of electroactive hybridization probes on gold surfaces of a disposable electrode were investigated as a technology for simple, sensitive, selective, and rapid gene identification. Hybridization to the ferrocene-labeled hairpin probes reproducibly diminished cyclic redox currents, presumably due to a displacement of the label from the electrode. Observed peak current densities were roughly 1000x greater than those observed in previous studies, such that results could easily be interpreted without the use of algorithms to correct for background polarization currents. Probes were sensitive to hybridization with a number of oligonucleotide sequences with varying homology, but target oligonucleotides could be distinguished from competing nontarget sequences based on unique "melting" profiles from the probe. Detection limits were demonstrated down to nearly 100 fM, which may be low enough to identify certain genetic conditions or infections without amplification. This technology has rich potential for use in field devices for gene identification as well as in gene microarrays.

  8. A new diketopyrrolopyrrole-based probe for sensitive and selective detection of sulfite in aqueous solution

    Science.gov (United States)

    Yang, Xiaofeng; Cui, Yu; Li, Yexin; Zheng, Luyi; Xie, Lijun; Ning, Rui; Liu, Zheng; Lu, Junling; Zhang, Gege; Liu, Chunxiang; Zhang, Guangyou

    2015-02-01

    A new probe was synthesized by incorporating an α,β -unsaturated ketone to a diketopyrrolopyrrole fluorophore. The probe had exhibited a selective and sensitive response to the sulfite against other thirteen anions and biothiols (Cys, Hcy and GSH), through the nucleophilic addition of sulfite to the alkene of probe with the detection limit of 0.1 μM in HEPES (10 mM, pH 7.4) THF/H2O (1:1, v/v). Meanwhile, it could be easily observed that the probe for sulfite changed from pink to colorless by the naked eye, and from pink to blue under UV lamp after the sulfite was added for 20 min. The NMR and Mass spectral analysis demonstrated the expected addition of sulfite to the Cdbnd C bonds.

  9. Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates

    Directory of Open Access Journals (Sweden)

    Najmul Arfin

    2013-11-01

    Full Text Available The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement ⟨R2⟩ exhibits a scaling with time as ⟨R2⟩ ∼ tα, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t, which follows the scaling, S(t ∼ tβ/ln (t. Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.

  10. Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates

    Science.gov (United States)

    Arfin, Najmul; Yadav, Avinash Chand; Bohidar, H. B.

    2013-11-01

    The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement ⟨R2⟩ exhibits a scaling with time as ⟨R2⟩ ˜ tα, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ˜ tβ/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.

  11. Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates

    Energy Technology Data Exchange (ETDEWEB)

    Arfin, Najmul [Polymer and Biophysics Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067 (India); Yadav, Avinash Chand [Nonlinear Dynamics Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067 (India); Bohidar, H. B., E-mail: bohi0700@mail.jnu.ac.in [Polymer and Biophysics Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067 (India); Special Centre for Nanosciences, Jawaharlal Nehru University, New Delhi-110067 (India)

    2013-11-15

    The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement 〈R{sup 2}〉 exhibits a scaling with time as 〈R{sup 2}〉 ∼ t{sup α}, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ∼ t{sup β}/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.

  12. Hydrazine selective dual signaling chemodosimetric probe in physiological conditions and its application in live cells

    Energy Technology Data Exchange (ETDEWEB)

    Nandi, Sandip; Sahana, Animesh; Mandal, Sandip [Department of Chemistry, The University of Burdwan, Burdwan, 713104 West Bengal (India); Sengupta, Archya; Chatterjee, Ansuman [Department of Zoology, Visva Bharati University, Santiniketan, West Bengal (India); Safin, Damir A., E-mail: damir.a.safin@gmail.com [Institute of Condensed Matter and Nanosciences, Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Place L. Pasteur 1, 1348 Louvain-la-Neuve (Belgium); Babashkina, Maria G.; Tumanov, Nikolay A.; Filinchuk, Yaroslav [Institute of Condensed Matter and Nanosciences, Molecules, Solids and Reactivity (IMCN/MOST), Université catholique de Louvain, Place L. Pasteur 1, 1348 Louvain-la-Neuve (Belgium); Das, Debasis, E-mail: ddas100in@yahoo.com [Department of Chemistry, The University of Burdwan, Burdwan, 713104 West Bengal (India)

    2015-09-17

    A rhodamine–cyanobenzene conjugate, (E)-4-((2-(3′,6′-bis(diethylamino)-3-oxospiro[isoindoline-1,9′-xanthene] -2-yl)ethylimino)methyl)benzonitrile (1), which structure has been elucidated by single crystal X-ray diffraction, was synthesized for selective fluorescent “turn-on” and colorimetric recognition of hydrazine at physiological pH 7.4. It was established that 1 detects hydrazine up to 58 nM. The probe is useful for the detection of intracellular hydrazine in the human breast cancer cells MCF-7 using a fluorescence microscope. Spirolactam ring opening of 1, followed by its hydrolysis, was established as a probable mechanism for the selective sensing of hydrazine. - Highlights: • A selective rhodamine–cyanobenzene conjugate is synthesized. • The conjugate is a selective dual signaling chemodosimetric probe towards hydrazine. • Spirolactam ring opening of the probe, followed by its hydrolysis, is the sensing mechanism. • The probe detects hydrazine in the human breast cancer cells MCF-7 imaging.

  13. Lipid-Bilayer Dynamics Probed by a Carbon Dot-Phospholipid Conjugate.

    Science.gov (United States)

    Nandi, Sukhendu; Malishev, Ravit; Bhunia, Susanta Kumar; Kolusheva, Sofiya; Jopp, Jürgen; Jelinek, Raz

    2016-05-10

    Elucidating the dynamic properties of membranes is important for understanding fundamental cellular processes and for shedding light on the interactions of proteins, drugs, and viruses with the cell surface. Dynamic studies of lipid bilayers have been constrained, however, by the relatively small number of pertinent molecular probes and the limited physicochemical properties of the probes. We show that a lipid conjugate comprised of a fluorescent carbon dot (C-dot) covalently attached to a phospholipid constitutes a versatile and effective vehicle for studying bilayer dynamics. The C-dot-modified phospholipids readily incorporated within biomimetic membranes, including solid-supported bilayers and small and giant vesicles, and inserted into actual cellular membranes. We employed the C-dot-phospholipid probe to elucidate the effects of polymyxin-B (a cytolytic peptide), valproic acid (a lipophilic drug), and amyloid-β (a peptide associated with Alzheimer's disease) upon bilayer fluidity and lipid dynamics through the application of various biophysical techniques.

  14. A highly selective and sensitive fluorescence probe for the hypochlorite anion.

    Science.gov (United States)

    Chen, Xinqi; Wang, Xiaochun; Wang, Shujuan; Shi, Wen; Wang, Ke; Ma, Huimin

    2008-01-01

    A new rhodamine B-based fluorescent probe for the hypochlorite anion (OCl(-)) has been designed, synthesized, and characterized. The probe comprises a spectroscopic unit of rhodamine B and an OCl(-)-specific reactive moiety of dibenzoylhydrazine. The probe itself is nearly nonfluorescent because of its spirolactam structure. Upon reaction with OCl(-), however, a largely enhanced fluorescence is produced due to the opening of the spirolactam ring by the oxidation of the exocyclic hydrazide and subsequently the formation of the hydrolytic product rhodamine B. Most notably, the fluorescence-on reaction shows high sensitivity and extremely high selectivity for OCl(-) over other common ions and oxidants, which makes it possible for OCl(-) to be detected directly in their presence. In addition, the reaction mechanism has been investigated and proposed. The OCl(-) anion selectively oxidizes the hydrazo group in the probe, and forms the analogue of dibenzoyl diimide, which in turn hydrolyzes and releases the fluorophore. The reaction mechanism that is described here might be useful in developing excellent spectroscopic probes with cleavable active bonds for other species.

  15. Digital Image Correlation with Dynamic Subset Selection

    Science.gov (United States)

    Hassan, Ghulam Mubashar; MacNish, Cara; Dyskin, Arcady; Shufrin, Igor

    2016-09-01

    The quality of the surface pattern and selection of subset size play a critical role in achieving high accuracy in Digital Image Correlation (DIC). The subset size in DIC is normally selected by testing different subset sizes across the entire image, which is a laborious procedure. This also leads to the problem that the worst region of the surface pattern influences the performance of DIC across the entire image. In order to avoid these limitations, a Dynamic Subset Selection (DSS) algorithm is proposed in this paper to optimize the subset size for each point in an image before optimizing the correlation parameters. The proposed DSS algorithm uses the local pattern around the point of interest to calculate a parameter called the Intensity Variation Ratio (Λ), which is used to optimize the subset size. The performance of the DSS algorithm is analyzed using numerically generated images and is compared with the results of traditional DIC. Images obtained from laboratory experiments are also used to demonstrate the utility of the DSS algorithm. Results illustrate that the DSS algorithm provides a better alternative to subset size "guessing" and finds an appropriate subset size for each point of interest according to the local pattern.

  16. Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases

    Directory of Open Access Journals (Sweden)

    Juan A. González-Vera

    2015-11-01

    Full Text Available Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes.

  17. Ultrafast pump-probe dynamics of iron oxide based earth pigments for applications to ancient pottery manufacture

    Science.gov (United States)

    Villafana, Tana E.; Brown, William; Warren, Warren S.; Fischer, Martin

    2015-06-01

    We demonstrate that ultrafast pump-probe microscopy provides unique dynamics for natural iron oxide and iron hydroxide earth pigments, despite their chemical similarity. First, we conducted a pump-probe spectroscopy study on heat-treated hematite (the pure red iron oxide mineral) and found the pump-probe dynamics to be temperature dependent. Second, we investigated pottery fired under known conditions and observed firing dependent pump-probe dynamics. Finally, we imaged a New World potshard from the North Carolina Museum of Art. Our results indicate that pump-probe microscopy could be a useful tool in elucidating pottery manufacture.

  18. Effect of disorder on ultrafast exciton dynamics probed by single molecule spectroscopy

    OpenAIRE

    Hernando Campos, Jordi; van Dijk, Erik M. H. P.; Hoogenboom, Jacob P.; García López, Juan José; Reinhoudt, David N.; Crego Calama, Mercedes; García Parajó, María F.; van Hulst, Niek F.

    2006-01-01

    We present a single-molecule study unraveling the effect of static disorder on the vibrational-assisted ultrafast exciton dynamics in multichromophoric systems. For every single complex, we probe the initial exciton relaxation process by an ultrafast pump-probe approach and the coupling to vibrational modes by emission spectra, while fluorescence lifetime analysis measures the amount of static disorder. Exploiting the wide range of disorder found from complex to complex, we demonstrate that s...

  19. Probing Li-ion Dynamics and Reactivity on the Nanoscale

    Energy Technology Data Exchange (ETDEWEB)

    Kalinin, Sergei V [ORNL; Balke, Nina [ORNL; Jesse, Stephen [ORNL; Tselev, Alexander [ORNL; Kumar, Amit [ORNL; Arruda, Thomas M [ORNL; Guo, Senli [ORNL; Proksch, Roger [Asylum Research, Santa Barbara, CA

    2011-01-01

    Progress in development and optimization of energy storage and conversion materials necessitates understanding their ionic and electrochemical functionality on the nanometer scale level of single grain cluster, grain, or extended defect. Classical electrochemical strategies based on Faradaic current detection are fundamentally limited on the nanoscale. Here, we review principles and recent applications of Electrochemical Strain Microscopy (ESM), a scanning probe microscopy (SPM) technique utilizing intrinsic coupling between ionic pehnomena and molar volumes. ESM imaging, as well as time and voltage spectroscopies, are illustrated for several Li-ion cathode and anode materials. Perspectives for future ESM development and applications to other ionic systems are discussed.

  20. Valley Carrier Dynamics in Monolayer Molybdenum Disulphide from Helicity Resolved Ultrafast Pump-probe Spectroscopy

    CERN Document Server

    Wang, Qinsheng; Li, Xiao; Qiu, Jun; Ji, Yanxin; Feng, Ji; Sun, Dong

    2013-01-01

    We investigate the valley related carrier dynamics in monolayer MoS2 using helicity resolved non-degenerate ultrafast pump-probe spectroscopy at the vicinity of the high-symmetry K point under the temperature down to 78 K. Monolayer MoS2 shows remarkable transient reflection signals, in stark contrast to bilayer and bulk MoS2 due to the enhancement of many-body effect at reduced dimensionality. The helicity resolved ultrafast time-resolved result shows that the valley polarization is preserved for only several ps before scattering process makes it undistinguishable. We suggest that the dynamical degradation of valley polarization is attributable primarily to the exciton trapping by defect states in the exfoliated MoS2 samples. Our experiment and a tight-binding model analysis also show that the perfect valley CD selectivity is fairly robust against disorder at the K point, but quickly decays from the high-symmetry point in the momentum space in the presence of disorder.

  1. Fabrication and buckling dynamics of nanoneedle AFM probes

    Energy Technology Data Exchange (ETDEWEB)

    Beard, J D; Gordeev, S N, E-mail: jdb28@bath.ac.uk [Department of Physics, University of Bath, Claverton Down, Bath BA2 7AY (United Kingdom)

    2011-04-29

    A new method for the fabrication of high-aspect-ratio probes by electron beam induced deposition is described. This technique allows the fabrication of cylindrical 'nanoneedle' structures on the atomic force microscope (AFM) probe tip which can be used for accurate imaging of surfaces with high steep features. Scanning electron microscope (SEM) imaging showed that needles with diameters in the range of 18-100 nm could be obtained by this technique. The needles were shown to undergo buckling deformation under large tip-sample forces. The deformation was observed to recover elastically under vertical deformations of up to {approx} 60% of the needle length, preventing damage to the needle. A technique of stabilizing the needle against buckling by coating it with additional electron beam deposited carbon was also investigated; it was shown that coated needles of 75 nm or greater total diameter did not buckle even under tip-sample forces of {approx} 1.5 {mu}N.

  2. A new hydroxynaphthyl benzothiazole derived fluorescent probe for highly selective and sensitive Cu2 + detection

    Science.gov (United States)

    Tang, Lijun; He, Ping; Zhong, Keli; Hou, Shuhua; Bian, Yanjiang

    2016-12-01

    A new reactive probe, 1-(benzo[d]thiazol-2-yl)naphthalen-2-yl-picolinate (BTNP), was designed and synthesized. BTNP acts as a highly selective probe to Cu2 + in DMSO/H2O (7/3, v/v, Tris-HCl 10 mM, pH = 7.4) solution based on Cu2 + catalyzed hydrolysis of the picolinate ester moiety in BTNP, which leads to the formation of an ESIPT active product with dual wavelength emission enhancement. The probe also possesses the advantages of simple synthesis, rapid response and high sensitivity. The pseudo-first-order reaction rate constant was calculated to be 0.205 min- 1. Moreover, application of BTNP to Cu2 + detection in living cells and real water samples was also explored.

  3. Optical probing of sodium dynamics in neurons and astrocytes.

    Science.gov (United States)

    Lamy, Christophe M; Chatton, Jean-Yves

    2011-09-15

    Changes in intracellular Na(+) concentration underlie essential neurobiological processes, but few reliable tools exist for their measurement. Here we characterize a new synthetic Na(+)-sensitive fluorescent dye, Asante Natrium Green (ANG), with unique properties. This indicator was excitable in the visible spectrum and by two-photon illumination, suffered little photobleaching and located to the cytosol were it remained for long durations without noticeable unwanted effects on basic cell properties. When used in brain tissue, ANG yielded a bright fluorescent signal during physiological Na(+) responses both in neurons and astrocytes. Synchronous electrophysiological and fluorometric recordings showed that ANG produced accurate Na(+) measurement in situ. This new Na(+) indicator opens innovative ways of probing neuronal circuits.

  4. Stability mechanisms of a thermophilic laccase probed by molecular dynamics

    DEFF Research Database (Denmark)

    Christensen, Niels Johan; Kepp, Kasper Planeta

    2013-01-01

    to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor...... of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K), probing structural changes associated with enthalpy-entropy compensation....... Approaching T opt (∼350 K) from 300 K, this change correlated with a beginning "unzipping" of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F(-) (but not Cl...

  5. A Thomson parabola ion imaging spectrometer designed to probe relativistic intensity ionization dynamics of nanoclusters.

    Science.gov (United States)

    Rajeev, R; Rishad, K P M; Trivikram, T Madhu; Narayanan, V; Krishnamurthy, M

    2011-08-01

    Conventional techniques of probing ionization dynamics at relativistic intensities for extended target systems such as clusters are difficult both due to problems of achieving good charge resolution and signal integration over the focal volume. Simultaneous measurement of arrival time, necessary for these systems, has normally involved complicated methods. We designed and developed a Thomson parabola imaging spectrometer that overcomes these problems. Intensity sampling method evolved in this report is proved to be mandatory for probing ionization dynamics of clusters at relativistic intensities. We use this method to measure charge resolved kinetic energy spectra of argon nanoclusters at intensities of 4 × 10(18) W cm(-2).

  6. A Thomson parabola ion imaging spectrometer designed to probe relativistic intensity ionization dynamics of nanoclusters

    Science.gov (United States)

    Rajeev, R.; Rishad, K. P. M.; Trivikram, T. Madhu; Narayanan, V.; Krishnamurthy, M.

    2011-08-01

    Conventional techniques of probing ionization dynamics at relativistic intensities for extended target systems such as clusters are difficult both due to problems of achieving good charge resolution and signal integration over the focal volume. Simultaneous measurement of arrival time, necessary for these systems, has normally involved complicated methods. We designed and developed a Thomson parabola imaging spectrometer that overcomes these problems. Intensity sampling method evolved in this report is proved to be mandatory for probing ionization dynamics of clusters at relativistic intensities. We use this method to measure charge resolved kinetic energy spectra of argon nanoclusters at intensities of 4 × 1018 W cm-2.

  7. Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics Simulations

    Science.gov (United States)

    2008-07-17

    Medical Research and Materiel Command, Fort Detrick, Maryland #Department of Cell Biology and Biochemistry , U.S. Army Medical Research Institute of...Molecular dynamics of n- alkanes ," J. Comput. Phys., vol. 23, pp. 327-341, 1977. [24] S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M

  8. Decoherence as a Probe of Coherent Quantum Dynamics

    CERN Document Server

    D'Arcy, M B; Summy, G S; Guarneri, I; Wimberger, S M; Fishman, S; Buchleitner, A; Arcy, Michael B. d'; Godun, Rachel M.; Summy, Gil S.; Guarneri, Italo; Wimberger, Sandro; Fishman, Shmuel; Buchleitner, Andreas

    2004-01-01

    The effect of decoherence, induced by spontaneous emission, on the dynamics of periodically kicked cold atoms at quantum resonance is experimentally and theoretically studied. We clarify the nature of the coherent evolution, and the way in which decoherence disrupts it, thereby resolving the puzzle of the observed enhancement of the atomic mean energy growth by decoherence [Phys. Rev. Lett. 87, 074102 (2001)].

  9. Hard gammas as a probe of nuclear dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Coniglione, R.; Sapienza, P.; Alba, R.; Agodi, C.; Maiolino, C.; Zoppo, A. Del; Colonna, M.; Bellia, G.; Finocchiaro, C.; Greco, V.; Loukachine, K.; Migneco, E.; Piattelli, P.; Santonocito, D. [INFN, Laboratorio Nazionale del Sud, Via A. Doria 44, Catania (Italy); Colonna, N. [INFN, Bari (Italy); Bruno, M.; D' Agostino, M.; Mastinu, P.F.; Vannini, G. [INFN and Dipartimento di Fisica, Bologna (Italy); Gramegna, F. [INFN, Laboratorio Nazionale di Legnaro, Padova (Italy); Iori, I.; Fabbietti, L.; Moroni, A. [INFN and Dipartimento di Fisica, Milano (Italy); Margagliotti, G.V.; Milazzo, P.M.; Rui, R. [INFN and Dipartimento di Fisica, Trieste (Italy); Blumenfeld, Y.; Scarpaci, J.A. [Institut de Physique Nucleaire, IN 2P 3 CNRS, F 91406 Orsay (France)

    2001-09-01

    Full text: Heavy ion collisions around the Fermi energy allow to investigate properties of nuclear matter far from stability at high density and temperature. To improve the comprehension of heavy ion reactions in these extreme conditions and to gather information on the EOS of nuclear matter, knowledge on the dynamics of the reactions is needed. It is well known that, in heavy ion reactions, hard gammas (E > 20 MeV) are mainly produced as Bremsstrahlung radiation in the n-p collisions occurring in the interaction zone. With the aim to study the reaction dynamics, that is strongly influenced by two body collisions, the energetic gamma emission has been measured for several reactions induced by {sup 58}Ni beams at 30 and 45 MeV/u performed with MEDEA and MULTICS apparatus (1) at the Laboratori Nazionali del Sud (Catania-Italy). An analysis in terms of energetic gammas, heavy residues and intermediate mass fragments and comparison with dynamical calculations, that explore the entire reaction dynamics, will be presented. (Author)

  10. Dynamic characterization of small fibers based on the flexural vibrations of a piezoelectric cantilever probe

    Science.gov (United States)

    Zhang, Xiaofei; Ye, Xuan; Li, Xide

    2016-08-01

    In this paper, we present a cantilever-probe system excited by a piezoelectric actuator, and use it to measure the dynamic mechanical properties of a micro- and nanoscale fiber. Coupling the fiber to the free end of the cantilever probe, we found the dynamic stiffness and damping coefficient of the fiber from the resonance frequency and the quality factor of the fiber-cantilever-probe system. The properties of Bacillus subtilis fibers measured using our proposed system agreed with tensile measurements, validating our method. Our measurements show that the piezoelectric actuator coupled to cantilever probe can be made equivalent to a clamped cantilever with an effective length, and calculated results show that the errors of measured natural frequency of the system can be ignored if the coupled fiber has an inclination angle of alignment of less than 10°. A sensitivity analysis indicates that the first or second resonant mode is the sensitive mode to test the sample’s dynamic stiffness, while the damping property has different sensitivities for the first four modes. Our theoretical analysis demonstrates that the double-cantilever probe is also an effective sensitive structure that can be used to perform dynamic loading and characterize dynamic response. Our method has the advantage of using amplitude-frequency curves to obtain the dynamic mechanical properties without directly measuring displacements and forces as in tensile tests, and it also avoids the effects of the complex surface structure and deformation presenting in contact resonance method. Our method is effective for measuring the dynamic mechanical properties of fiber-like one-dimensional (1D) materials.

  11. Probing Molecular Organization and Electronic Dynamics at Buried Organic Interfaces

    Science.gov (United States)

    Roberts, Sean

    2015-03-01

    Organic semiconductors are a promising class of materials due to their ability to meld the charge transport capabilities of semiconductors with many of the processing advantages of plastics. In thin film organic devices, interfacial charge transfer often comprises a crucial step in device operation. As molecular materials, the density of states within organic semiconductors often reflect their intermolecular organization. Truncation of the bulk structure of an organic semiconductor at an interface with another material can lead to substantial changes in the density of states near the interface that can significantly impact rates for interfacial charge and energy transfer. Here, we will present the results of experiments that utilize electronic sum frequency generation (ESFG) to probe buried interfaces in these materials. Within the electric dipole approximation, ESFG is only sensitive to regions of a sample that experience a breakage of symmetry, which occurs naturally at material interfaces. Through modeling of signals measured for thin organic films using a transfer matrix-based formalism, signals from buried interfaces between two materials can be isolated and used to uncover the interfacial density of states.

  12. Probing the structural dynamics of proteins and nucleic acids with optical tweezers.

    Science.gov (United States)

    Ritchie, Dustin B; Woodside, Michael T

    2015-10-01

    Conformational changes are an essential feature of most molecular processes in biology. Optical tweezers have emerged as a powerful tool for probing conformational dynamics at the single-molecule level because of their high resolution and sensitivity, opening new windows on phenomena ranging from folding and ligand binding to enzyme function, molecular machines, and protein aggregation. By measuring conformational changes induced in a molecule by forces applied by optical tweezers, new insight has been gained into the relationship between dynamics and function. We discuss recent advances from studies of how structure forms in proteins and RNA, including non-native structures, fluctuations in disordered proteins, and interactions with chaperones assisting native folding. We also review the development of assays probing the dynamics of complex protein-nucleic acid and protein-protein assemblies that reveal the dynamic interactions between biomolecular machines and their substrates.

  13. METHODS OF SOIL TESTING BY UNIVERSAL DYNAMIC PROBE OF LRN & TP

    Directory of Open Access Journals (Sweden)

    SEDIN V. L.

    2016-02-01

    Full Text Available Problem statement. Nowadays the survey organizations need in facilities of light type not being produced mass.But they are necessary for the accelerated testing of soil with the possibility of use in cramped conditions. Described below probe and test procedures is one of the possible solutions to this problem. Purpose. To acquaint with a description of the constructional features and testing methods of soil dynamic universal probe, developed in the laboratory of research of nuclear and thermal power plants (LRNTP of Pridneprovsk scientific and educational institution of innovative technologies in construction. Conclusion. The proposed probe intended to determine the mechanical properties of soils and allows to provide the express assessment of the soil properties of natural foundations to explore the changes of the properties of soil foundation under the operative objects in the process of their operation. Universal feature of the probe is the possibility to use disposable standard cones and of the composite construction of hammer (if it is necessary to reduce the weight of the hammer. As well as the possibility of carrying out tests on foreign standards, in particular on standard for the SPT (Standard Probe Test. Results of probing are drawn up as a standard continuous step schedule of change of depth value of conditional dynamic resistance of soils Pq, followed by averaging schedule and calculating of weighted index of probing for each layer land constructions. This probe and the following technique, fill a niche of the lack of manual small facilities and can contribute to the expansion of technical capabilities of survey organizations.

  14. Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

    Science.gov (United States)

    Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

  15. Investigation Solvation Dynamics and Isomerization of Dye IR-140 Using pump supercontinuum-probing Technique

    CERN Document Server

    Wang, D; Wu, S; Yang, H; Xiang, Q G J; Xu, G; Wang, Danling; Jiang, Hongbing; Wu, Songjiang; Yang, Hong; Xiang, Qihuang Gong Junfeng; Xu, Guangzhi

    2001-01-01

    The solvation dynamics and isomerization process of an organic dye, IR-140, in polar solvents and nonpolar solvents have been investigated using pump supercontinuum-probing (PSCP) technique. In all solvents, the dynamics exhibits solvent-dependent. Solvent induced spectral shifts of the absorption and emission spectra of IR-140 have also been studied in a variety of solvents. At the same time, the photoisomerization process has been examined. The approximate energy-band structure of IR-140 was also supposed firstly.

  16. Dynamic nuclear polarization studies on deuterated nitroxyl spin probes.

    Science.gov (United States)

    David Jebaraj, D; Utsumi, Hideo; Milton Franklin Benial, A

    2017-10-01

    Detailed dynamic nuclear polarization and electron spin resonance studies were carried out for 3-carbamoyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl, 3-carboxy-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl,3-methoxycarbonyl-2,2,5,5-tetramethy pyrolidine-1-oxyl nitroxyl radicals and their corresponding deuterated nitroxyl radicals, used in Overhauser-enhanced magnetic resonance imaging for the first time. The dynamic nuclear polarization parameters such as dynamic nuclear polarization (DNP) factor, longitudinal relaxivity, saturation parameter, leakage factor and coupling factor were estimated for deuterated nitroxyl radicals. DNP enhancement increases with agent concentration up to 3 mm and decreases above 3 mm. The proton spin-lattice relaxation time and the longitudinal relaxivity parameters were estimated. The leakage factor increases with increasing agent concentration up to 3 mm and reaches plateau in the region 3-5 mm. The coupling parameter shows the interaction between the electron and nuclear spins to be mainly dipolar in origin. DNP spectrum exhibits that the full width at half maximum values are higher for undeuterated nitroxyl radicals compared with deuterated nitroxyl radicals, which leads to the increase in DNP enhancement. The ESR parameters such as, the line width, line shape, signal intensity ratio, rotational correlation time, hyperfine coupling constant and g-factor were calculated. The narrow line width was observed for deuterated nitroxyl radicals compared with undeuterated nitroxyl radicals, which leads to the higher saturation parameter value and DNP enhancement. The novelty of the work permits clear understanding of the DNP parameters determining the higher DNP enhancement compared with the undeuterated nitroxyl radicals. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  17. Real-Time Probing of Structural Dynamics by Interaction between Chromophores

    DEFF Research Database (Denmark)

    Brogaard, Rasmus Y.; Møller, Klaus Braagaard; Sølling, Theis Ivan

    2011-01-01

    We present an investigation of structural dynamics in excited-state cations probed in real-time by femtosecond timeresolved ion photofragmentation spectroscopy. From photoelectron spectroscopy data on 1,3-dibromopropane we conclude that the pump pulse ionizes the molecule, populating an excited...

  18. Investigation on Dynamic Calibration for an Optical-Fiber Solids Concentration Probe in Gas-Solid Two-Phase Flows

    OpenAIRE

    Changsui Zhao; Liu Shen; Pan Xu; Xiaoping Chen; Daoyin Liu; Cai Liang; Guiling Xu

    2013-01-01

    This paper presents a review and analysis of the research that has been carried out on dynamic calibration for optical-fiber solids concentration probes. An introduction to the optical-fiber solids concentration probe was given. Different calibration methods of optical-fiber solids concentration probes reported in the literature were reviewed. In addition, a reflection-type optical-fiber solids concentration probe was uniquely calibrated at nearly full range of the solids concentration from 0...

  19. Probing C84-embedded Si Substrate Using Scanning Probe Microscopy and Molecular Dynamics.

    Science.gov (United States)

    Ho, Mon-Shu; Huang, Chih-Pong; Tsai, Jyun-Hwei; Chou, Che-Fu; Lee, Wen-Jay

    2016-09-28

    This paper reports an array-designed C84-embedded Si substrate fabricated using a controlled self-assembly method in an ultra-high vacuum chamber. The characteristics of the C84-embedded Si surface, such as atomic resolution topography, local electronic density of states, band gap energy, field emission properties, nanomechanical stiffness, and surface magnetism, were examined using a variety of surface analysis techniques under ultra, high vacuum (UHV) conditions as well as in an atmospheric system. Experimental results demonstrate the high uniformity of the C84-embedded Si surface fabricated using a controlled self-assembly nanotechnology mechanism, represents an important development in the application of field emission display (FED), optoelectronic device fabrication, MEMS cutting tools, and in efforts to find a suitable replacement for carbide semiconductors. Molecular dynamics (MD) method with semi-empirical potential can be used to study the nanoindentation of C84-embedded Si substrate. A detailed description for performing MD simulation is presented here. Details for a comprehensive study on mechanical analysis of MD simulation such as indentation force, Young's modulus, surface stiffness, atomic stress, and atomic strain are included. The atomic stress and von-Mises strain distributions of the indentation model can be calculated to monitor deformation mechanism with time evaluation in atomistic level.

  20. Molecular Frame Photoemission: Probe of the Photoionization Dynamics for Molecules in the Gas Phase

    Institute of Scientific and Technical Information of China (English)

    D. Dowek; Y. J. Picard; P. Billaud; C. Elkharrat; J. C. Houver

    2009-01-01

    Molecular frame photoemission is a very sensitive probe of the photoionization (PI) dynamics of molecules. This paper reports a comparative study of non-resonant and resonant photoionization of D2 induced by VUV circularly polarized synchrotron radiation at SOLEIL at the level of the molecular frame photoelectron angular distributions (MFPADs). We use the vector correlation method which combines imaging and time-of-flight resolved electron-ion coincidence techniques, and a generalized formalism for the expression of the I(X, θe,φe)MFPADs.where X is the orientation of the molecular axis with respect to the light quantization axis and (θe,φe) the electron emission direction in the molecular frame. Selected MFPADs for a molecule aligned parallel or perpendicular to linearly polarized light, or perpendicular to the propagation axis of circularly polarizcd light, are presented for dissociative photoionization (DPI) of D2 at two photon excitation energies, hv=19 eV, where direct PI is the only channel opened, and hv=32.5 eV, i.e. in the region involving resonant excitation of Q1 and Q2 doubly excited state series. We discuss in particular the properties of the circular dichroism characterizing photoemission in the molecular frame for direct and resonant PI. In the latter case, a remarkable behavior is observed which may be attributed to the interference occurring between undistinguishable autoionization decay channels.

  1. Can causal dynamical triangulations probe factor-ordering issues?

    CERN Document Server

    Maitra, R L

    2009-01-01

    The causal dynamical triangulations (CDT) program has for the first time allowed for path-integral computation of correlation functions in full general relativity without symmetry reductions and taking into account Lorentzian signature. One of the most exciting recent results in CDT is the strong agreement of these computations with (minisuperspace) path integral calculations in quantum cosmology. Herein I will describe my current project to compute minisuperspace (Friedman-Robertson-Walker) path integrals with a range of different measures corresponding to various factor orderings of the Friedman-Robertson-Walker Hamiltonian. The aim is to compare with CDT results and ask whether CDT can shed light on factor-ordering ambiguities in quantum cosmology models.

  2. A magmatic probe of dynamic topography beneath western North America

    Science.gov (United States)

    Klöcking, M.; White, N. J.; Maclennan, J.

    2014-12-01

    A region centered on the Yellowstone hotspot and encompassing the Colorado Plateau sits at an elevation 2 km higher than the cratonic North America. This difference broadly coincides with tomographically observed variations in lithospheric thickness: ~120 km beneath western North America, ~240 km beneath the craton. Thermochronology of the Grand Canyon area, sedimentary flux to the Gulf of Mexico, and river profile inversion all suggest that regional uplift occurred in at least two separate stages. High resolution seismic tomographic models, using USArray data, have identified a ring of low velocity material beneath the edges of the Colorado Plateau. Magmatism coincides with these low velocity zones and shows distinct phases: an overall increase in volume around 40 Ma and a change from lithospheric to asthenospheric signatures around 5 Ma. Volcanism is also observed to migrate north-east with time. Here, we attempt to integrate these different observations with lithospheric thickness. A dynamic topography model of progressive lithospheric erosion over a hot mantle plume might account for uplift as well as the temporal and spatial distribution of magmatism across western North America. Thinning of the lithosphere around the edges of the Colorado Plateau in combination with the hotter mantle potential temperature of a plume could create isostatic and dynamic uplift as well as allowing for melt production. To test this model, we have analysed around 100 samples from volcanic centers across western North America by ICP-MS for rare earth elements (REE). Most of the samples are younger than 5 Ma, and all of them have previously been analysed by XRF. Using trace element ratios such as La/Yb and Nb/Y we assess depth of melting and melt fraction, respectively. In addition, we use REE inversion modelling to estimate melt fractions as a function of depth and temperature of melting. The results are compared to existing constraints on lithospheric thickness and mantle potential

  3. An Amidochlorin-Based Colorimetric Fluorescent Probe for Selective Cu2+ Detection

    Directory of Open Access Journals (Sweden)

    Wenting Li

    2016-01-01

    Full Text Available The design and synthesis of selective and sensitive chemosensors for the quantification of environmentally and biologically important ionic species has attracted widespread attention. Amidochlorin p6 (ACP; an effective colorimetric and fluorescent probe for copper ions (Cu2+ in aqueous solution derived from methyl pheophorbide-a (MPa was designed and synthesized. A remarkable color change from pale yellow to blue was easily observed by the naked eye upon addition of Cu2+; and a fluorescence quenching was also determined. The research of fluorescent quenching of ACP-Cu2+ complexation showed the detection limit was 7.5 × 10−8 mol/L; which suggested that ACP can act as a high sensitive probe for Cu2+ and can be used to quantitatively detect low levels of Cu2+ in aqueous solution. In aqueous solution the probe exhibits excellent selectivity and sensitivity toward Cu2+ ions over other metal ions (M = Zn2+; Ni2+; Ba2+; Ag+; Co2+; Na+; K+; Mg2+; Cd2+; Pb2+; Mn2+; Fe3+; and Ca2+. The obvious change from pale yellow to blue upon the addition of Cu2+ could make it a suitable “naked eye” indicator for Cu2+.

  4. Heterodyne pump probe measurements of nonlinear dynamics in an indium phosphide photonic crystal cavity

    DEFF Research Database (Denmark)

    Heuck, Mikkel; Combrié, S.; Lehoucq, G.

    2013-01-01

    Using a sensitive two-color heterodyne pump-probe technique, we investigate the carrier dynamics of an InP photonic crystal nanocavity. The heterodyne technique provides unambiguous results for all wavelength configurations, including the degenerate case, which cannot be investigated with the wid...... with the widely used homodyne technique. A model based on coupled mode theory including two carrier distributions is introduced to account for the relaxation dynamics, which is assumed to be governed by both diffusion and recombination.......Using a sensitive two-color heterodyne pump-probe technique, we investigate the carrier dynamics of an InP photonic crystal nanocavity. The heterodyne technique provides unambiguous results for all wavelength configurations, including the degenerate case, which cannot be investigated...

  5. Highly selective "Off-On" fluorescent probe for histidine and its imaging in living cells.

    Science.gov (United States)

    Chen, Tiantian; Yin, Liyan; Huang, Chusen; Qin, Yiqiao; Zhu, Weiping; Xu, Yufang; Qian, Xuhong

    2015-04-15

    A naphthalimide-based fluorescent probe CP has been synthesized with simple steps. It can selectively and sensitively recognize copper ions (Cu(2+)) in HEPES buffer (50mM, pH 7.2). The fluorescence intensity of CP is linearly proportional to the concentration of Cu(2+) ranging from 0-8.3μM (correlation coefficient R(2)=0.9808). The resulted complex CP@Cu can serve as a turn-on fluorescent probe for the detection of histidine and histidine rich proteins in broad pH application range. Upon the addition of histidine, the fluorescence intensity of CP@Cu exhibits a linear correlation with the concentration of histidine ranging from 0-200μM (correlation coefficient R(2)=0.9912). Moreover, CP@Cu has potential for imaging histidine in vitro experiments and has promise in real sample applications with great validity.

  6. Probing bonding and dynamics at heterogeneous adsorbate/graphene interfaces

    Science.gov (United States)

    Mattson, Eric

    Graphene-based materials are becoming an astoundingly promising choice for many relevant technological and environmental applications. Deriving graphene from the reduction of graphene oxide (GO) is becoming a popular and inexpensive route toward the synthesis of these materials. While the desired product from GO reduction is pristine graphene, defects and residual oxygen functional groups inherited from the parent GO render reduced graphene oxide (RGO) distinct from graphene. In this work, the structure and bonding for GO and RGO is investigated to the end of a working understanding of the composition and properties of these materials. In situ selected area electron diffraction and ex situ IR microspectroscopy are used to study, respectively, thermal and chemical reduction of GO. The residual oxygen functional groups are found to be predominantly epoxide, C-O-C, bonded oxygen. The role of these oxygen functional groups and the collective RGO in gas sensing applications is investigated by performing in situ IR spectromicroscopy studies of molecular adsorption onto RGO. NO2 and NH3 are the target molecules of interest; NH3 due to its widespread use in industry and NO2 is a a common byproducts in combustion reactions. Following adsorption of both molecules, numerous species are identified on the surface due to the heterogeneity of the substrate. Residual epoxide groups participate in reactions with the target molecules to produce additional surface species that have varying impacts on the conductivity of the substrate.

  7. Metal-organic framework based highly selective fluorescence turn-on probe for hydrogen sulphide

    Science.gov (United States)

    Nagarkar, Sanjog S.; Saha, Tanmoy; Desai, Aamod V.; Talukdar, Pinaki; Ghosh, Sujit K.

    2014-11-01

    Hydrogen sulphide (H2S) is known to play a vital role in human physiology and pathology which stimulated interest in understanding complex behaviour of H2S. Discerning the pathways of H2S production and its mode of action is still a challenge owing to its volatile and reactive nature. Herein we report azide functionalized metal-organic framework (MOF) as a selective turn-on fluorescent probe for H2S detection. The MOF shows highly selective and fast response towards H2S even in presence of other relevant biomolecules. Low cytotoxicity and H2S detection in live cells, demonstrate the potential of MOF towards monitoring H2S chemistry in biological system. To the best of our knowledge this is the first example of MOF that exhibit fast and highly selective fluorescence turn-on response towards H2S under physiological conditions.

  8. The importance of cantilever dynamics in the interpretation of Kelvin probe force microscopy.

    Science.gov (United States)

    Satzinger, Kevin J; Brown, Keith A; Westervelt, Robert M

    2012-09-15

    A realistic interpretation of the measured contact potential difference (CPD) in Kelvin probe force microscopy (KPFM) is crucial in order to extract meaningful information about the sample. Central to this interpretation is a method to include contributions from the macroscopic cantilever arm, as well as the cone and sharp tip of a KPFM probe. Here, three models of the electrostatic interaction between a KPFM probe and a sample are tested through an electrostatic simulation and compared with experiment. In contrast with previous studies that treat the KPFM cantilever as a rigid object, we allow the cantilever to bend and rotate; accounting for cantilever bending provides the closest agreement between theory and experiment. We demonstrate that cantilever dynamics play a major role in CPD measurements and provide a simulation technique to explore this phenomenon.

  9. Novel coumarin-based fluorescent probe for selective detection of Cu(II)

    Science.gov (United States)

    Bekhradnia, Ahmadreza; Domehri, Elham; Khosravi, Masome

    2016-01-01

    We report an efficient and convenient method for preparing nitro-3-carboxamide coumarin derivatives, proposed as novel fluorescent chemosensor, through microwave irradiation. This compound can be used as fluorescent probe for Cu2+ with selectivity over other metal ions in aqueous solution. The fluorescence of 6-nitro-N-[2-(dimethylamino)ethyl]-2-oxo-2H-chromene-3-carboxamide(3) is the highest in the presence of Cu2+, with stronger excitation at λ = 320 nm than for the other cations tested.

  10. A Fast Response Highly Selective Probe for the Detection of Glutathione in Human Blood Plasma

    Directory of Open Access Journals (Sweden)

    Robert M. Strongin

    2012-05-01

    Full Text Available A fluorescent probe for glutathione (GSH detection was developed. Our study indicates a possible mechanism which couples a conjugate addition and micelle-catalyzed large membered ring formation/elimination sequence. This method enables excellent selectivity towards GSH over other biological thiols such as cysteine (Cys and homocysteine (Hcy. The proposed method is precise with a relative standard deviation (R.S.D lower than 6% (n = 3 and has been successfully applied to determine GSH in human plasma with recoveries between 99.2% and 102.3%.

  11. Planar dynamical systems selected classical problems

    CERN Document Server

    Liu, Yirong; Huang, Wentao

    2014-01-01

    This book presents in an elementary way the recent significant developments in the qualitative theory of planar dynamical systems. The subjects are covered as follows: the studies of center and isochronous center problems, multiple Hopf bifurcations and local and global bifurcations of the equivariant planar vector fields which concern with Hilbert's 16th problem. This book is intended for graduate students, post-doctors and researchers in the area of theories and applications of dynamical systems. For all engineers who are interested the theory of dynamical systems, it is also a reasona

  12. A highly selective long-wavelength fluorescent probe for hydrazine and its application in living cell imaging

    Science.gov (United States)

    Hao, Yuanqiang; Zhang, Yintang; Ruan, Kehong; Meng, Fanteng; Li, Ting; Guan, Jinsheng; Du, Lulu; Qu, Peng; Xu, Maotian

    2017-09-01

    A highly selective long-wavelength turn-on fluorescent probe has been developed for the detection of N2H4. The probe was prepared by conjugation the tricyanofuran-based D-π-A system with a recognizing moiety of acetyl group. In the presence of N2H4, the probe can be effectively hydrazinolysized and produce a turn-on fluorescent emission at 610 nm as well as a large red-shift in the absorption spectrum corresponding to a color change from yellow to blue. The sensing mechanism was confirmed by HPLC, MS, UV-vis, emission spectroscopic and theoretical calculation studies. The probe displayed high selectivity and sensitivity for N2H4 with a LOD (limit of detection) of 0.16 μM. Moreover, the probe was successfully utilized for the detection of hydrazine in living cells.

  13. Maximum-Likelihood Sequence Detector for Dynamic Mode High Density Probe Storage

    CERN Document Server

    Kumar, Naveen; Ramamoorthy, Aditya; Salapaka, Murti

    2009-01-01

    There is an ever increasing need for storing data in smaller and smaller form factors driven by the ubiquitous use and increased demands of consumer electronics. A new approach of achieving a few Tb per in2 areal densities, utilizes a cantilever probe with a sharp tip that can be used to deform and assess the topography of the material. The information may be encoded by means of topographic profiles on a polymer medium. The prevalent mode of using the cantilever probe is the static mode that is known to be harsh on the probe and the media. In this paper, the high quality factor dynamic mode operation, which is known to be less harsh on the media and the probe, is analyzed for probe based high density data storage purposes. It is demonstrated that an appropriate level of abstraction is possible that obviates the need for an involved physical model. The read operation is modeled as a communication channel which incorporates the inherent system memory due to the intersymbol interference and the cantilever state ...

  14. Probing the dynamics of Andreev states in a coherent normal/superconducting ring.

    Science.gov (United States)

    Chiodi, F; Ferrier, M; Tikhonov, K; Virtanen, P; Heikkilä, T T; Feigelman, M; Guéron, S; Bouchiat, H

    2011-01-01

    The supercurrent that establishes between two superconductors connected through a normal N mesoscopic link is carried by quasiparticule states localized within the link, the "Andreev bound states (ABS)". Whereas the dc properties of this supercurrent in SNS junctions are now well understood, its dynamical properties are still an unresolved issue. In this letter we probe this dynamics by inductively coupling an NS ring to a multimode superconducting resonator, thereby implementing both a phase bias and current detection at high frequency. Whereas at very low temperatures we essentially measure the phase derivative of the supercurrent, at higher temperature we find a surprisingly strong frequency dependence in the current response of the ring: the ABS do not follow adiabatically the phase modulation. This experiment also illustrates a new tool to probe the fundamental time scales of phase coherent systems that are decoupled from macroscopic normal contacts and thermal baths.

  15. Using XFELs for Probing of Complex Interaction Dynamics of Ultra-Intense Lasers with Solid Matter

    CERN Document Server

    Kluge, Thomas; Huang, Lingen; Metzkes, Josefine; Schramm, Ulrich; Bussmann, Michael; Cowan, Thomas E

    2013-01-01

    We demonstrate the potential of X-ray free-electron lasers (XFEL) to advancethe understanding of complex plasma dynamics by allowing for the first time nanometer and femtosecond resolution at the same time in plasma diagnostics. Plasma phenomena on such short timescales are of high relevance for many fields of physics, in particular in the ultra-intense ultra-short laser interaction with matter. Highly relevant yet only partially understood phenomena may become directly accessible in experiment. These include relativistic laser absorption at solid targets, creation of energetic electrons and electron transport in warm dense matter, including the seeding and development of surface and beam instabilities, ambipolar expansion, shock formation, and dynamics at the surfaces or at buried layers. We demonstrate the potentials of XFEL plasma probing for high power laser matter interactions using exemplary the small angle X-ray scattering technique, focusing on general considerations for XFEL probing.

  16. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes.

    Science.gov (United States)

    Li, Y; Zakharov, D; Zhao, S; Tappero, R; Jung, U; Elsen, A; Baumann, Ph; Nuzzo, R G; Stach, E A; Frenkel, A I

    2015-06-29

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction-ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.

  17. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    Science.gov (United States)

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R. G.; Stach, E. A.; Frenkel, A. I.

    2015-06-01

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction--ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.

  18. Real-time ultrafast dynamics of dense, hot matter measured by pump-probe Doppler spectrometry

    Science.gov (United States)

    Lad, Amit D.; Mondal, S.; Narayanan, V.; Ahmed, Saima; Rajeev, P. P.; Robinson, A. P. L.; Pasley, J.; Kumar, G. Ravindra

    2010-08-01

    A detailed understanding of the critical surface motion of high intensity laser produced plasma is very crucial for understanding the interaction. We employ the two colour pump-probe technique to report the first ever femtosecond scale ultrafast dynamics measurement of the critical surface of a solid plasma produced by a relativistically intense, femtosecond pump laser beam (1018 W/cm2, 30 fs, 800 nm) on an aluminium target. We observe the Doppler shift of a time delayed probe laser beam (1012 W/cm2, 80 fs, 400 nm) up to delays of 30 ps. Such unravelling of dynamics has not been possible in earlier measurements, which typically used the self reflection of a powerful pump pulse. We observe time dependent red and blue shifts and measure their magnitudes to infer plasma expansion velocity and acceleration and thereby the plasma profile. Our results are very well reproduced by 1D hydrodynamic simulation (HYADES code).

  19. A ratiometric fluorescence probe for selective visual sensing of Zn2+.

    Science.gov (United States)

    Ajayaghosh, Ayyappanpillai; Carol, Priya; Sreejith, Sivaramapanicker

    2005-11-02

    A simple ratiometric fluorescence probe based on vinylpyrrole end-capped bipyridine for the visual sensing of Zn2+ under aqueous physiological pH (6.8-7.4) is described. The fluorophores 3a-c showed strong emission around 537 nm in acetonitrile with a quantum yield of 0.4. In buffered (HEPES, pH 7.2) acetonitrile-water mixture (9:1 v/v), titration of transition metal salts to 3c showed strong quenching of the emission at 547 nm except in the case of Zn2+, which resulted in a red-shifted emission at 637 nm. Alkali and alkaline earth metal salts could not induce any considerable changes to the emission behavior of 3a-c. The binding of Zn2+ was highly selective in the presence of a variety of other metal ions. Though Cu2+ quenches the emission of 3c, in the presence of Zn2+, a red emission prevails, indicating the preference of 3c toward Zn2+. Job plot and Benesi-Hildebrand analysis revealed a 1:1 complexation between the probe and the metal ion. The selective visual sensing of Zn2+ with a red emission is ideally suited for the imaging of biological specimens.

  20. First-order reversal curve probing of spatially resolved polarization switching dynamics in ferroelectric nanocapacitors.

    Science.gov (United States)

    Kim, Yunseok; Kumar, Amit; Ovchinnikov, Oleg; Jesse, Stephen; Han, Hee; Pantel, Daniel; Vrejoiu, Ionela; Lee, Woo; Hesse, Dietrich; Alexe, Marin; Kalinin, Sergei V

    2012-01-24

    Spatially resolved polarization switching in ferroelectric nanocapacitors was studied on the sub-25 nm scale using the first-order reversal curve (FORC) method. The chosen capacitor geometry allows both high-veracity observation of the domain structure and mapping of polarization switching in a uniform field, synergistically combining microstructural observations and probing of uniform-field polarization responses as relevant to device operation. A classical Kolmogorov-Avrami-Ishibashi model has been adapted to the voltage domain, and the individual switching dynamics of the FORC response curves are well approximated by the adapted model. The comparison with microstructures suggests a strong spatial variability of the switching dynamics inside the nanocapacitors.

  1. Probe conformational dynamics of proteins in aqueous solutions by terahertz spectroscopy

    Science.gov (United States)

    Vinh, Nguyen Q.

    2016-10-01

    Proteins solvated in their biologically milieu are expected to exhibit strong absorption in the terahertz frequencies, that contain information on their global and sub-global collective vibrational modes (conformational dynamics) and global dynamic correlations among solvent water and proteins. The dynamics play an important role in enzymatic activities of proteins, but obtaining an accurate and quantitative pictures of these activities, however, is challenging due to the strong absorption of water. In response, we have developed the world's highest precision, highest sensitivity terahertz-frequency domain spectrometer and a standard terahertz-time domain system to probe the collective dynamics of proteins in aqueous solutions. Operating over the frequency range from 5 GHz up to 3 THz, our spectrometers provide an unparalleled ability to probe directly such questions as the hydration level, the dynamics of water and hydrated proteins over the 100 fs to 1 ns timescale. Employing an effective medium approximation to describe the complex dielectric response of the solvated proteins in solution we find that proteins are surrounded by a loosely and tightly held layers of water molecules that behave as if they are an integral part of the protein. The number of water molecules in the protein hydration shells varies with proteins, which can tell us the average surface structure of proteins. These measurements shed light on the macromolecular motions of proteins in their biologically relevant environment.

  2. Genetically encoded fluorescent probe to visualize intracellular phosphatidylinositol 3,5-bisphosphate localization and dynamics.

    Science.gov (United States)

    Li, Xinran; Wang, Xiang; Zhang, Xiaoli; Zhao, Mingkun; Tsang, Wai Lok; Zhang, Yanling; Yau, Richard Gar Wai; Weisman, Lois S; Xu, Haoxing

    2013-12-24

    Phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2] is a low-abundance phosphoinositide presumed to be localized to endosomes and lysosomes, where it recruits cytoplasmic peripheral proteins and regulates endolysosome-localized membrane channel activity. Cells lacking PI(3,5)P2 exhibit lysosomal trafficking defects, and human mutations in the PI(3,5)P2-metabolizing enzymes cause lysosome-related diseases. The spatial and temporal dynamics of PI(3,5)P2, however, remain unclear due to the lack of a reliable detection method. Of the seven known phosphoinositides, only PI(3,5)P2 binds, in the low nanomolar range, to a cytoplasmic phosphoinositide-interacting domain (ML1N) to activate late endosome and lysosome (LEL)-localized transient receptor potential Mucolipin 1 (TRPML1) channels. Here, we report the generation and characterization of a PI(3,5)P2-specific probe, generated by the fusion of fluorescence tags to the tandem repeats of ML1N. The probe was mainly localized to the membranes of Lamp1-positive compartments, and the localization pattern was dynamically altered by either mutations in the probe, or by genetically or pharmacologically manipulating the cellular levels of PI(3,5)P2. Through the use of time-lapse live-cell imaging, we found that the localization of the PI(3,5)P2 probe was regulated by serum withdrawal/addition, undergoing rapid changes immediately before membrane fusion of two LELs. Our development of a PI(3,5)P2-specific probe may facilitate studies of both intracellular signal transduction and membrane trafficking in the endosomes and lysosomes.

  3. The ML1Nx2 Phosphatidylinositol 3,5-Bisphosphate Probe Shows Poor Selectivity in Cells.

    Science.gov (United States)

    Hammond, Gerald R V; Takasuga, Shunsuke; Sasaki, Takehiko; Balla, Tamas

    2015-01-01

    Phosphatidylinositol (3,5)-bisphosphate (PtdIns(3,5)P2) is a quantitatively minor phospholipid in eukaryotic cells that plays a fundamental role in regulating endocytic membrane traffic. Despite its clear importance for cellular function and organism physiology, mechanistic details of its biology have so far not been fully elucidated. In part, this is due to a lack of experimental tools that specifically probe for PtdIns(3,5)P2 in cells to unambiguously identify its dynamics and site(s) of action. In this study, we have evaluated a recently reported PtdIns(3,5)P2 biosensor, GFP-ML1Nx2, for its veracity as such a probe. We report that, in live cells, the localization of this biosensor to sub-cellular compartments is largely independent of PtdIns(3,5)P2, as assessed after pharmacological, chemical genetic or genomic interventions that block the lipid's synthesis. We therefore conclude that it is unwise to interpret the localization of ML1Nx2 as a true and unbiased biosensor for PtdIns(3,5)P2.

  4. Geochemical dynamics in selected Yellowstone hydrothermal features

    Science.gov (United States)

    Druschel, G.; Kamyshny, A.; Findlay, A.; Nuzzio, D.

    2010-12-01

    Yellowstone National Park has a wide diversity of thermal features, and includes springs with a range of pH conditions that significantly impact sulfur speciation. We have utilized a combination of voltammetric and spectroscopic techniques to characterize the intermediate sulfur chemistry of Cinder Pool, Evening Primrose, Ojo Caliente, Frying Pan, Azure, and Dragon thermal springs. These measurements additionally have demonstrated the geochemical dynamics inherent in these systems; significant variability in chemical speciation occur in many of these thermal features due to changes in gas supply rates, fluid discharge rates, and thermal differences that occur on second time scales. The dynamics of the geochemical settings shown may significantly impact how microorganisms interact with the sulfur forms in these systems.

  5. Dynamic Channel Selection for Cognitive Femtocells

    DEFF Research Database (Denmark)

    Da Costa, Gustavo Wagner Oliveira; Cattoni, Andrea Fabio; Mogensen, Preben;

    2014-01-01

    , but not least, the possibility of having closed-subscriber-groups aggravates the inter-cell interference problems. In order to tackle these issues we consider the implementation of some aspects of cognitive radio technology into femtocells, leading to the concept of cognitive femtocells. This chapter focuses...... on state-of-art techniques to manage the radio resources in order to cope with inter-cell interference in cognitive femtocells. Different techniques are presented as examples of gradually increasing sophistication of the cognitive femtocells, allowing for dynamic channel allocation, dynamic reuse...... the traditional planning and optimization techniques. This leads to uncoordinated deployment by the end-user. Second, the high density of femtocells, including vertical reuse, leads to very different inter-cell interference patterns than the ones traditionally considered in cellular networks. And last...

  6. A rhodamine chromene-based turn-on fluorescence probe for selectively imaging Cu²+ in living cell.

    Science.gov (United States)

    Liu, Wei-Yong; Li, Hai-Ying; Lv, Hong-Shui; Zhao, Bao-Xiang; Miao, Jun-Ying

    2012-09-01

    We describe the development of a rhodamine chromene-based turn-on fluorescence probe to monitor the intracellular Cu(2+) level in living cells. The new fluorescent probe with a chlorine group in chromene moiety exhibits good membrane-permeable property than previous reported because the predicted lipophilicity of present probe 4 is stronger than that of methoxyl substituted probe in our previous work (CLogP of 4: 8.313, CLogP of methoxyl substituted probe: 7.706), and a fluorescence response toward Cu(2+) under physiological conditions with high sensitivity and selectivity, and facilitates naked-eye detection of Cu(2+). The fluorescence intensity was remarkably increased upon the addition of Cu(2+) within 1 or 2 min, while the other sixteen metal ions caused no significant effect. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Dynamic characterization of silicon nanowires using a terahertz optical asymmetric demultiplexer-based pump-probe scheme

    DEFF Research Database (Denmark)

    Ji, Hua; Cleary, C. S.; Dailey, J. M.;

    2012-01-01

    Dynamic phase and amplitude all-optical responses of silicon nanowires are characterized using a terahertz optical asymmetric demultiplexer (TOAD) based pump-probe scheme. Ultra-fast recovery is observed for moderate pump powers....

  8. Vibrational dynamics of aqueous hydroxide solutions probed using broadband 2DIR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mandal, Aritra [Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637 (United States); Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Tokmakoff, Andrei, E-mail: tokmakoff@uchicago.edu [Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637 (United States)

    2015-11-21

    We employed ultrafast transient absorption and broadband 2DIR spectroscopy to study the vibrational dynamics of aqueous hydroxide solutions by exciting the O–H stretch vibrations of the strongly hydrogen-bonded hydroxide solvation shell water and probing the continuum absorption of the solvated ion between 1500 and 3800 cm{sup −1}. We observe rapid vibrational relaxation processes on 150–250 fs time scales across the entire probed spectral region as well as slower vibrational dynamics on 1–2 ps time scales. Furthermore, the O–H stretch excitation loses its frequency memory in 180 fs, and vibrational energy exchange between bulk-like water vibrations and hydroxide-associated water vibrations occurs in ∼200 fs. The fast dynamics in this system originate in strong nonlinear coupling between intra- and intermolecular vibrations and are explained in terms of non-adiabatic vibrational relaxation. These measurements indicate that the vibrational dynamics of the aqueous hydroxide complex are faster than the time scales reported for long-range transport of protons in aqueous hydroxide solutions.

  9. Exciton Dynamics in LH1 and LH2 of Rhodopseudomonas Acidophila and Rhodobium Marinum Probed with Accumulated Photon Echo and Pump-Probe Measurements

    NARCIS (Netherlands)

    Lampoura, Stefania S.; Grondelle, Rienk van; Stokkum, Ivo H.M. van; Cogdell, Richard J.; Wiersma, Douwe A.; Duppen, Koos; van Stokkum, I.H.N.

    2000-01-01

    Exciton dynamics in the B850 and B875 bands of isolated complexes of Rhodopseudomonas acidophila (strain 10050 and 7050) and in the B875 band of isolated complexes of Rhodobium marinum were investigated by means of accumulated photon echo and pump-probe techniques at different temperatures and wavel

  10. Comparison of vibrational dynamics between non-ionic and ionic vibrational probes in water: Experimental study with two-dimensional infrared and infrared pump-probe spectroscopies

    Science.gov (United States)

    Okuda, Masaki; Ohta, Kaoru; Tominaga, Keisuke

    2016-09-01

    Dynamics of the hydration structure around small vibrational probes have been extensively studied over the past few decades. However, we need to gain insight into how vibrational dynamics is affected by the molecular nature of the probe molecules in water. In this study, 2-nitro-5-thiocyanate benzoic acid (NTBA), which has an SCN group attached to an aromatic ring, and thiocyanate ion (SCN-) were used to investigate the vibrational dynamics of two vibrational probes, including vibrational frequency fluctuations and rotational relaxation. By performing two-dimensional infrared spectroscopic measurements, the vibrational frequency fluctuations of the SCN anti-stretching modes of these solutes were compared. The frequency-frequency time correlation function (FFTCF) of these solutes can be modeled by a delta function plus an exponential function and a constant. The FFTCF of NTBA was characterized by a time constant of 1.1 ps, which is similar to that of SCN-. Moreover, no component was longer than this constant. Consequently, the loss of the correlation in frequency fluctuations of the SCN anti-stretching mode of NTBA may be controlled by a mechanism similar to that of the ionic probe, which involves the hydrogen bonding dynamics of water. Polarization-controlled IR pump-probe measurements were performed for these vibrational probes in water to study the vibrational energy relaxation (VER) and reorientational relaxation processes. The VER rate of NTBA is much smaller than that of SCN-, which indicates that the intramolecular relaxation process is significant for VER of NTBA. Based on the rotational relaxation time of NTBA being shorter than that of SCN-, the internal rotational motion of the SCN group around the Cphenyl-S bond axis, where Cphenyl denotes a carbon atom of the aromatic ring to which the SCN group is attached, may play an important role in the anisotropic decay of NTBA in H2O.

  11. GAS PHASE MOLECULAR DYNAMICS: HIGH-RESOLUTION SPECTROSCOPIC PROBES OF CHEMICAL DYNAMICS.

    Energy Technology Data Exchange (ETDEWEB)

    HALL, G.E.

    2006-05-30

    This research is carried out as part of the Gas Phase Molecular Dynamics group program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopic tools are developed and applied to problems in chemical dynamics. Recent topics have included the state-resolved studies of collision-induced electronic energy transfer, dynamics of barrierless unimolecular reactions, and the kinetics and spectroscopy of transient species.

  12. A multi writable thiophene-based selective and reversible chromogenic fluoride probe with dual -NH functionality

    Science.gov (United States)

    Vishwakarma, Siddharth; Kumar, Ajit; Pandey, Abha; Upadhyay, K. K.

    2017-01-01

    A chromogenic fluoride probe bearing bis imine groups having dual -NH functionality (BSB) has been designed, synthesised and structurally characterized by its single crystal X-ray diffraction studies. The BSB could visually and spectroscopically recognise F- with high selectivity over other anions by exhibiting intense chromogenic response (from colourless to red) for F- in acetonitrile solution. The UV-visible titration and 1H NMR titration experiments indicated that the observed changes occur via a combined process including hydrogen bonding and deprotonation between the BSB and F-. Moreover theoretical calculations at the Density Functional Theory (DFT) level shed further light upon probe design strategy and the nature of interactions between BSB and F-. The limit of detection and binding constant of BSB towards F- were found to be 6.9 × 10- 7 M and 1.42 ± 0.069 × 108 M- 2 respectively. Finally, by using F- and H+ as chemical inputs and the absorbance as output, a INHIBIT logic gate was constructed, which exhibits "Multi-write" ability without obvious degradation in its optical output.

  13. Two rhodamine lactam modulated lysosome-targetable fluorescence probes for sensitively and selectively monitoring subcellular organelle pH change

    Energy Technology Data Exchange (ETDEWEB)

    Li, Hongmei [Ministry of Education Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, College of Chemistry & Materials Science, Northwest University, Xi' an 710069 (China); Wang, Cuiling [Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi' an 710069 (China); She, Mengyao; Zhu, Yuelu; Zhang, Jidong; Yang, Zheng [Ministry of Education Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, College of Chemistry & Materials Science, Northwest University, Xi' an 710069 (China); Liu, Ping, E-mail: liuping@nwu.edu.cn [Ministry of Education Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, College of Chemistry & Materials Science, Northwest University, Xi' an 710069 (China); Wang, Yaoyu [Ministry of Education Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, College of Chemistry & Materials Science, Northwest University, Xi' an 710069 (China); Li, Jianli, E-mail: lijianli@nwu.edu.cn [Ministry of Education Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, College of Chemistry & Materials Science, Northwest University, Xi' an 710069 (China)

    2015-11-05

    Be a powerful technique for convenient detection of pH change in living cells, especially at subcellular level, fluorescent probes has attracted more and more attention. In this work, we designed and synthesized three rhodamine lactam modulated fluorescent probes RS1, RS2 and RS3, which all respond sensitively toward weak acidity (pH range 4–6) via the photophysical property in buffer solution without interference from the other metal ions, and they also show ideal pKa values and excellent reversibility. Particularly, by changing the lone pair electrons distribution of lactam-N atom with different conjugations, RS2 and RS3 exhibit high quantum yield, negligible cytotoxicity and excellent permeability. They are suitable to stain selectively lysosomes of tumor cells and monitor its pH changes sensitively via optical molecular imaging. The above findings suggest that the probes we designed could act as ideal and easy method for investigating the pivotal role of H{sup +} in lysosomes and are potential pH detectors in disease diagnosis through direct intracellular imaging. - Highlights: • Two probes for sensitively and selectively monitoring weak acidic pH change. • The pKa of the probes was highly suitable for staining lysosomes in tumor cells. • The properties of those probes were changed by different conjugate system. • These probes have negligible cytotoxicity and good sensitivity in vivo.

  14. Probing Properties of Glassy Water and Other Liquids with Site Selective Spectroscopies

    Energy Technology Data Exchange (ETDEWEB)

    Dang, Nhan Chuong [Iowa State Univ., Ames, IA (United States)

    2005-01-01

    The standard non-photochemical hole burning (NPHB) mechanism, which involves phonon-assisted tunneling in the electronically excited state, was originally proposed to explain the light-induced frequency change of chemically stable molecules in glassy solids at liquid helium temperatures by this research group more than two decades ago. The NPHB mechanism was then further elucidated and the concept of intrinsic to glass configurational relaxation processes as pre-mediating step to the hole burning process was introduced. The latter provided the theoretical basis for NPHB to evolve into a powerful tool probing the dynamics and nature of amorphous media, which aside from ''simple'' inorganic glasses may include also ''complex'' biological systems such as living cells and cancerous/normal tissues. Presented in this dissertation are the experimental and theoretical results of hole burning properties of aluminum phthalocyanine tetrasulphonate (APT) in several different matrices: (1) hyperquenched glassy water (HGW); (2) cubic ice (Ic); and (3) water confined into poly(2-hydroxyethylmethacrylate) (poly-HEMA). In addition, results of photochemical hole burning (PHB) studies obtained for phthalocyanine tetrasulphonate (PcT) in HGW and free base phthalocyanine (Pc) in ortho-dichlorobenzene (DCB) glass are reported. The goal of this dissertation was to provide further evidence supporting the NPHB mechanism and to provide more insight that leads to a better understanding of the kinetic events (dynamics) in glasses, and various dynamical processes of different fluorescent chromorphores in various amorphous solids and the liquid that exist above the glass transition temperature (Tg). The following issues are addressed in detail: (1) time evolution of hole being burned under different conditions and in different hole burning systems; (2) temperature dependent hole profile; and (3) the structure/dynamics

  15. Real-Time Probing of Electron Dynamics Using Attosecond Time-Resolved Spectroscopy

    Science.gov (United States)

    Ramasesha, Krupa; Leone, Stephen R.; Neumark, Daniel M.

    2016-05-01

    Attosecond science has paved the way for direct probing of electron dynamics in gases and solids. This review provides an overview of recent attosecond measurements, focusing on the wealth of knowledge obtained by the application of isolated attosecond pulses in studying dynamics in gases and solid-state systems. Attosecond photoelectron and photoion measurements in atoms reveal strong-field tunneling ionization and a delay in the photoemission from different electronic states. These measurements applied to molecules have shed light on ultrafast intramolecular charge migration. Similar approaches are used to understand photoemission processes from core and delocalized electronic states in metal surfaces. Attosecond transient absorption spectroscopy is used to follow the real-time motion of valence electrons and to measure the lifetimes of autoionizing channels in atoms. In solids, it provides the first measurements of bulk electron dynamics, revealing important phenomena such as the timescales governing the switching from an insulator to a metallic state and carrier-carrier interactions.

  16. Structural dynamics inside a functionalized metal–organic framework probed by ultrafast 2D IR spectroscopy

    Science.gov (United States)

    Nishida, Jun; Tamimi, Amr; Fei, Honghan; Pullen, Sonja; Ott, Sascha; Cohen, Seth M.; Fayer, Michael D.

    2014-01-01

    The structural elasticity of metal–organic frameworks (MOFs) is a key property for their functionality. Here, we show that 2D IR spectroscopy with pulse-shaping techniques can probe the ultrafast structural fluctuations of MOFs. 2D IR data, obtained from a vibrational probe attached to the linkers of UiO-66 MOF in low concentration, revealed that the structural fluctuations have time constants of 7 and 670 ps with no solvent. Filling the MOF pores with dimethylformamide (DMF) slows the structural fluctuations by reducing the ability of the MOF to undergo deformations, and the dynamics of the DMF molecules are also greatly restricted. Methodology advances were required to remove the severe light scattering caused by the macroscopic-sized MOF particles, eliminate interfering oscillatory components from the 2D IR data, and address Förster vibrational excitation transfer. PMID:25512539

  17. Probing the Dynamics of a Superradiant Quantum Phase Transition with a Single Trapped Ion.

    Science.gov (United States)

    Puebla, Ricardo; Hwang, Myung-Joong; Casanova, Jorge; Plenio, Martin B

    2017-02-17

    We demonstrate that the quantum phase transition (QPT) of the Rabi model and critical dynamics near the QPT can be probed in the setup of a single trapped ion. We first demonstrate that there exists equilibrium and nonequilibrium scaling functions of the Rabi model by finding a proper rescaling of the system parameters and observables, and show that those scaling functions are representative of the universality class to which the Rabi model belongs. We then propose a scheme that can faithfully realize the Rabi model in the limit of a large ratio of the effective atomic transition frequency to the oscillator frequency using a single trapped ion and, therefore, the QPT. It is demonstrated that the predicted universal functions can indeed be observed based on our scheme. Finally, the effects of realistic noise sources on probing the universal functions in experiments are examined.

  18. Probing the Dynamics of a Superradiant Quantum Phase Transition with a Single Trapped Ion

    Science.gov (United States)

    Puebla, Ricardo; Hwang, Myung-Joong; Casanova, Jorge; Plenio, Martin B.

    2017-02-01

    We demonstrate that the quantum phase transition (QPT) of the Rabi model and critical dynamics near the QPT can be probed in the setup of a single trapped ion. We first demonstrate that there exists equilibrium and nonequilibrium scaling functions of the Rabi model by finding a proper rescaling of the system parameters and observables, and show that those scaling functions are representative of the universality class to which the Rabi model belongs. We then propose a scheme that can faithfully realize the Rabi model in the limit of a large ratio of the effective atomic transition frequency to the oscillator frequency using a single trapped ion and, therefore, the QPT. It is demonstrated that the predicted universal functions can indeed be observed based on our scheme. Finally, the effects of realistic noise sources on probing the universal functions in experiments are examined.

  19. Weather conditions drive dynamic habitat selection in a generalist predator

    DEFF Research Database (Denmark)

    Sunde, Peter; Thorup, Kasper; Jacobsen, Lars B.;

    2014-01-01

    Despite the dynamic nature of habitat selection, temporal variation as arising from factors such as weather are rarely quantified in species-habitat relationships. We analysed habitat use and selection (use/availability) of foraging, radio-tagged little owls (Athene noctua), a nocturnal, year-rou...

  20. Probing cosmology with weak lensing selected clusters II: Dark energy and f(R) gravity models

    CERN Document Server

    Shirasaki, Masato; Yoshida, Naoki

    2015-01-01

    Ongoing and future wide-field galaxy surveys can be used to locate a number of clusters of galaxies with cosmic shear measurement alone. We study constraints on cosmological models using statistics of weak lensing selected galaxy clusters. We extend our previous theoretical framework to model the statistical properties of clusters in variants of cosmological models as well as in the standard LCDM model. Weak lensing selection of clusters does not rely on the conventional assumption such as the relation between luminosity and mass and/or hydrostatic equilibrium, but a number of observational effects compromise robust identification. We use a large set of realistic mock weak-lensing catalogs as well as analytic models to perform a Fisher analysis and make forecast for constraining two competing cosmological models, wCDM model and f(R) model proposed by Hu & Sawicki, with our lensing statistics. We show that weak lensing selected clusters are excellent probe of cosmology when combined with cosmic shear power...

  1. A two-dimensional coordination compound as a zinc ion selective luminescent probe for biological applications.

    Science.gov (United States)

    Dhara, Koushik; Karan, Santanu; Ratha, Jagnyeswar; Roy, Partha; Chandra, Goutam; Manassero, Mario; Mallik, Biswanath; Banerjee, Pradyot

    2007-09-01

    A 2D coordination compound {[Cu2(HL)(N3)]ClO4}infinity (1; H3L = 2,6-bis(hydroxyethyliminoethyl)-4-methyl phenol) was synthesized and characterized by single-crystal X-ray diffraction to be a polymer in the crystalline state. Each [Cu2(HL)(N3)]+ species is connected to its adjacent unit by a bridging alkoxide oxygen atom of the ligand to form a helical propagation along the crystallographic a axis. The adjacent helical frameworks are connected by a ligand alcoholic oxygen atom along the crystallographic b axis to produce pleated 2D sheets. In solution, 1 dissociates into [Cu2(HL)2(H3L)]2H2O (2); the monomer displays high selectivity for Zn2+ and can be used in HEPES buffer (pH 7.4) as a zinc ion selective luminescent probe for biological application. The system shows a nearly 19-fold Zn2+-selective chelation-enhanced fluorescence response in the working buffer. Application of 2 to cultured living cells (B16F10 mouse melanoma and A375 human melanoma) and rat hippocampal slices was also studied by fluorescence microscopy.

  2. Femtosecond Excited State Dynamics of Size Selected Neutral Molecular Clusters.

    Science.gov (United States)

    Montero, Raúl; León, Iker; Fernández, José A; Longarte, Asier

    2016-07-21

    The work describes a novel experimental approach to track the relaxation dynamics of an electronically excited distribution of neutral molecular clusters formed in a supersonic expansion, by pump-probe femtosecond ionization. The introduced method overcomes fragmentation issues and makes possible to retrieve the dynamical signature of a particular cluster from each mass channel, by associating it to an IR transition of the targeted structure. We have applied the technique to study the nonadiabatic relaxation of pyrrole homoclusters. The results obtained exciting at 243 nm, near the origin of the bare pyrrole electronic absorption, allow us to identify the dynamical signature of the dimer (Py)2, which exhibits a distinctive lifetime of τ1 ∼ 270 fs, considerably longer than the decays recorded for the monomer and bigger size clusters (Py)n>2. A possible relationship between the measured lifetime and the clusters geometries is tentatively discussed.

  3. Differential selectivity of cytochrome P450 inhibitors against probe substrates in human and rat liver microsomes

    Science.gov (United States)

    Eagling, Victoria A; Tjia, John F; Back, David J

    1998-01-01

    Aims Chemical inhibitors of cytochrome P450 (CYP) are a useful tool in defining the role of individual CYPs involved in drug metabolism. The aim of the present study was to evaluate the selectivity and rank the order of potency of a range of isoform-selective CYP inhibitors and to compare directly the effects of these inhibitors in human and rat hepatic microsomes. Methods Four chemical inhibitors of human cytochrome P450 isoforms, furafylline (CYP1A2), sulphaphenazole (CYP2C9), diethyldithiocarbamate (CYP2E1), and ketoconazole (CYP3A4) were screened for their inhibitory specificity towards CYP-mediated reactions in both human and rat liver microsomal preparations. Phenacetin O-deethylation, tolbutamide 4-hydroxylation, chlorzoxazone 6-hydroxylation and testosterone 6β-hydroxylation were monitored for enzyme activity. Results Furafylline was a potent, selective inhibitor of phenacetin O-deethylation (CYP1A2-mediated) in human liver microsomes (IC50 = 0.48 μm), but inhibited both phenacetin O-deethylation and tolbutamide 4-hydroxylation (CYP2C9-mediated) at equimolar concentrations in rat liver microsomes (IC50 = 20.8 and 24.0 μm respectively). Sulphaphenazole demonstrated selective inhibition of tolbutamide hydroxylation in human liver microsomes but failed to inhibit this reaction in rat liver microsomes. DDC demonstrated a low level of selectivity as an inhibitory probe for chlorzoxazone 6-hydroxylation (CYP2E1-mediated). DDC also inhibited testosterone 6β-hydroxylation (CYP3A-mediated) in man and rat, and tolbutamide 4-hydroxylase activity in rat. Ketoconazole was a very potent, selective inhibitor of CYP3A4 activity in human liver (IC50 = 0.04 μm). Although inhibiting CYP3A in rat liver it also inhibited all other reactions at concentrations ≤5 μm. Conclusions It is evident that CYP inhibitors do not exhibit the same selectivity in human and rat liver microsomes. This is due to differential selectivity of the inhibitors and/or differences in the CYP

  4. Probing of the assembly structure and dynamics within nanoparticles during interaction with blood proteins.

    Science.gov (United States)

    Li, Yuanpei; Budamagunta, Madhu S; Luo, Juntao; Xiao, Wenwu; Voss, John C; Lam, Kit S

    2012-11-27

    Fully understanding the influence of blood proteins on the assembly structure and dynamics within nanoparticles is difficult because of the complexity of the system and the difficulty in probing the diverse elements and milieus involved. Here we show the use of site-specific labeling with spin probes and fluorophores combined with electron paramagnetic resonance (EPR) spectroscopy and fluorescence resonance energy transfer (FRET) measurements to provide insights into the molecular architecture and dynamics within nanoparticles. These tools are especially useful for determining nanoparticle stability in the context of blood proteins and lipoproteins and have allowed us to quantitatively analyze the dynamic changes in assembly structure, local stability, and cargo diffusion of a class of novel telodendrimer-based micellar nanoparticles. When combined with human plasma and individual plasma components, we find that non-cross-linked nanoparticles immediately lose their original assembly structure and release their payload upon interaction with lipoproteins. In contrast, serum albumins and immunoglobulin gamma have moderate affects on the integrity of the nanoparticles. Disulfide cross-linked nanoparticles show minimal interaction with lipoproteins and can better retain their assembly structure and payload in vitro and in vivo. We further demonstrate how the enhanced stability and release property of disulfide cross-linked nanoparticles can be reversed in reductive conditions. These findings identify factors that are crucial to the performance of nanomedicines and provide design modes to control their interplay with blood factors.

  5. Ultrafast excited-state dynamics at interfaces: fluorescent DNA probes at the dodecane/water interface

    Science.gov (United States)

    Licari, Giuseppe; Vauthey, Eric

    2015-08-01

    Although the interfaces between two isotropic media are of primary importance in many areas of science and technology, their properties are only partially understood. Our strategy to obtain an insight into these properties is to investigate the ultrafast excited-state dynamics of environment-sensitive molecular probes at liquid interfaces using time-resolved surface second harmonic generation, and to compare it with the dynamics of the same molecules in bulk solutions. Additionally, this approach gives rich information on how the chemical reactivity may change when going from the bulk phase to the interface. This is illustrated by an investigation performed with a series of fluorescent DNA probes at the dodecane/water interface without and with the presence of DNA in the aqueous phase. Substantial differences in the conformation of these cyanine dyes (aggregated or not) and in the excited-state dynamics are observed when going from bulk solutions to the interface. Moreover, the presence of double-stranded DNA in the aqueous phase induces some chirality at the interface.

  6. Initial Dynamics of The Norrish Type I Reaction in Acetone: Probing Wave Packet Motion

    DEFF Research Database (Denmark)

    Brogaard, Rasmus Y.; Sølling, Theis I.; Møller, Klaus Braagaard

    2011-01-01

    agreement with the experimental signals. We can explain the ultrafast decay of the experimental signals in the following manner: the wave packet simply travels, mainly along the deplanarization coordinate, out of the detection window of the ionizing probe. This window is so narrow that subsequent revival...... of the signal due to the coherent deplanarization vibration is not observed, meaning that from the point of view of the experiment the wave packets travels directly to the S1 minimum. This result stresses the importance of pursuing a closer link to the experimental signal when using molecular dynamics...

  7. Trace element associations with Fe- and Mn-oxides in soil nodules: Comparison of selective dissolution with electron probe microanalysis

    Energy Technology Data Exchange (ETDEWEB)

    Neaman, Alexander [Area de Medio Ambiente, Facultad de Agronomia, Pontificia Universidad Catolica de Valparaiso, Casilla 4-D, Quillota (Chile); Centro Regional de Estudios en Alimentos Saludables, Region de Valparaiso (Chile)], E-mail: alexander.neaman@ucv.cl; Martinez, Carmen Enid [Department of Crop and Soil Sciences, Pennsylvania State University, University Park, PA 16802 (United States); Trolard, Fabienne; Bourrie, Guilhem [INRA, UR 1119, Geochimie des Sols et des Eaux, BP 80, 13545 Aix-en-Provence cedex 04 (France)

    2008-04-15

    Selective dissolution methods have been largely used to get insight on trace element association with solid phases. Modern instrumental techniques offer many tools to test the validity of selective dissolution methods and should be systematically used to this end. The association of trace elements with Fe- and Mn-oxides in soil nodules has been studied here by electron probe microanalysis. The results were compared with findings from an earlier study on selective dissolution of the same nodules by hydroxylamine hydrochloride, acidified hydrogen peroxide, and Na-citrate-bicarbonate-dithionite. Electron probe microanalysis results were consistent with previous findings using selective dissolution and showed that P, As and Cr were mainly present in Fe-oxides, while Co was mainly associated with Mn-oxide phases. These results support the applicability of the studied selective dissolution methods for fractionation of trace elements in soils and sediments containing appreciable amounts of Fe and Mn-oxide phases.

  8. Highly selective fluorescent probe for the detection of tin (IV) Ion

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Leiming; Yang, Jing; Wang, Qiusheng, E-mail: wangqsh@tjut.edu.cn; Zeng, Lintao, E-mail: zlt1981@126.com

    2014-04-15

    A novel fluorescent compound, 7-diethylamino-3-(2'-(1H-imidazo[4,5-b]phenazine)yl)coumarin (DIPC), was synthesized and employed as a fluorescent probe for detecting tin (IV) ion. Upon addition of tin (IV) ion to the solution of DIPC in DMSO–water (9:1, v/v), DIPC exhibited a considerable red-shift in its absorption spectrum and a decrease in fluorescence intensity. These changes result from tin (IV) ion binding to carbonyl oxygen of coumarin and nitrogen of imidazole, reflecting an enhanced ICT process from N,N-diethylamino unit to imidazole unit. The tin (IV) ion selective response was clearly observed by the naked eye through color change. We also studied the bioimaging application of DIPC for detecting tin (IV) ion in Hela cells. And a significant decrease of the fluorescence from the intracellular area was observed. -- Highlights: • We synthesized a novel coumarin derivative (DIPC). • DIPC was used to detect tin (IV) ion selectively. • The detection process was studied upon UV–vis and fluorescence spectrum. • We studied the bioimaging application of DIPC for detecting Sn{sup 4+} ion in cells.

  9. Molecular probes to visualize the location, organization and dynamics of lipids.

    Science.gov (United States)

    Maekawa, Masashi; Fairn, Gregory D

    2014-11-15

    Cellular lipids play crucial roles in the cell, including in energy storage, the formation of cellular membranes, and in signaling and vesicular trafficking. To understand the functions and characteristics of lipids within cells, various methods to image lipids have been established. In this Commentary, we discuss the four main types of molecular probes that have significantly contributed to our understanding of the cell biology of lipids. In particular, genetically encoded biosensors and antibodies will be discussed, and how they have been used extensively with traditional light and electron microscopy to determine the subcellular localization of lipids and their spatial and temporal regulation. We highlight some of the recent studies that have investigated the distribution of lipids and their ability to cluster using super-resolution and electron microscopy. We also examine methods for analyzing the movement and dynamics of lipids, including single-particle tracking (SPT), fluorescence recovery after photobleaching (FRAP) and fluorescence correlation spectroscopy (FCS). Although the combination of these lipid probes and the various microscopic techniques is very powerful, we also point out several potential caveats and limitations. Finally, we discuss the need for new probes for a variety of phospholipids and cholesterol.

  10. Cryogenic sample exchange NMR probe for magic angle spinning dynamic nuclear polarization

    Science.gov (United States)

    Barnes, Alexander B.; Mak-Jurkauskas, Melody L.; Matsuki, Yoh; Bajaj, Vikram S.; van der Wel, Patrick C. A.; DeRocher, Ronald; Bryant, Jeffrey; Sirigiri, Jagadishwar R.; Temkin, Richard J.; Lugtenburg, Johan; Herzfeld, Judith; Griffin, Robert G.

    2009-01-01

    We describe a cryogenic sample exchange system that dramatically improves the efficiency of magic angle spinning (MAS) dynamic nuclear polarization (DNP) experiments by reducing the time required to change samples and by improving long-term instrument stability. Changing samples in conventional cryogenic MAS DNP/NMR experiments involves warming the probe to room temperature, detaching all cryogenic, RF, and microwave connections, removing the probe from the magnet, replacing the sample, and reversing all the previous steps, with the entire cycle requiring a few hours. The sample exchange system described here — which relies on an eject pipe attached to the front of the MAS stator and a vacuum jacketed dewar with a bellowed hole — circumvents these procedures. To demonstrate the excellent sensitivity, resolution, and stability achieved with this quadruple resonance sample exchange probe, we have performed high precision distance measurements on the active site of the membrane protein bacteriorhodopsin. We also include a spectrum of the tripeptide N-f-MLF-OH at 100 K which shows 30 Hz linewidths. PMID:19356957

  11. Molecular dynamics in rod-like liquid crystals probed by muon spin resonance spectroscopy.

    Science.gov (United States)

    McKenzie, Iain; Scheuermann, Robert; Sedlak, Kamil; Stoykov, Alexey

    2011-08-01

    Muoniated spin probes were produced by the addition of muonium (Mu) to two rod-like liquid crystals: N-(4-methoxybenzylidene)-4'-n-butylaniline (MBBA) and cholesteryl nonanoate (CN). Avoided level crossing muon spin resonance spectroscopy was used to characterize the muoniated spin probes and to probe dynamics at the molecular level. In MBBA Mu adds predominantly to the carbon of the bridging imine group and the muon and methylene proton hyperfine coupling constants (hfccs) of the resulting radical shift in the nematic phase due to the dipolar hyperfine coupling, the ordering of the molecules along the applied magnetic field and fluctuations about the local director. The amplitude of these fluctuations in in the nematic phase of MBBA is determined from the temperature dependence of the methylene proton hfcc. Mu adds to the double bond of the steroidal ring system of CN and the temperature dependence of the Δ(1) line width provides information about the amplitude of the fluctuations about the local director in the chiral nematic phase and the slow isotropic reorientation in the isotropic phase.

  12. Excited state X-ray absorption spectroscopy: Probing both electronic and structural dynamics

    Science.gov (United States)

    Neville, Simon P.; Averbukh, Vitali; Ruberti, Marco; Yun, Renjie; Patchkovskii, Serguei; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

    2016-10-01

    We investigate the sensitivity of X-ray absorption spectra, simulated using a general method, to properties of molecular excited states. Recently, Averbukh and co-workers [M. Ruberti et al., J. Chem. Phys. 140, 184107 (2014)] introduced an efficient and accurate L 2 method for the calculation of excited state valence photoionization cross-sections based on the application of Stieltjes imaging to the Lanczos pseudo-spectrum of the algebraic diagrammatic construction (ADC) representation of the electronic Hamiltonian. In this paper, we report an extension of this method to the calculation of excited state core photoionization cross-sections. We demonstrate that, at the ADC(2)x level of theory, ground state X-ray absorption spectra may be accurately reproduced, validating the method. Significantly, the calculated X-ray absorption spectra of the excited states are found to be sensitive to both geometric distortions (structural dynamics) and the electronic character (electronic dynamics) of the initial state, suggesting that core excitation spectroscopies will be useful probes of excited state non-adiabatic dynamics. We anticipate that the method presented here can be combined with ab initio molecular dynamics calculations to simulate the time-resolved X-ray spectroscopy of excited state molecular wavepacket dynamics.

  13. Computer selection of oligonucleotide probes from amino acid sequences for use in gene library screening.

    Science.gov (United States)

    Yang, J H; Ye, J H; Wallace, D C

    1984-01-11

    We present a computer program, FINPROBE, which utilizes known amino acid sequence data to deduce minimum redundancy oligonucleotide probes for use in screening cDNA or genomic libraries or in primer extension. The user enters the amino acid sequence of interest, the desired probe length, the number of probes sought, and the constraints on oligonucleotide synthesis. The computer generates a table of possible probes listed in increasing order of redundancy and provides the location of each probe in the protein and mRNA coding sequence. Activation of a next function provides the amino acid and mRNA sequences of each probe of interest as well as the complementary sequence and the minimum dissociation temperature of the probe. A final routine prints out the amino acid sequence of the protein in parallel with the mRNA sequence listing all possible codons for each amino acid.

  14. Investigations of ultrafast charge dynamics in laser-irradiated targets by a self probing technique employing laser driven protons

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, H. [School of Mathematics and Physics, Queen' s University Belfast, BT7 1NN (United Kingdom); Kar, S., E-mail: s.kar@qub.ac.uk [School of Mathematics and Physics, Queen' s University Belfast, BT7 1NN (United Kingdom); Cantono, G. [School of Mathematics and Physics, Queen' s University Belfast, BT7 1NN (United Kingdom); Department of Physics “E. Fermi”, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Consiglio Nazionale delle Ricerche, Istituto Nazionale di Ottica, Research Unit Adriano Gozzini, via G. Moruzzi 1, Pisa 56124 (Italy); Nersisyan, G. [School of Mathematics and Physics, Queen' s University Belfast, BT7 1NN (United Kingdom); Brauckmann, S. [Institut für Laser-und Plasmaphysik, Heinrich-Heine-Universität, Düsseldorf (Germany); Doria, D.; Gwynne, D. [School of Mathematics and Physics, Queen' s University Belfast, BT7 1NN (United Kingdom); Macchi, A. [Department of Physics “E. Fermi”, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Consiglio Nazionale delle Ricerche, Istituto Nazionale di Ottica, Research Unit Adriano Gozzini, via G. Moruzzi 1, Pisa 56124 (Italy); Naughton, K. [School of Mathematics and Physics, Queen' s University Belfast, BT7 1NN (United Kingdom); Willi, O. [Institut für Laser-und Plasmaphysik, Heinrich-Heine-Universität, Düsseldorf (Germany); Lewis, C.L.S.; Borghesi, M. [School of Mathematics and Physics, Queen' s University Belfast, BT7 1NN (United Kingdom)

    2016-09-01

    The divergent and broadband proton beams produced by the target normal sheath acceleration mechanism provide the unique opportunity to probe, in a point-projection imaging scheme, the dynamics of the transient electric and magnetic fields produced during laser-plasma interactions. Commonly such experimental setup entails two intense laser beams, where the interaction produced by one beam is probed with the protons produced by the second. We present here experimental studies of the ultra-fast charge dynamics along a wire connected to laser irradiated target carried out by employing a ‘self’ proton probing arrangement – i.e. by connecting the wire to the target generating the probe protons. The experimental data shows that an electromagnetic pulse carrying a significant amount of charge is launched along the wire, which travels as a unified pulse of 10s of ps duration with a velocity close to speed of light. The experimental capabilities and the analysis procedure of this specific type of proton probing technique are discussed. - Highlights: • Prompt charging of laser irradiated target generates ultra-short EM pulses. • Its ultrafast propagation along a wire was studied by self-proton probing technique. • Self-proton probing technique is the proton probing with one laser pulse. • Pulse temporal profile and speed along the wire were measured with high resolution.

  15. Dynamic Interactions of CdSe/ZnS Quantum Dots with Cyclic Solvents Probed by Femtosecond Four-Wave Mixing

    Directory of Open Access Journals (Sweden)

    Biju V.

    2013-03-01

    Full Text Available We studied dynamic interactions between CdSe/ZnS quantum dots (QDs and cyclic solvents probed by femtosecond four-wave mixing. We found that the dynamic interactions of QDs strongly depend on the existence of π-bonds in solvent molecules.

  16. An aldehyde group-based P-acid probe for selective fluorescence turn-on sensing of cysteine and homocysteine.

    Science.gov (United States)

    Yang, Chunlei; Wang, Xiu; Shen, Lei; Deng, Wenping; Liu, Haiyun; Ge, Shenguang; Yan, Mei; Song, Xianrang

    2016-06-15

    A highly sensitive and selective turn on fluorescent probe P-acid-aldehyde (P-CHO) is developed for the determination of cysteine (Cys) and homocysteine (Hcy). The probe is designed and synthesized by incorporating the specific functional group aldehyde group for thiols into a stable π-conjugated material 4,4'-(2,5-dimethoxy-1,4-phenylene) bis(ethyne-2,1-diyl) dibenzoic acid (P-acid). The probe fluorescence is quenched through donor photoinduced electron transfer (d-PET) between the fluorophore (P-acid) and the recognition group (aldehyde group). In the presence of thiols, Cys and Hcy can selectively react with aldehyde group of the probe because the inhibition of d-PET between fluorophore and recognition group. Therefore, a turn-on fluorescent sensor was established for the fluorescence recovery. Under the optimized conditions, the fluorescence response of probe is directly proportional to the concentration of Cys in the range of 4-95 NM L(-1), with a detection limit 3.0 nM. In addition, the sensing system exhibits good selectively toward Cys and Hcy in the presence of other amino acids. It has been successfully applied for bioimaging of Cys and Hcy in living cells with low cell toxicity.

  17. Dynamic Service Selection in Workflows Using Performance Data

    Directory of Open Access Journals (Sweden)

    David W. Walker

    2007-01-01

    Full Text Available An approach to dynamic workflow management and optimisation using near-realtime performance data is presented. Strategies are discussed for choosing an optimal service (based on user-specified criteria from several semantically equivalent Web services. Such an approach may involve finding "similar" services, by first pruning the set of discovered services based on service metadata, and subsequently selecting an optimal service based on performance data. The current implementation of the prototype workflow framework is described, and demonstrated with a simple workflow. Performance results are presented that show the performance benefits of dynamic service selection. A statistical analysis based on the first order statistic is used to investigate the likely improvement in service response time arising from dynamic service selection.

  18. Carrier dynamics and terahertz photoconductivity of doped silicon measured by femtosecond pump-terahertz probe spectroscopy

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The carrier dynamics and terahertz photoconductivity in the n-type silicon (n-Si) as well as in the p-type Silicon (p-Si) have been investigated by using femtosecond pump-terahertz probe technique. The measurements show that the relative change of terahertz transmission of p-Si at low pump power is slightly smaller than that of n-Si,due to the lower carrier density induced by the recombination of original holes in the p-type material and the photogenerated electrons. At high pump power,the bigger change of terahertz transmission of p-Si originates from the greater mobility of the carriers compared to n-Si. The transient photoconductivities are calculated and fit well with the Drude-Smith model,showing that the mobility of the photogenerated carriers decreases with the increasing pump power. The obtained results indicate that femtosecond pump-terahertz probe technique is a promising method to investigate the carrier dynamics of semiconductors.

  19. Carrier dynamics and terahertz photoconductivity of doped silicon measured by femtosecond pump-terahertz probe spectroscopy

    Institute of Scientific and Technical Information of China (English)

    ZHOU QingLi; SHI YuLei; LI Tong; JIN Bin; ZHAO DongMei; ZHANG CunLin

    2009-01-01

    The carrier dynamics and terahertz photoconductivity in the n-type silicon (n-Si) as well as in the p-type Silicon (pSi) have been investigated by using femtoaecond pump-terahertz probe technique. The measurements show that the relative change of terahertz transmission of p-Si at low pump power is slightly smaller than that of n-Si, due to the lower carrier density induced by the recombination of original holes in the p-type material and the photogenerated electrons. At high pump power, the bigger change of terahertz transmission of p-Si originates from the greater mobility of the carriers compared to n-Si. The transient photoconductivities are calculated and fit well with the Drude-Smith model, showing that the mobility of the photogenerated carriers decreases with the increasing pump power. The obtained results indicate that femtosecond pump-terahertz probe technique is a promising method to investigate the carrier dynamics of semiconductors.

  20. Towards pump-probe experiments of defect dynamics with short ion beam pulses

    Science.gov (United States)

    Schenkel, T.; Lidia, S. M.; Weis, C. D.; Waldron, W. L.; Schwartz, J.; Minor, A. M.; Hosemann, P.; Kwan, J. W.

    2013-11-01

    A novel, induction type linear accelerator, the Neutralized Drift Compression eXperiment (NDCX-II), is currently being commissioned at Berkeley Lab. This accelerator is designed to deliver intense (up to 3 × 1011 ions/pulse), 0.6 to ∼600 ns duration pulses of 0.05-1.2 MeV lithium ions at a rate of about 2 pulses per minute onto 1-10 mm scale target areas. When focused to mm-diameter spots, the beam is predicted to volumetrically heat micrometer thick foils to temperatures of ∼30,000 °K. At lower beam power densities, the short excitation pulse with tunable intensity and time profile enables pump-probe type studies of defect dynamics in a broad range of materials. We briefly describe the accelerator concept and design, present results from beam pulse shaping experiments and discuss examples of pump-probe type studies of defect dynamics following irradiation of materials with intense, short ion beam pulses from NDCX-II.

  1. Towards pump probe experiments of defect dynamics with short ion beam pulses

    Energy Technology Data Exchange (ETDEWEB)

    Schenkel, T. [Lawrence Berkeley National Laboratory (LBNL); Lidia, S. [Lawrence Berkeley National Laboratory (LBNL); Weis, C. D. [Lawrence Berkeley National Laboratory (LBNL); Waldron, W. L. [Lawrence Berkeley National Laboratory (LBNL); Schwartz, J. [Lawrence Berkeley National Laboratory (LBNL); Minor, Andrew [Lawrence Berkeley National Laboratory (LBNL); Hosemann, P [University of California, Berkeley; Kwan, J. W. [Lawrence Berkeley National Laboratory (LBNL)

    2013-01-01

    A novel, induction type linear accelerator, the Neutralized Drift Compression eXperiment (NDCX-II), is currently being commissioned at Berkeley Lab. This accelerator is designed to deliver intense (up to 3 1011 ions/pulse), 0.6 to 600 ns duration pulses of 0.05 1.2 MeV lithium ions at a rate of about 2 pulses per minute onto 1 10 mm scale target areas. When focused to mm-diameter spots, the beam is predicted to volumetrically heat micrometer thick foils to temperatures of 30,000 K. At lower beam power densities, the short excitation pulse with tunable intensity and time profile enables pump probe type studies of defect dynamics in a broad range of materials. We briefly describe the accelerator concept and design, present results from beam pulse shaping experiments and discuss examples of pump probe type studies of defect dynamics following irradiation of materials with intense, short ion beam pulses from NDCX-II.

  2. Towards pump–probe experiments of defect dynamics with short ion beam pulses

    Energy Technology Data Exchange (ETDEWEB)

    Schenkel, T., E-mail: t_schenkel@lbl.gov [Accelerator and Fusion Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 5R121, Berkeley, CA 94720 (United States); Lidia, S.M.; Weis, C.D.; Waldron, W.L.; Schwartz, J. [Accelerator and Fusion Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 5R121, Berkeley, CA 94720 (United States); Minor, A.M. [Materials Science Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 (United States); Department of Materials Science and Engineering, University of California, Berkeley, CA 94720 (United States); Hosemann, P. [Materials Science Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 (United States); Nuclear Engineering Department, University of California, Berkeley, CA 94720 (United States); Kwan, J.W. [Accelerator and Fusion Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, 5R121, Berkeley, CA 94720 (United States)

    2013-11-15

    A novel, induction type linear accelerator, the Neutralized Drift Compression eXperiment (NDCX-II), is currently being commissioned at Berkeley Lab. This accelerator is designed to deliver intense (up to 3 × 10{sup 11} ions/pulse), 0.6 to ∼600 ns duration pulses of 0.05–1.2 MeV lithium ions at a rate of about 2 pulses per minute onto 1–10 mm scale target areas. When focused to mm-diameter spots, the beam is predicted to volumetrically heat micrometer thick foils to temperatures of ∼30,000 °K. At lower beam power densities, the short excitation pulse with tunable intensity and time profile enables pump–probe type studies of defect dynamics in a broad range of materials. We briefly describe the accelerator concept and design, present results from beam pulse shaping experiments and discuss examples of pump–probe type studies of defect dynamics following irradiation of materials with intense, short ion beam pulses from NDCX-II.

  3. PLASTICITY OF SELECTED METALLIC MATERIALS IN DYNAMIC DEFORMATION CONDITIONS

    OpenAIRE

    2014-01-01

    Characteristics of a modernized flywheel machine has been presented in the paper. The laboratory stand enables to perform dynamic tensile tests and impact bending with a linear velocity of the enforcing element in the range of 5÷40 m/s. A new data acquisition system, based on the tensometric sensors, allows for significant qualitative improvement of registered signals. Some preliminary dynamic forming tests were performed for the selected group of metallic materials. Subsequent microstruct...

  4. A Zn2+-specific fluorescent molecular probe for the selective detection of endogenous cyanide in biorelevant samples.

    Science.gov (United States)

    Divya, Kizhumuri P; Sreejith, Sivaramapanicker; Balakrishna, Bugga; Jayamurthy, Purushothaman; Anees, Palappuravan; Ajayaghosh, Ayyappanpillai

    2010-09-07

    A Zn(2+)-specific molecular probe 3 was developed for the selective detection of CN(-) under aqueous conditions. The fluorescent Zn(2+) complex of 3 upon CN(-) addition generates a bright blue fluorescence that allows the detection of the latter and is useful for the screening of natural products with and without endogenous cyanide content.

  5. Development and Optimization of Piperidyl-1,2,3-Triazole Ureas as Selective Chemical Probes of Endocannabinoid Biosynthesis

    Science.gov (United States)

    Hsu, Ku-Lung; Tsuboi, Katsunori; Whitby, Landon R.; Speers, Anna E.; Pugh, Holly; Inloes, Jordon; Cravatt, Benjamin F.

    2014-01-01

    We have previously shown that 1,2,3-triazole ureas (1,2,3-TUs) act as versatile class of irreversible serine hydrolase inhibitors that can be tuned to create selective probes for diverse members of this large enzyme class, including diacylglycerol lipase-β (DAGLβ), a principal biosynthetic enzyme for the endocannabinoid 2-arachidonoylglycerol (2-AG). Here, we provide a detailed account of the discovery, synthesis, and structure-activity relationship (SAR) of (2-substituted)-piperidyl-1,2,3-TUs that selectively inactivate DAGLβ in living systems. Key to success was the use of activity-based protein profiling (ABPP) with broad-spectrum and tailored activity-based probes to guide our medicinal chemistry efforts. We also describe an expanded repertoire of DAGL-tailored activity-based probes that includes biotinylated and alkyne agents for enzyme enrichment coupled with mass spectrometry-based proteomics and assessment of proteome-wide selectivity. Our findings highlight the broad utility of 1,2,3-TUs for serine hydrolase inhibitor development and their application to create selective probes of endocannabinoid biosynthetic pathways. PMID:24152245

  6. Probing nuclear dynamics and architecture using single-walled carbon nanotubes

    Science.gov (United States)

    Jung, Yoon; Li, Junang; Fakhri, Nikta

    Chromatin is a multiscale dynamic architecture that acts as a template for many biochemical processes such as transcription and DNA replication. Recent developments such as Hi-C technology enable an identification of chromatin interactions across an entire genome. However, a single cell dynamic view of chromatin organization is far from understood. We discuss a new live cell imaging technique to probe the dynamics of the nucleus at a single cell level using single-walled carbon nanotubes (SWNTs). SWNTs are non-perturbing rigid rods (diameter of 1 nm and length of roughly 100 nm) that fluoresce in the near infrared region. Due to their high aspect ratio, they can diffuse in tight spaces and report on the architecture and dynamics of the nucleoplasm. We develop 3D imaging and tracking of SWNTs in the volume of the nucleus using double helix point spread function microscopy (DH-PSF) and discuss the capabilities of the DH-PSF for inferring the 3D orientation of nanotubes based on vectorial diffraction theory.

  7. Probing the dynamics of high-viscosity entangled polymers under shear using Neutron Spin Echo spectroscopy

    Science.gov (United States)

    Kawecki, M.; Gutfreund, P.; Adlmann, F. A.; Lindholm, E.; Longeville, S.; Lapp, A.; Wolff, M.

    2016-09-01

    Neutron Spin Echo spectroscopy provides unique insight into molecular and submolecular dynamics as well as intra- and inter-molecular interactions in soft matter. These dynamics may change drastically under shear flow. In particular in polymer physics a stress plateau is observed, which might be explained by an entanglement-disentanglement transition. However, such a transition is difficult to identify directly by experiments. Neutron Spin Echo has been proven to provide information about entanglement length and degree by probing the local dynamics of the polymer chains. Combining shear experiments and neutron spin echo is challenging since, first the beam polarisation has to be preserved during scattering and second, Doppler scattered neutrons may cause inelastic scattering. In this paper we present a new shear device adapted for these needs. We demonstrate that a high beam polarisation can be preserved and present first data on an entangled polymer solution under shear. To complement the experiments on the dynamics we present novel SANS data revealing shear- induced conformational changes in highly entangled polymers.

  8. Selectivity among two lectins: probing the effect of topology, multivalency and flexibility of "clicked" multivalent glycoclusters.

    Science.gov (United States)

    Cecioni, Samy; Faure, Sophie; Darbost, Ulrich; Bonnamour, Isabelle; Parrot-Lopez, Hélène; Roy, Olivier; Taillefumier, Claude; Wimmerová, Michaela; Praly, Jean-Pierre; Imberty, Anne; Vidal, Sébastien

    2011-02-11

    The design of multivalent glycoconjugates has been developed over the past decades to obtain high-affinity ligands for lectin receptors. While multivalency frequently increases the affinity of a ligand for its lectin through the so-called "glycoside cluster effect", the binding profiles towards different lectins have been much less investigated. We have designed a series of multivalent galactosylated glycoconjugates and studied their binding properties towards two lectins, from plant and bacterial origins, to determine their potential selectivity. The synthesis was achieved through copper(I)-catalysed azide-alkyne cycloaddition (CuAAC) under microwave activation between propargylated multivalent scaffolds and an azido-functionalised carbohydrate derivative. The interactions of two galactose-binding lectins from Pseudomonas aeruginosa (PA-IL) and Erythrina cristagalli (ECA) with the synthesized glycoclusters were studied by hemagglutination inhibition assays (HIA), surface plasmon resonance (SPR) and isothermal titration microcalorimetry (ITC). The results obtained illustrate the influence of the scaffold's geometry on the affinity towards the lectin and also on the relative potency in comparison with a monovalent galactoside reference probe.

  9. Popularity and Adolescent Friendship Networks : Selection and Influence Dynamics

    NARCIS (Netherlands)

    Dijkstra, Jan Kornelis; Cillessen, Antonius H. N.; Borch, Casey

    2013-01-01

    This study examined the dynamics of popularity in adolescent friendship networks across 3 years in middle school. Longitudinal social network modeling was used to identify selection and influence in the similarity of popularity among friends. It was argued that lower status adolescents strive to enh

  10. Popularity and Adolescent Friendship Networks: Selection and Influence Dynamics

    Science.gov (United States)

    Dijkstra, Jan Kornelis; Cillessen, Antonius H. N.; Borch, Casey

    2013-01-01

    This study examined the dynamics of popularity in adolescent friendship networks across 3 years in middle school. Longitudinal social network modeling was used to identify selection and influence in the similarity of popularity among friends. It was argued that lower status adolescents strive to enhance their status through befriending higher…

  11. Forecasting house prices in the 50 states using Dynamic Model Averaging and Dynamic Model Selection

    DEFF Research Database (Denmark)

    Bork, Lasse; Møller, Stig Vinther

    2015-01-01

    We examine house price forecastability across the 50 states using Dynamic Model Averaging and Dynamic Model Selection, which allow for model change and parameter shifts. By allowing the entire forecasting model to change over time and across locations, the forecasting accuracy improves...

  12. A cysteine probe with high selectivity and sensitivity promoted by response-assisted electrostatic attraction.

    Science.gov (United States)

    Zhou, Xin; Jin, Xuejun; Sun, Guangyan; Li, Donghao; Wu, Xue

    2012-09-11

    A new turn-on fluorescent probe for fast detection of cysteine in physiological conditions, based on a new response-assisted electrostatic attraction strategy, is reported. The practical utility of the probe in fluorescent protein labeling and subcellular imaging is also demonstrated.

  13. A water-soluble sulfonate-BODIPY based fluorescent probe for selective detection of HOCl/OCl⁻ in aqueous media.

    Science.gov (United States)

    Kim, Jiyoung; Kim, Youngmi

    2014-06-21

    A new, water-soluble BODIPY dye 1, bearing sulfonate groups at the 2- and 6-positions was found to be a sensitive and selective fluorescent probe for the detection of HOCl/OCl(-) in aqueous buffer solution. The probe, which displays extremely weak fluorescence owing to efficient singlet excited state quenching by photoinduced electron transfer (PeT) from an electron-rich catechol group at a meso-position, responds to HOCl/OCl(-) through a dramatic enhancement of its fluorescence intensity.

  14. Nonlinear dynamics of direction-selective recurrent neural media.

    Science.gov (United States)

    Xie, Xiaohui; Giese, Martin A

    2002-05-01

    The direction selectivity of cortical neurons can be accounted for by asymmetric lateral connections. Such lateral connectivity leads to a network dynamics with characteristic properties that can be exploited for distinguishing in neurophysiological experiments this mechanism for direction selectivity from other possible mechanisms. We present a mathematical analysis for a class of direction-selective neural models with asymmetric lateral connections. Contrasting with earlier theoretical studies that have analyzed approximations of the network dynamics by neglecting nonlinearities using methods from linear systems theory, we study the network dynamics with nonlinearity taken into consideration. We show that asymmetrically coupled networks can stabilize stimulus-locked traveling pulse solutions that are appropriate for the modeling of the responses of direction-selective neurons. In addition, our analysis shows that outside a certain regime of stimulus speeds the stability of these solutions breaks down, giving rise to lurching activity waves with specific spatiotemporal periodicity. These solutions, and the bifurcation by which they arise, cannot be easily accounted for by classical models for direction selectivity.

  15. A Simple and Effective Ratiometric Fluorescent Probe for the Selective Detection of Cysteine and Homocysteine in Aqueous Media

    Directory of Open Access Journals (Sweden)

    Risong Na

    2016-08-01

    Full Text Available Biothiols such as cysteine (Cys and homocysteine (Hcy are essential biomolecules participating in molecular and physiological processes in an organism. However, their selective detection remains challenging. In this study, ethyl 2-(3-formyl-4-hydroxyphenyl-4-methylthiazole-5-carboxylate (NL was synthesized as a ratiometric fluorescent probe for the rapid and selective detection of Cys and Hcy over glutathione (GSH and other amino acids. The fluorescence intensity of the probe in the presence of Cys/Hcy increased about 3-fold at a concentration of 20 equiv. of the probe, compared with that in the absence of these chemicals in aqueous media. The limits of detection of the fluorescent assay were 0.911 μM and 0.828 μM of Cys and Hcy, respectively. 1H-NMR and MS analyses indicated that an excited-state intramolecular proton transfer is the mechanism of fluorescence sensing. This ratiometric probe is structurally simple and highly selective. The results suggest that it has useful applications in analytical chemistry and diagnostics.

  16. Tracing molecular dynamics at the femto-/atto-second boundary through extreme-ultraviolet pump-probe spectroscopy

    CERN Document Server

    Carpeggiani, P A; Palacios, A; Gray, D; Martín, F; Charalambidis, D

    2013-01-01

    Coherent light pulses of few to hundreds of femtoseconds (fs) duration have prolifically served the field of ultrafast phenomena. While fs pulses address mainly dynamics of nuclear motion in molecules or lattices in the gas, liquid or condensed matter phase, the advent of attosecond pulses has in recent years provided direct experimental access to ultrafast electron dynamics. However, there are processes involving nuclear motion in molecules and in particular coupled electronic and nuclear motion that possess few fs or even sub-fs dynamics. In the present work we have succeeded in addressing simultaneously vibrational and electronic dynamics in molecular Hydrogen. Utilizing a broadband extreme-ultraviolet (XUV) continuum the entire, Frank-Condon allowed spectrum of H2 is coherently excited. Vibrational, electronic and ionization 1fs scale dynamics are subsequently tracked by means of XUV-pump-XUV-probe measurements. These reflect the intrinsic molecular behavior as the XUV probe pulse hardly distorts the mole...

  17. Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology.

    Science.gov (United States)

    Galdeano, Carles; Ciulli, Alessio

    2016-09-01

    Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity.

  18. The Juno and Cassini gravity measurements: probing the interior dynamics of Jupiter and Saturn

    Science.gov (United States)

    Kaspi, Y.; Galanti, E.; Hubbard, W. B.; Davighi, J. E.

    2015-10-01

    During 2016-2017 both the Juno and Cassini spacecraft will enter into close-by polar orbits of Jupiter and Saturn, respectively. Using Doppler tracking from Earth these flybys will allow high precision gravity measurements of these planets [1]. These will include high order gravity harmonics (at least up to J10), and the yet to be measured odd gravity spectrum. As the dynamics of deep flows relate to perturbations in the density of the planets, this data can be used to probe for the first time the atmospheric and interior flows on these planets [4, 5, 8]. Particularly, this may allow addressing one of the longest-standing questions in planetary atmospheric dynamics regarding the depth of the observed strong east-west jets-streams on Jupiter and Saturn. In this talk we review different approaches to analyze the gravity measurements, discuss the proposed models relating the gravity fields to the dynamics, and the implications of the results for understanding the mechanisms governing the interiors and atmospheres of Jupiter and Saturn.

  19. Black-hole horizons as probes of black-hole dynamics II: geometrical insights

    CERN Document Server

    Jaramillo, José Luis; Moesta, o Philipp; Rezzolla, Luciano

    2011-01-01

    In a companion paper [1], we have presented a cross-correlation approach to near-horizon physics in which bulk dynamics is probed through the correlation of quantities defined at inner and outer spacetime hypersurfaces acting as test screens. More specifically, dynamical horizons provide appropriate inner screens in a 3+1 setting and, in this context, we have shown that an effective-curvature vector measured at the common horizon produced in a head-on collision merger can be correlated with the flux of linear Bondi-momentum at null infinity. In this paper we provide a more sound geometric basis to this picture. First, we show that a rigidity property of dynamical horizons, namely foliation uniqueness, leads to a preferred class of null tetrads and Weyl scalars on these hypersurfaces. Second, we identify a heuristic horizon news-like function, depending only on the geometry of spatial sections of the horizon. Fluxes constructed from this function offer refined geometric quantities to be correlated with Bondi f...

  20. Experimental probing of conical intersection dynamics in the photodissociation of thioanisole.

    Science.gov (United States)

    Lim, Jeong Sik; Kim, Sang Kyu

    2010-08-01

    Chemical reactions that occur in the ground electronic state are described well by invoking the Born-Oppenheimer approximation, which allows their development to be rationalized by nuclear rearrangements that smoothly traverse an adiabatic potential energy surface. The situation is different, however, for reactions in electronically excited states, where non-adiabatic transitions occur between adiabatic surfaces. The conical intersection, in which two adiabatic surfaces touch, is accepted widely as the dynamic funnel for efficient non-adiabatic transitions, but its direct experimental probing is rare. Here, we investigate the photodissociation of thioanisole and observe a striking dependence of the relative yields of two reaction channels on the photoexcitation energy as indicated by a dynamic resonance in the product branching ratio. This results from the interference of two different adiabatic states that are in close proximity in the region of a conical intersection. The location of the observed resonance on the multidimensional potential energy surface thus reveals the nuclear configuration of the conical intersection and its dynamic role in the non-adiabatic transition.

  1. Nano-confined water in the interlayers of hydrocalumite: Reorientational dynamics probed by neutron spectroscopy and molecular dynamics computer simulations

    Science.gov (United States)

    Kalinichev, A. G.; Faraone, A.; Udovic, T.; Kolesnikov, A. I.; de Souza, N. R.; Reinholdt, M. X.; Kirkpatrick, R.

    2008-12-01

    Layered double hydroxides (LDHs, anionic clays) represent excellent model systems for detailed molecular- level studies of the structure, dynamics, and energetics of nano-confined water in mineral interlayers and nano-pores, because LDH interlayers can have a well-defined structures and contain H2O molecules and a wide variety of anions in structurally well-defined positions and coordinations. [Ca2Al(OH)6]Cl·2H2O, also known as hydrocalumite or Friedel's salt, has a well- ordered Ca,Al distribution in the hydroxide layer and a very high degree of H2O,Cl ordering in the interlayer. It is also one of the only LDH phase for which a single crystal structure refinement is available. Thus, it is currently the best model compound for understanding the structure and dynamical behavior of interlayer and surface species in other, less-ordered, LDHs. We investigated the structural and dynamic behavior of water in the interlayers of hydrocalumite using inelastic (INS) and quasielastic (QENS) neutron scattering and molecular dynamics computer simulations. The comperehensive neutron scattering studies were performed for one fully hydrated and one dehydrated sample of hydrocalumite using several complementary instruments (HFBS, DCS and FANS at NCNR; HRMECS and QENS at IPNS) at temperatures above and below the previously discovered order-disorder interlayer phase transition. Together the experimental and molecular modeling results capture the important details of the dynamics of nano-confined water and the effects of the orientational ordering of H2O molecules above and below the phase transition. They provide otherwise unobtainable experimental information about the transformation of H2O librational and diffusional modes across the order-disorder phase transition and significantly add to our current understanding of the structure and dynamics of water in LDH phases based on the earlier NMR, IR, X-ray, and calorimetric measurements. The approach can now be extended to probe the

  2. Rupture mechanism of aromatic systems from graphite probed with molecular dynamics simulations.

    Science.gov (United States)

    Leng, Yumin; Chen, Jian; Zhou, Beifei; Gräter, Frauke

    2010-07-01

    Intermolecular interactions involving aromatic rings are of pivotal importance in many areas of chemistry, biology and materials science. Mimicking recent atomic force microscopy (AFM) experiments that measured the adhesion forces of single pi-pi complexes, here interactions between pyrene/coronene and graphite have been probed by force-probe molecular dynamics (FPMD) simulations. The pyrene or coronene molecule was connected to a virtual spring through a flexible poly(ethylene glycol) (PEG) linker and was pulled away from graphite in water under constant velocity. Pyrene and coronene showed similar unbinding pathways featuring four states, with a transition and an intermediate state connecting the bound and unbound states in terms of distance and interplanar angles. Transient conformations with tilted orientations (approximately 40 degrees) and with one side of the aromatic structure still in contact with the graphite surface (approximately 70 degrees) were identified as the transition and intermediate states, respectively, similar to previously observed perpendicularly stacked benzene dimers. The distance to transition state x(tr) was determined to be 0.23 +/- 0.03 nm both for pyrene/graphite and coronene/graphite. The complexes share similar unbinding pathways, but coronene binds to graphite more strongly than to pyrene.

  3. Retrieval of spectral and dynamic properties from two-dimensional infrared pump-probe experiments.

    Science.gov (United States)

    Chelli, Riccardo; Volkov, Victor V; Righini, Roberto

    2008-07-15

    We have developed a fitting algorithm able to extract spectral and dynamic properties of a three level oscillator from a two-dimensional infrared spectrum (2D-IR) detected in time resolved nonlinear experiments. Such properties go from the frequencies of the ground-to-first and first-to-second vibrational transitions (and hence anharmonicity) to the frequency-fluctuation correlation function. This last is represented through a general expression that allows one to approach the various strategies of modeling proposed in the literature. The model is based on the Kubo picture of stochastic fluctuations of the transition frequency as a result of perturbations by a fluctuating surrounding. To account for the line-shape broadening due to pump pulse spectral width in double-resonance measurements, we supply the fitting algorithm with the option to perform the convolution of the spectral signal with a Lorentzian function in the pump-frequency dimension. The algorithm is tested here on 2D-IR pump-probe spectra of a Gly-Ala dipeptide recorded at various pump-probe delay times. Speedup benchmarks have been performed on a small Beowulf cluster. The program is written in FORTRAN language for both serial and parallel architectures and is available free of charge to the interested reader.

  4. Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study.

    Science.gov (United States)

    do Canto, António M T M; Robalo, João R; Santos, Patrícia D; Carvalho, Alfredo J Palace; Ramalho, J P Prates; Loura, Luís M S

    2016-11-01

    Fluorescence spectroscopy and microscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in these membranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3-4Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using them as membrane reporters. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Observational constraints on viable f(R) parametrizations with geometrical and dynamical probes

    CERN Document Server

    Basilakos, Spyros; Perivolaropoulos, Leandros

    2013-01-01

    We demonstrate that a wide range of viable f(R) parameterizations (including the Hu & Sawicki and the Starobinsky models) can be expressed as perturbations deviating from the LCDM Lagrangian. We constrain the deviation parameter b using a combination of geometrical and dynamical observational probes. In particular, we perform a joint likelihood analysis of the recent Supernovae Type Ia data, the Cosmic Microwave Background shift parameters, the Baryonic Acoustic Oscillations and the growth rate data provided by the various galaxy surveys. This analysis provides constraints for the following parameters: the matter density Omega_{m0}, the deviation from LCDM parameter b and the growth index gamma(z). We parametrize the growth index gamma(z) in three manners (constant, Taylor expansion around z=0, and Taylor expansion around the scale factor). We point out the numerical difficulty for solving the generalized f(R) Friedman equation at high redshifts due to stiffness of the resulting ordinary differential equa...

  6. Dynamic Probe Window Based Optimization for Surveillance in Home Security System

    Directory of Open Access Journals (Sweden)

    Bhaskar Kapoor

    2010-02-01

    Full Text Available Tracking of a moving object is very important for video surveillance in a real time scenario. The proposedalgorithm uses dynamic probe window based approach & combines the conventional edge based and framedifferencing approach to achieve better algorithmic time complexity as well as improved results. First itcomputes the edge map of two consecutive frames with the help of first order differential sobel operator dueto its noise resistant attributes and applies the frame differencing method between the two consecutive edgemaps. Apart from the above optimization, our method doesn’t differentiate between the scenario when motionoccurs and when it doesn’t, that is, almost same computation overhead is required even if motion is not thereso it reduces the time complexity of the algorithm when no motion is detected. The effectiveness of theproposed motion detection algorithm is demonstrated in a real time environment and the evaluation resultsare reported.

  7. Molecular Frame Photoelectron Angular Distributions as a Probe of Geometry and Auger Dissociation Dynamics

    Science.gov (United States)

    Trevisan, Cynthia S.; Rescigno, Thomas N.; McCurdy, C. William

    2012-06-01

    Compex Kohn variational calculations of the molecular frame photoelectron distributions (MFPADs) for 1s core ionization of CH4, NH3, and H2O are presented for ejected electron energies below 25 eV. Surprisingly, in these three cases there are energy ranges in which the photoelectron MFPADs effectively form ``images'' of the molecular geometry. Comparison with recent momentum imaging experiments on methane at the Advanced Light Source verify this effect. Simultaneous double Auger decay in these molecules can produce dissociation into three charged fragments, e.g., CH2^+ + 2 H^+, allowing the complete orientation of the molecule and therefore the measurement of 3D MFPADs that test these predictions. In other Auger decay channels the measurement of 3D MFPADs verifies axial recoil (prompt dissociation) or probes its absence in the Auger dissociation dynamics of small molecules.

  8. Probing molecular dynamics at the nanoscale via an individual paramagnetic center

    Science.gov (United States)

    Staudacher, Tobias; Raatz, Nicole; Pezzagna, Sebastien; Meijer, Jan; Reinhard, Friedemann; Meriles, Carlos; Wrachtrup, Joerg

    We use shallow NVs to probe mesoscale proton ensembles from different substances deposited on the diamond surface. We resort to a form of correlation spectroscopy to reconstruct the equivalent of a nuclear ``free-induction-decay'' (FID), which, unlike the NMR counterpart, does not require nuclear spin pre-polarization. This pseudo FID has a limit decay time governed by the NV spin-lattice relaxation time T1 (typically longer than the NV coherence lifetime T2), which allows us to attain spectral resolution superior to that possible with standard magnetometry techniques. Upon applying this scheme to solid- and liquid-state substances we find substantial differences in the correlation signal lifetime, which we associate with the presumably different molecular dynamics governing these systems. In particular, we observe long-lived 1H signals from oil molecules, likely a consequence of the interplay between fast molecular tumbling and slow self-diffusion.

  9. Probing spin-orbit-interaction-induced electron dynamics in the carbon atom by multiphoton ionization

    Science.gov (United States)

    Rey, H. F.; van der Hart, H. W.

    2014-09-01

    We use R-matrix theory with time dependence (RMT) to investigate multiphoton ionization of ground-state atomic carbon with initial orbital magnetic quantum number ML=0 and ML=1 at a laser wavelength of 390 nm and peak intensity of 1014W/cm2. Significant differences in ionization yield and ejected-electron momentum distribution are observed between the two values for ML. We use our theoretical results to model how the spin-orbit interaction affects electron emission along the laser polarization axis. Under the assumption that an initial C atom is prepared at zero time delay with ML=0, the dynamics with respect to time delay of an ionizing probe pulse modeled by using RMT theory is found to be in good agreement with available experimental data.

  10. Probing how initial retinal configuration controls photochemical dynamics in retinal proteins

    Directory of Open Access Journals (Sweden)

    Sheves M.

    2013-03-01

    Full Text Available The effects of the initial retinal configuration and the active isomerization coordinate on the photochemistry of retinal proteins (RPs are assessed by comparing photochemical dynamics of two stable retinal ground state configurations (all-trans,15-anti vs. 13-cis,15-syn, within two RPs: Bacteriorhodopsin (BR and Anabaena Sensory Rhodopsin (ASR. Hyperspectral pump-probe spectroscopy shows that photochemistry starting from 13-cis retinal in both proteins is 3-10 times faster than when started in the all-trans state, suggesting that the hastening is ubiquitous to microbial RPs, regardless of their different biological functions and origin. This may also relate to the known disparity of photochemical rates between microbial RPs and visual pigments. Importance and possible underlying mechanisms are discussed as well.

  11. Dynamic angle selection in X-ray computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Dabravolski, Andrei, E-mail: andrei.dabravolski@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Batenburg, Kees Joost, E-mail: joost.batenburg@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Centrum Wiskunde and Informatica (CWI), Science Park 123, 1098 XG Amsterdam (Netherlands); Sijbers, Jan, E-mail: jan.sijbers@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium)

    2014-04-01

    Highlights: • We propose the dynamic angle selection algorithm for CT scanning. • The approach is based on the concept of information gain over a set of solutions. • Projection angles are selected based on the already available projection data. • The approach can lead to more accurate results from fewer projections. - Abstract: In X-ray tomography, a number of radiographs (projections) are recorded from which a tomogram is then reconstructed. Conventionally, these projections are acquired equiangularly, resulting in an unbiased sampling of the Radon space. However, especially in case when only a limited number of projections can be acquired, the selection of the angles has a large impact on the quality of the reconstructed image. In this paper, a dynamic algorithm is proposed, in which new projection angles are selected by maximizing the information gain about the object, given the set of possible new angles. Experiments show that this approach can select projection angles for which the accuracy of the reconstructed image is significantly higher compared to the standard angle selections schemes.

  12. PLASTICITY OF SELECTED METALLIC MATERIALS IN DYNAMIC DEFORMATION CONDITIONS

    Directory of Open Access Journals (Sweden)

    Jacek PAWLICKI

    2014-06-01

    Full Text Available Characteristics of a modernized flywheel machine has been presented in the paper. The laboratory stand enables to perform dynamic tensile tests and impact bending with a linear velocity of the enforcing element in the range of 5÷40 m/s. A new data acquisition system, based on the tensometric sensors, allows for significant qualitative improvement of registered signals. Some preliminary dynamic forming tests were performed for the selected group of metallic materials. Subsequent microstructural examinations and identification of the fracture type enabled to describe a correlation between strain rate, strain and microstructure.

  13. A carbon dot-based "off-on" fluorescent probe for highly selective and sensitive detection of phytic acid.

    Science.gov (United States)

    Gao, Zhao; Wang, Libing; Su, Rongxin; Huang, Renliang; Qi, Wei; He, Zhimin

    2015-08-15

    We herein report a facile, one-step pyrolysis synthesis of photoluminescent carbon dots (CDs) using citric acid as the carbon source and lysine as the surface passivation reagent. The as-prepared CDs show narrow size distribution, excellent blue fluorescence and good photo-stability and water dispersivity. The fluorescence of the CDs was found to be effectively quenched by ferric (Fe(III)) ions with high selectivity via a photo-induced electron transfer (PET) process. Upon addition of phytic acid (PA) to the CDs/Fe(III) complex dispersion, the fluorescence of the CDs was significantly recovered, arising from the release of Fe(III) ions from the CDs/Fe(III) complex because PA has a higher affinity for Fe(III) ions compared to CDs. Furthermore, we developed an "off-on" fluorescence assay method for the detection of phytic acid using CDs/Fe(III) as a fluorescent probe. This probe enables the selective detection of PA with a linear range of 0.68-18.69 μM and a limit of detection (signal-to-noise ratio is 3) of 0.36 μM. The assay method demonstrates high selectivity, repeatability, stability and recovery ratio in the detection of the standard and real PA samples. We believe that the facile operation, low-cost, high sensitivity and selectivity render this CD-based "off-on" fluorescent probe an ideal sensing platform for the detection of PA.

  14. Functional network macroscopes for probing past and present Earth system dynamics (Invited)

    Science.gov (United States)

    Donges, J. F.

    2013-12-01

    probing past and present Earth system dynamics: Complex hierarchical interactions, tipping points, and beyond" by J.F. Donges, Humboldt University, Berlin, Germany, 2012. URL: http://nbn-resolving.de/urn:nbn:de:kobv:11-100207126.

  15. Strategy selection in evolutionary game dynamics on group interaction networks.

    Science.gov (United States)

    Tan, Shaolin; Feng, Shasha; Wang, Pei; Chen, Yao

    2014-11-01

    Evolutionary game theory provides an appropriate tool for investigating the competition and diffusion of behavioral traits in biological or social populations. A core challenge in evolutionary game theory is the strategy selection problem: Given two strategies, which one is favored by the population? Recent studies suggest that the answer depends not only on the payoff functions of strategies but also on the interaction structure of the population. Group interactions are one of the fundamental interactive modes within populations. This work aims to investigate the strategy selection problem in evolutionary game dynamics on group interaction networks. In detail, the strategy selection conditions are obtained for some typical networks with group interactions. Furthermore, the obtained conditions are applied to investigate selection between cooperation and defection in populations. The conditions for evolution of cooperation are derived for both the public goods game and volunteer's dilemma game. Numerical experiments validate the above analytical results.

  16. Bases for time-resolved probing of transient carrier dynamics by optical pump-probe scanning tunneling microscopy.

    Science.gov (United States)

    Yokota, Munenori; Yoshida, Shoji; Mera, Yutaka; Takeuchi, Osamu; Oigawa, Haruhiro; Shigekawa, Hidemi

    2013-10-07

    The tangled mechanism that produces optical pump-probe scanning tunneling microscopy spectra from semiconductors was analyzed by comparing model simulation data with experimental data. The nonlinearities reflected in the spectra, namely, the excitations generated by paired laser pulses with a delay time, the logarithmic relationship between carrier density and surface photovoltage (SPV), and the effect of the change in tunneling barrier height depending on SPV, were examined along with the delay-time-dependent integration process used in measurement. The optimum conditions required to realize reliable measurement, as well as the validity of the microscopy technique, were demonstrated for the first time.

  17. Protocols for dynamically probing topological edge states and dimerization with fermionic atoms in optical potentials

    Science.gov (United States)

    Metcalf, Mekena; Lai, Chen-Yen; Wright, Kevin; Chien, Chih-Chun

    2017-06-01

    Topological behavior has been observed in quantum systems including ultracold atoms. However, background harmonic traps for cold atoms hinder the direct detection of topological edge states arising at the boundary because the distortion fuses the edge states into the bulk. We propose experimentally feasible protocols to probe localized edge states and dimerization of ultracold fermions. By confining cold atoms in a ring lattice and changing the boundary condition from periodic to open using an off-resonant laser sheet to cut open the ring, topological edge states can be generated. A lattice in a topological configuration can trap a single particle released at the edge as the system evolves in time. Alternatively, depleting an initially filled lattice away from the boundary reveals the occupied edge states. Signatures of dimerization in the presence of contact interactions can be found in selected correlations as the system boundary suddenly changes from periodic to open and exhibit memory effects of the initial state distinguishing different configurations.

  18. Role of strongly modulated coherence in transient evolution dynamics of probe absorption in a three-level atomic system

    Science.gov (United States)

    Panchadhyayee, Pradipta

    2013-11-01

    We investigate the dynamical behaviour of atomic response in a closed three-level V-type atomic system with the variation of different relevant parameters to exhibit transient evolution of absorption, gain and transparency in the probe response. The oscillations in probe absorption and gain can be efficiently modulated by changing the values of the Rabi frequency, detuning and the collective phase involved in the system. The interesting outcome of the work is the generation of coherence controlled loop-structure with varying amplitudes in the oscillatory probe response of the probe field at various parameter conditions. The prominence of these structures is observed when the coherence induced in a one-photon excitation path is strongly modified by two-step excitations driven by the coherent fields operating in closed interaction contour. In contrast to purely resonant case, the time interval between two successive loops gets significantly reduced with the application of non-zero detuning in the coherent fields.

  19. The Selection and Use of Sorghum (Sorghum propinquum Bacterial Artificial Chromosomes as Cytogenetic FISH Probes for Maize (Zea mays L.

    Directory of Open Access Journals (Sweden)

    Debbie M. Figueroa

    2011-01-01

    Full Text Available The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescence in situ hybridization (FISH maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and compared in silico BAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented along with an example of transgenomic BAC FISH mapping. This strategy has been used to facilitate the integration of RFLP and FISH maps in other large-genome species.

  20. The selection and use of sorghum (Sorghum propinquum) bacterial artificial chromosomes as cytogenetic FISH probes for maize (Zea mays L.).

    Science.gov (United States)

    Figueroa, Debbie M; Davis, James D; Strobel, Cornelia; Conejo, Maria S; Beckham, Katherine D; Ring, Brian C; Bass, Hank W

    2011-01-01

    The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescence in situ hybridization (FISH) maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP) probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and compared in silico BAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented along with an example of transgenomic BAC FISH mapping. This strategy has been used to facilitate the integration of RFLP and FISH maps in other large-genome species.

  1. Carbon-deuterium bonds as non-perturbative infrared probes of protein dynamics, electrostatics, heterogeneity, and folding.

    Science.gov (United States)

    Zimmermann, Jörg; Romesberg, Floyd E

    2014-01-01

    Vibrational spectroscopy is uniquely able to characterize protein dynamics and microenvironmental heterogeneity because it possesses an inherently high temporal resolution and employs probes of ultimately high structural resolution-the bonds themselves. The use of carbon-deuterium (C-D) bonds as vibrational labels circumvents the spectral congestion that otherwise precludes the use of vibrational spectroscopy to proteins and makes the observation of single vibrations within a protein possible while being wholly non-perturbative. Thus, C-D probes can be used to site-specifically characterize conformational heterogeneity and thermodynamic stability. C-D probes are also uniquely useful in characterizing the electrostatic microenvironment experienced by a specific residue side chain or backbone due to its effect on the C-D absorption frequency. In this chapter we describe the experimental procedures required to use C-D bonds and FT IR spectroscopy to characterize protein dynamics, structural and electrostatic heterogeneity, ligand binding, and folding.

  2. Optically induced lattice dynamics probed with ultrafast x-ray diffraction

    Science.gov (United States)

    Lee, H. J.; Workman, J.; Wark, J. S.; Averitt, R. D.; Taylor, A. J.; Roberts, J.; McCulloch, Q.; Hof, D. E.; Hur, N.; Cheong, S.-W.; Funk, D. J.

    2008-04-01

    We have studied the picosecond lattice dynamics of optically pumped hexagonal LuMnO3 by using ultrafast x-ray diffraction. The results show a shift and broadening of the diffraction curve due to the stimulated lattice expansion. To understand the transient response of the lattice, the measured time- and angle-resolved diffraction curves are compared to a theoretical calculation based on the dynamical diffraction theory of coherent phonon propagation modified for the hexagonal crystal structure of LuMnO3 . Our simulations reveal that a large coupling coefficient (c13) between the a-b plane and the c axis is required to fit the data. Though we interpret the transient response within the framework of thermal coherent phonons, we do not exclude the possibility of strong nonthermal coupling of the electronic excitation to the atomic framework. We compare this result to our previous coherent phonon studies of LuMnO3 in which we used optical pump-probe spectroscopy.

  3. Understanding Earth's radiation belt electron dynamics: Van Allen Probes observations and simulations

    Science.gov (United States)

    Li, Wen; Ma, Qianli; Thorne, Richard; Bortnik, Jacob; Zhang, Xiaojia

    2016-10-01

    Various physical processes are known to cause acceleration, loss, and transport of energetic electrons in the Earth's radiation belts, but their quantitative roles in different time and space need further investigation. In the present paper, we evaluate the relative roles of various physical processes during geomagnetic storms using a 3D diffusion simulation. By quantitatively comparing the electron evolution observed by Van Allen Probes and simulation, we found that whistler-mode chorus waves play a critical role in accelerating electrons up to several MeV through efficient energy diffusion. By only including radial diffusion driven by ultra-low-frequency waves, the simulation underestimates the observed electron acceleration, while radial diffusion plays an important role in redistributing electrons. Although an additional loss process is required to fully explain the overestimated electron fluxes at multi-MeV, the combined physical processes of radial diffusion and scattering by whistler-mode waves reproduce the observed electron dynamics remarkably well, suggesting that quasi-linear diffusion theory is reasonable to evaluate radiation belt electron dynamics, and the importance of nonlinear wave-particle interaction may still remain as an open question. We would like to acknowledge AFOSR Award FA9550-15-1-0158, NASA Grants NNX15AI96G, NNX15AF61G, and the NSF Grant AGS 1564510 for supporting this research.

  4. Probing initial-stages of ALD growth with dynamic in situ spectroscopic ellipsometry

    Energy Technology Data Exchange (ETDEWEB)

    Muneshwar, Triratna, E-mail: muneshwa@ualberta.ca; Cadien, Ken

    2015-02-15

    Graphical abstract: - Highlights: • Dynamic in situ spectroscopic ellipsometry to study ALD growth initiation. • Sub-monolayer ALD growth is modeled as diffusive film growth mode. • Bruggeman's EMA model used to analyze d-iSE data. • Plasma enhanced ALD of ZrN is presented as example. • Surface coverage of ZrN film is calculated after every ALD cycle. - Abstract: The initial stages of ALD surface reactions are probed using dynamic in situ spectroscopic ellipsometry (d-iSE) technique during plasma-enhanced ALD of zirconium nitride (ZrN) thin films in spectral range of 0.73–6.4 eV. The measured change in the ellipsometry parameter Δ, with every precursor (TDMAZr) and reactant (forming gas plasma) exposure is interpreted as the combined effect of film growth and change in surface chemistry during ALD. We present application of Bruggeman's effective-medium approximation (B-EMA) in the analysis of d-iSE data to determine fractional surface coverage (θ) of ALD grown film at the end of every deposition cycle. During the deposition of first few ZrN monolayers, d-iSE datasets are analyzed on the basis of surface diffusion enhanced ALD growth, where the surface adsorbed precursor molecules can diffuse over substrate surface to occupy energetically favorable surface sites. The determined surface coverage of ZrN films highlights the effects of substrate enhanced ALD growth.

  5. Initial dynamics of the Norrish Type I reaction in acetone: probing wave packet motion.

    Science.gov (United States)

    Brogaard, Rasmus Y; Sølling, Theis I; Møller, Klaus B

    2011-02-10

    The Norrish Type I reaction in the S(1) (nπ*) state of acetone is a prototype case of ketone photochemistry. On the basis of results from time-resolved mass spectrometry (TRMS) and photoelectron spectroscopy (TRPES) experiments, it was recently suggested that after excitation the wave packet travels toward the S(1) minimum in less than 30 fs and stays there for more than 100 picoseconds [Chem. Phys. Lett.2008, 461, 193]. In this work we present simulated TRMS and TRPES signals based on ab initio multiple spawning simulations of the dynamics during the first 200 fs after excitation, getting quite good agreement with the experimental signals. We can explain the ultrafast decay of the experimental signals in the following manner: the wave packet simply travels, mainly along the deplanarization coordinate, out of the detection window of the ionizing probe. This window is so narrow that subsequent revival of the signal due to the coherent deplanarization vibration is not observed, meaning that from the point of view of the experiment the wave packets travels directly to the S(1) minimum. This result stresses the importance of pursuing a closer link to the experimental signal when using molecular dynamics simulations in interpreting experimental results.

  6. Van Allen Probes observations of EMIC events triggered by solar wind dynamic pressure enhancements

    Science.gov (United States)

    Lee, D. Y.; Cho, J.; Roh, S. J.; Shin, D. K.; Hwang, J.; Kim, K. C.; Choi, C.; Kletzing, C.; Wygant, J. R.; Thaller, S. A.; Larsen, B.; Skoug, R. M.

    2015-12-01

    Electromagnetic ion cyclotron (EMIC) waves are one of the key plasma waves that can affect charged particle dynamics in the Earth's inner magnetosphere. One of the generation mechanisms of EMIC waves has long been known to be due to magnetospheric compression due to impact by enhanced solar wind dynamic pressure Pdyn. With the Van Allen Probes observations, we have identified 4 EMIC wave events that are triggered by Pdyn enhancements under northward IMF, prolonged quiet time conditions. We find the following features of the EMIC events. (1) They are triggered immediately at the Pdyn impact and remain active during the same period as the enhanced Pdyn duration. (2) They occur in either H band or He band or both. (3) Two events occur inside the plasmasphere and the other two outside the plasmasphere. (4) The wave polarization, either R or L, are highly elliptical, being close to be linear. (5) The wave normal angles are quite large, well away from being field-aligned. (6) About 10 - 50 keV proton fluxes indicate enhanced flux state with ~90 deg-peaked anisotropy in velocity distribution after the Pdyn impact. (7) From low altitude NOAA POES satellite observations of particles we find no obvious evidence for relativistic electron precipitation due to these Pdyn-triggered EMIC events. We will discuss implications of these observations on wave generation mechanism and interaction with radiation belt electrons.

  7. Multi-probe relaxation dispersion measurements increase sensitivity to protein dynamics.

    Science.gov (United States)

    Fenwick, R Bryn; Oyen, David; Wright, Peter E

    2016-02-17

    Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion measurements are a valuable tool for the characterization of structural transitions on the micro-millisecond timescale. While the measurement of (15)N relaxation dispersion is now routine, the measurements with alternative nuclei remain limited. Here we report (15)N as well as (1)H R2 relaxation dispersion measurements of the N23PP/S148A "dynamic knockout" mutant of dihydrofolate reductase. The (1)H dispersion measurements are complementary to (15)N data as many additional residues are observed to have dispersive behavior for the (1)H nucleus. Simultaneous fitting of the dispersion profiles for the two nuclei increases the accuracy of exchange parameters determined for individual residues and clustered groups of residues. The different sensitivity of the two nuclei to changes in backbone torsional angles, ring currents, and hydrogen bonding effects provides important insights into the nature of the structural changes that take place during the exchange process. We observe clear evidence of direct and indirect hydrogen bond effects for the (15)N and (1)H chemical shift changes in the active-site, modulation of ring current shielding in the CD-loop and backbone torsional changes in a cluster of residues associated with the C-terminus. This work demonstrates the power of combined (1)H and (15)N probes for the study of backbone dynamics on the micro-millisecond timescale though the analysis of chemical shift changes.

  8. Spin tune mapping as a novel tool to probe the spin dynamics in storage rings

    Science.gov (United States)

    Saleev, A.; Nikolaev, N. N.; Rathmann, F.; Augustyniak, W.; Bagdasarian, Z.; Bai, M.; Barion, L.; Berz, M.; Chekmenev, S.; Ciullo, G.; Dymov, S.; Eversmann, D.; Gaisser, M.; Gebel, R.; Grigoryev, K.; Grzonka, D.; Guidoboni, G.; Heberling, D.; Hejny, V.; Hempelmann, N.; Hetzel, J.; Hinder, F.; Kacharava, A.; Kamerdzhiev, V.; Keshelashvili, I.; Koop, I.; Kulikov, A.; Lehrach, A.; Lenisa, P.; Lomidze, N.; Lorentz, B.; Maanen, P.; Macharashvili, G.; Magiera, A.; Mchedlishvili, D.; Mey, S.; Müller, F.; Nass, A.; Pesce, A.; Prasuhn, D.; Pretz, J.; Rosenthal, M.; Schmidt, V.; Semertzidis, Y.; Senichev, Y.; Shmakova, V.; Silenko, A.; Slim, J.; Soltner, H.; Stahl, A.; Stassen, R.; Stephenson, E.; Stockhorst, H.; Ströher, H.; Tabidze, M.; Tagliente, G.; Talman, R.; Engblom, P. Thörngren; Trinkel, F.; Uzikov, Yu.; Valdau, Yu.; Valetov, E.; Vassiliev, A.; Weidemann, C.; Wrońska, A.; Wüstner, P.; Zuprański, P.; Zurek, M.; JEDI Collaboration

    2017-07-01

    Precision experiments, such as the search for electric dipole moments of charged particles using storage rings, demand for an understanding of the spin dynamics with unprecedented accuracy. The ultimate aim is to measure the electric dipole moments with a sensitivity up to 15 orders in magnitude better than the magnetic dipole moment of the stored particles. This formidable task requires an understanding of the background to the signal of the electric dipole from rotations of the spins in the spurious magnetic fields of a storage ring. One of the observables, especially sensitive to the imperfection magnetic fields in the ring is the angular orientation of stable spin axis. Up to now, the stable spin axis has never been determined experimentally, and in addition, the JEDI collaboration for the first time succeeded to quantify the background signals that stem from false rotations of the magnetic dipole moments in the horizontal and longitudinal imperfection magnetic fields of the storage ring. To this end, we developed a new method based on the spin tune response of a machine to artificially applied longitudinal magnetic fields. This novel technique, called spin tune mapping, emerges as a very powerful tool to probe the spin dynamics in storage rings. The technique was experimentally tested in 2014 using polarized deuterons stored in the cooler synchrotron COSY, and for the first time, the angular orientation of the stable spin axis at two different locations in the ring has been determined to an unprecedented accuracy of better than 2.8 μ rad .

  9. A dynamic data source selection system for smartwatch platform.

    Science.gov (United States)

    Nemati, Ebrahim; Sideris, Konstantinos; Kalantarian, Haik; Sarrafzadeh, Majid

    2016-08-01

    A novel data source selection algorithm is proposed for ambulatory activity tracking of elderly people. The algorithm introduces the concept of dynamic switching between the data collection modules (a smartwatch and a smartphone) to improve accuracy and battery life using contextual information. We show that by making offloading decisions as a function of activity, the proposed algorithm improves power consumption and accuracy of the previous work by 7 hours and 5% respectively compared to the baseline.

  10. Selected topics in nonlinear dynamics and theoretical electrical engineering

    Energy Technology Data Exchange (ETDEWEB)

    Kyamakya, Kyandoghere; Chedjou, Jean Camberlain [Kalgenfurt Univ. (Austria); Halang, Wolfgang A.; Li, Zhong [Hagen Fernuniv. (Germany); Mathis, Wolfgang (eds.) [Leibniz Univ. Hannover (Germany). Inst. fuer Theoretische Elektrotechnik

    2013-02-01

    Post proceedings of Joint Conference INDS 2011 and ISTET 2011. Recent advances in nonlinear Dynamics and Synchronization as well as in Theoretical Electrical Engineering. Written by leading experts in the field. This book contains a collection of recent advanced contributions in the field of nonlinear dynamics and synchronization, including selected applications in the area of theoretical electrical engineering. The present book is divided into twenty-one chapters grouped in five parts. The first part focuses on theoretical issues related to chaos and synchronization and their potential applications in mechanics, transportation, communication and security. The second part handles dynamic systems modelling and simulation with special applications to real physical systems and phenomena. The third part discusses some fundamentals of electromagnetics (EM) and addresses the modelling and simulation in some real physical electromagnetic scenarios. The fourth part mainly addresses stability concerns. Finally, the last part assembles some sample applications in the area of optimization, data mining, pattern recognition and image processing.

  11. Selective reflection technique as a probe to monitor the growth of a metallic thin film on dielectric surfaces

    CERN Document Server

    Martins, Weliton Soares; Chevrollier, Martine; de Silans, Thierry Passerat

    2013-01-01

    Controlling thin film formation is technologically challenging. The knowledge of physical properties of the film and of the atoms in the surface vicinity can help improve control over the film growth. We investigate the use of the well-established selective reflection technique to probe the thin film during its growth, simultaneously monitoring the film thickness, the atom-surface van der Waals interaction and the vapor properties in the surface vicinity.

  12. Nanoscale thermal, acoustic, and magnetic dynamics probed with soft x-ray light

    Science.gov (United States)

    Siemens, Mark E.

    This thesis discusses the application of coherent, ultrafast beams of soft x-ray light from high-order harmonic generation (HHG) to study thermal, acoustic, and magnetic processes in nanostructures. This short-wavelength light is a uniquely powerful probe of surface dynamics since it has both a very short wavelength and duration. First, this thesis reports the first observation and quantitative measurements of the transition from diffusive to ballistic thermal transport for the case of heat flow away from a heated nanostructure into a bulk substrate. This measurement provides insight into the fundamentals of thermal energy transport away from nanoscale hot spots, and demonstrates a fundamental limit to the energy dissipation capability of nanostructures. Further, we propose a straightforward correction to the Fourier law for heat diffusion, necessary for thermal management in nanoelectronics, nano-enabled energy systems, nanomanufacturing, and nanomedicine. Second, this work discusses dynamic measurements of ultra-high frequency surface acoustic waves (SAW) and the first SAW dispersion measurement in a nanostructured system. These results are directly applicable to adhesion and thickness diagnostics of very thin films. Finally, this thesis reports the first use of light from HHG to study magnetic orientation. Using the transverse magneto-optic Kerr effect and soft x-ray light near the M-absorption edges of Fe, Co, and Ni, magnetic asymmetries up to 8% are observed from thin Permalloy (Ni80Fe20) films. This signal is 1-2 orders of magnitude higher than that observed using optical methods, showing great promise for dynamic imaging of domain flipping at the 100 nm level.

  13. Probing equilibrium by nonequilibrium dynamics: Aging in Co/Cr superlattices

    Science.gov (United States)

    Binek, Christian

    2013-03-01

    Magnetic aging phenomena are investigated in a structurally ordered Co/Cr superlattice through measurements of magnetization relaxation, magnetic susceptibility, and hysteresis at various temperatures above and below the onset of collective magnetic order. We take advantage of the fact that controlled growth of magnetic multilayer thin films via molecular beam epitaxy allows tailoring the intra and inter-layer exchange interaction and thus enables tuning of magnetic properties including the spin-fluctuation spectra. Tailored nanoscale periodicity in Co/Cr multilayers creates mesoscopic spatial magnetic correlations with slow relaxation dynamics when quenching the system into a nonequilibrium state. Magnetization relaxation in weakly correlated spin systems depends on the microscopic spin-flip time of about 10 ns and is therefore a fast process. The spin correlations in our Co/Cr superlattice bring the magnetization dynamics to experimentally better accessible time scales of seconds or hours. In contrast to spin-glasses, where slow dynamics due to disorder and frustration is a well-known phenomenon, we tune and increase relaxation times in ordered structures. This is achieved by increasing spin-spin correlation between mesoscopically correlated regions rather than individual atomic spins, a concept with some similarity to block spin renormalization. Magnetization transients are measured after exposing the Co/Cr heterostructure to a magnetic set field for various waiting times. Scaling analysis reveals an asymptotic power-law behavior in accordance with a full aging scenario. The temperature dependence of the relaxation exponent shows pronounced anomalies at the equilibrium phase transitions of the antiferromagnetic superstructure and the ferromagnetic to paramagnetic transition of the Co layers. The latter leaves only weak fingerprints in the equilibrium magnetic behavior but gives rise to a prominent change in nonequilibrium properties. Our findings suggest that

  14. Capsid structure and dynamics of a human rhinovirus probed by hydrogen exchange mass spectrometry.

    Science.gov (United States)

    Wang, Lintao; Smith, David L

    2005-06-01

    Viral capsids are dynamic protein assemblies surrounding viral genomes. Despite the high-resolution structures determined by X-ray crystallography and cryo-electron microscopy, their in-solution structure and dynamics can be probed by hydrogen exchange. We report here using hydrogen exchange combined with protein enzymatic fragmentation and mass spectrometry to determine the capsid structure and dynamics of a human rhinovirus, HRV14. Capsid proteins (VP1-4) were labeled with deuterium by incubating intact virus in D(2)O buffer at neutral pH. The labeled proteins were digested by immobilized pepsin to give peptides analyzed by capillary reverse-phase HPLC coupled with nano-electrospray mass spectrometry. Deuterium levels incorporated at amide linkages in peptic fragments were measured for different exchange times from 12 sec to 30 h to assess the amide hydrogen exchange rates along each of the four protein backbones. Exchange results generally agree with the crystal structure of VP1-4,with extended, flexible terminal and surface-loop regions in fast exchange and folded helical and sheet structures in slow exchange. In addition, three alpha-helices, one from each of VP1-3, exhibited very slow exchange, indicating high stability of the protomeric interface. The beta-strands at VP3 N terminus also had very slow exchange, suggesting stable pentamer contacts. It was noted, however, that the interface around the fivefold axis had fast and intermediate exchange, indicating relatively more flexibility. Even faster exchange rates were found in the N terminus of VP1 and most segments of VP4, suggesting high flexibilities, which may correspond to their potential roles in virus uncoating.

  15. Plasma membrane organization and dynamics is probe and cell line dependent.

    Science.gov (United States)

    Huang, Shuangru; Lim, Shi Ying; Gupta, Anjali; Bag, Nirmalya; Wohland, Thorsten

    2017-09-01

    The action and interaction of membrane receptor proteins take place within the plasma membrane. The plasma membrane, however, is not a passive matrix. It rather takes an active role and regulates receptor distribution and function by its composition and the interaction of its lipid components with embedded and surrounding proteins. Furthermore, it is not a homogenous fluid but contains lipid and protein domains of various sizes and characteristic lifetimes which are important in regulating receptor function and signaling. The precise lateral organization of the plasma membrane, the differences between the inner and outer leaflet, and the influence of the cytoskeleton are still debated. Furthermore, there is a lack of comparisons of the organization and dynamics of the plasma membrane of different cell types. Therefore, we used four different specific membrane markers to test the lateral organization, the differences between the inner and outer membrane leaflet, and the influence of the cytoskeleton of up to five different cell lines, including Chinese hamster ovary (CHO-K1), Human cervical carcinoma (HeLa), neuroblastoma (SH-SY5Y), fibroblast (WI-38) and rat basophilic leukemia (RBL-2H3) cells by Imaging Total Internal Reflection (ITIR)-Fluorescence Correlation Spectroscopy (FCS). We measure diffusion in the temperature range of 298-310K to measure the Arrhenius activation energy (EArr) of diffusion and apply the FCS diffusion law to obtain information on the spatial organization of the probe molecules on the various cell membranes. Our results show clear differences of the FCS diffusion law and EArr for the different probes in dependence of their localization. These differences are similar in the outer and inner leaflet of the membrane. However, these values can differ significantly between different cell lines raising the question how molecular plasma membrane events measured in different cell lines can be compared. This article is part of a Special Issue

  16. Weather Conditions Drive Dynamic Habitat Selection in a Generalist Predator

    DEFF Research Database (Denmark)

    Sunde, Peter; Thorup, Kasper; Jacobsen, Lars Bo

    2014-01-01

    Despite the dynamic nature of habitat selection, temporal variation as arising from factors such as weather are rarely quantified in species-habitat relationships. We analysed habitat use and selection (use/availability) of foraging, radio-tagged little owls (Athene noctua), a nocturnal, year......-round resident generalist predator, to see how this varied as a function of weather, season and availability. Use of the two most frequently used land cover types, gardens/buildings and cultivated fields varied more than 3-fold as a simple function of season and weather through linear effects of wind...... with temperature and was proportional to their availability. The study shows that habitat selection by generalist foragers may be highly dependent on temporal variables such as weather, probably because such foragers switch between weather dependent feeding opportunities offered by different land cover types...

  17. Weather Conditions Drive Dynamic Habitat Selection in a Generalist Predator

    DEFF Research Database (Denmark)

    Sunde, Peter; Thorup, Kasper; Jacobsen, Lars Bo;

    2014-01-01

    Despite the dynamic nature of habitat selection, temporal variation as arising from factors such as weather are rarely quantified in species-habitat relationships. We analysed habitat use and selection (use/availability) of foraging, radio-tagged little owls (Athene noctua), a nocturnal, year......-round resident generalist predator, to see how this varied as a function of weather, season and availability. Use of the two most frequently used land cover types, gardens/buildings and cultivated fields varied more than 3-fold as a simple function of season and weather through linear effects of wind...... with temperature and was proportional to their availability. The study shows that habitat selection by generalist foragers may be highly dependent on temporal variables such as weather, probably because such foragers switch between weather dependent feeding opportunities offered by different land cover types...

  18. Beyond structure: ultrafast X-ray absorption spectroscopy as a probe of non-adiabatic wavepacket dynamics.

    Science.gov (United States)

    Neville, Simon P; Averbukh, Vitali; Patchkovskii, Serguei; Ruberti, Marco; Yun, Renjie; Chergui, Majed; Stolow, Albert; Schuurman, Michael S

    2016-12-16

    The excited state non-adiabatic dynamics of polyatomic molecules, leading to the coupling of structural and electronic dynamics, is a fundamentally important yet challenging problem for both experiment and theory. Ongoing developments in ultrafast extreme vacuum ultraviolet (XUV) and soft X-ray sources present new probes of coupled electronic-structural dynamics because of their novel and desirable characteristics. As one example, inner-shell spectroscopy offers localized, atom-specific probes of evolving electronic structure and bonding (via chemical shifts). In this work, we present the first on-the-fly ultrafast X-ray time-resolved absorption spectrum simulations of excited state wavepacket dynamics: photo-excited ethylene. This was achieved by coupling the ab initio multiple spawning (AIMS) method, employing on-the-fly dynamics simulations, with high-level algebraic diagrammatic construction (ADC) X-ray absorption cross-section calculations. Using the excited state dynamics of ethylene as a test case, we assessed the ability of X-ray absorption spectroscopy to project out the electronic character of complex wavepacket dynamics, and evaluated the sensitivity of the calculated spectra to large amplitude nuclear motion. In particular, we demonstrate the pronounced sensitivity of the pre-edge region of the X-ray absorption spectrum to the electronic and structural evolution of the excited-state wavepacket. We conclude that ultrafast time-resolved X-ray absorption spectroscopy may become a powerful tool in the interrogation of excited state non-adiabatic molecular dynamics.

  19. Calcium dynamics in root cells of Arabidopsis thaliana visualized with selective plane illumination microscopy.

    Directory of Open Access Journals (Sweden)

    Alex Costa

    Full Text Available Selective Plane Illumination Microscopy (SPIM is an imaging technique particularly suited for long term in-vivo analysis of transparent specimens, able to visualize small organs or entire organisms, at cellular and eventually even subcellular resolution. Here we report the application of SPIM in Calcium imaging based on Förster Resonance Energy Transfer (FRET. Transgenic Arabidopsis plants expressing the genetically encoded-FRET-based Ca(2+ probe Cameleon, in the cytosol or nucleus, were used to demonstrate that SPIM enables ratiometric fluorescence imaging at high spatial and temporal resolution, both at tissue and single cell level. The SPIM-FRET technique enabled us to follow nuclear and cytosolic Ca(2+ dynamics in Arabidopsis root tip cells, deep inside the organ, in response to different stimuli. A relevant physiological phenomenon, namely Ca(2+ signal percolation, predicted in previous studies, has been directly visualized.

  20. Blue Straggler Stars in Globular Clusters: a powerful tool to probe the internal dynamical evolution of stellar systems

    CERN Document Server

    Ferraro, Francesco R; Dalessandro, Emanuele; Mucciarelli, Alessio; Lovisi, Loredana

    2014-01-01

    This chapter presents an overview of the main observational results obtained to date about Blue Straggler Stars (BSSs) in Galactic Globular Clusters (GCs). The BSS specific frequency, radial distribution, chemical composition and rotational properties are presented and discussed in the framework of using this stellar population as probe of GC internal dynamics. In particular, the shape of the BSS radial distribution has been found to be a powerful tracer of the dynamical age of stellar systems, thus allowing the definition of the first empirical "dynamical clock".

  1. Stiffening hydrogels to probe short- and long-term cellular responses to dynamic mechanics.

    Science.gov (United States)

    Guvendiren, Murat; Burdick, Jason A

    2012-04-24

    Biological processes are dynamic in nature, and growing evidence suggests that matrix stiffening is particularly decisive during development, wound healing and disease; yet, nearly all in vitro models are static. Here we introduce a step-wise approach, addition then light-mediated crosslinking, to fabricate hydrogels that stiffen (for example, ~3-30 kPa) in the presence of cells, and investigated the short-term (minutes-to-hours) and long-term (days-to-weeks) cell response to dynamic stiffening. When substrates are stiffened, adhered human mesenchymal stem cells increase their area from ~500 to 3,000 μm(2) and exhibit greater traction from ~1 to 10 kPa over a timescale of hours. For longer cultures up to 14 days, human mesenchymal stem cells selectively differentiate based on the period of culture, before or after stiffening, such that adipogenic differentiation is favoured for later stiffening, whereas osteogenic differentiation is favoured for earlier stiffening.

  2. A multifunctional probe with aggregation-induced emission characteristics for selective fluorescence imaging and photodynamic killing of bacteria over mammalian cells.

    Science.gov (United States)

    Gao, Meng; Hu, Qinglian; Feng, Guangxue; Tomczak, Nikodem; Liu, Rongrong; Xing, Bengang; Tang, Ben Zhong; Liu, Bin

    2015-04-02

    A multifunctional probe aggregation-induced emission-Zinc(II)-dipicolylamine (AIE-ZnDPA) is developed for selective targeting, fluorescence imaging, and photodynamic killing of both Gram-positive and Gram-negative bacteria over mammalian cells. The probe has significant advantages in simple probe design, enhanced fluorescence upon bacteria binding, excellent photostability, and broad-spectrum antibacterial activity with almost no harm to mammalian cells.

  3. Selective Incorporation of Nitrile-Based Infrared Probes into Proteins via Cysteine Alkylation

    Science.gov (United States)

    Jo, Hyunil; Culik, Robert M.; Korendovych, Ivan V.; DeGrado, William F.; Gai, Feng

    2010-01-01

    The nitrile stretching vibration is increasingly used as a sensitive infrared probe of local protein environments. However, site-specific incorporation of a nitrile moiety into proteins is difficult. Here we show that various aromatic nitriles can be easily incorporated into peptides and proteins via either thiol alkylation or arylation reaction. PMID:21077670

  4. Robust hybridization-based genotyping probes for HPV 6, 11, 16 and 18 obtained via in vitro selection

    Directory of Open Access Journals (Sweden)

    Ivan B. Brukner

    2010-04-01

    Full Text Available This paper describes the technical and analytical performance of a novel set of hybridization probes for the four GARDASIL® vaccine-relevant HPV types (6, 11, 16 and 18. These probes are obtained through in vitro selection from a pool of random oligonucleotides, rather than the traditional “rational design” approach typically used as the initial step in assay development. The type-specific segment of the HPV genome was amplified using a GP5+/6+ PCR protocol and 39 synthetic oligonucleotide templates derived from each of the HPV types, as PCR targets. The robust performance of the 4 selected hybridization probes was demonstrated by monitoring the preservation of the specificity and sensitivity of the typing assay over all 39 HPV types, using a different spectrum of HPV (genome equivalent: 103-109 and human DNA concentrations (10-100 ng as well as temperature and buffer composition variations. To the Authors’ knowledge, this is a unique hybridization-based multiplex typing assay. It performs at ambient temperatures, does not require the strict temperature control of hybridization conditions, and is functional with a number of different non-denaturing buffers, thereby offering downstream compatibility with a variety of detection methods. Studies aimed at demonstrating clinical performance are needed to validate the applicability of this strategy.

  5. Weather conditions drive dynamic habitat selection in a generalist predator.

    Directory of Open Access Journals (Sweden)

    Peter Sunde

    Full Text Available Despite the dynamic nature of habitat selection, temporal variation as arising from factors such as weather are rarely quantified in species-habitat relationships. We analysed habitat use and selection (use/availability of foraging, radio-tagged little owls (Athene noctua, a nocturnal, year-round resident generalist predator, to see how this varied as a function of weather, season and availability. Use of the two most frequently used land cover types, gardens/buildings and cultivated fields varied more than 3-fold as a simple function of season and weather through linear effects of wind and quadratic effects of temperature. Even when controlling for the temporal context, both land cover types were used more evenly than predicted from variation in availability (functional response in habitat selection. Use of two other land cover categories (pastures and moist areas increased linearly with temperature and was proportional to their availability. The study shows that habitat selection by generalist foragers may be highly dependent on temporal variables such as weather, probably because such foragers switch between weather dependent feeding opportunities offered by different land cover types. An opportunistic foraging strategy in a landscape with erratically appearing feeding opportunities in different land cover types, may possibly also explain decreasing selection of the two most frequently used land cover types with increasing availability.

  6. Weather conditions drive dynamic habitat selection in a generalist predator.

    Science.gov (United States)

    Sunde, Peter; Thorup, Kasper; Jacobsen, Lars B; Rahbek, Carsten

    2014-01-01

    Despite the dynamic nature of habitat selection, temporal variation as arising from factors such as weather are rarely quantified in species-habitat relationships. We analysed habitat use and selection (use/availability) of foraging, radio-tagged little owls (Athene noctua), a nocturnal, year-round resident generalist predator, to see how this varied as a function of weather, season and availability. Use of the two most frequently used land cover types, gardens/buildings and cultivated fields varied more than 3-fold as a simple function of season and weather through linear effects of wind and quadratic effects of temperature. Even when controlling for the temporal context, both land cover types were used more evenly than predicted from variation in availability (functional response in habitat selection). Use of two other land cover categories (pastures and moist areas) increased linearly with temperature and was proportional to their availability. The study shows that habitat selection by generalist foragers may be highly dependent on temporal variables such as weather, probably because such foragers switch between weather dependent feeding opportunities offered by different land cover types. An opportunistic foraging strategy in a landscape with erratically appearing feeding opportunities in different land cover types, may possibly also explain decreasing selection of the two most frequently used land cover types with increasing availability.

  7. Probing charge transfer and hot carrier dynamics in organic solar cells with terahertz spectroscopy

    Science.gov (United States)

    Cunningham, Paul D.; Lane, Paul A.; Melinger, Joseph S.; Esenturk, Okan; Heilweil, Edwin J.

    2016-04-01

    Time-resolved terahertz spectroscopy (TRTS) was used to explore charge generation, transfer, and the role of hot carriers in organic solar cell materials. Two model molecular photovoltaic systems were investigated: with zinc phthalocyanine (ZnPc) or alpha-sexathiophene (α-6T) as the electron donors and buckminsterfullerene (C60) as the electron acceptor. TRTS provides charge carrier conductivity dynamics comprised of changes in both population and mobility. By using time-resolved optical spectroscopy in conjunction with TRTS, these two contributions can be disentangled. The sub-picosecond photo-induced conductivity decay dynamics of C60 were revealed to be caused by auto-ionization: the intrinsic process by which charge is generated in molecular solids. In donor-acceptor blends, the long-lived photo-induced conductivity is used for weight fraction optimization of the constituents. In nanoscale multilayer films, the photo-induced conductivity identifies optimal layer thicknesses. In films of ZnPc/C60, electron transfer from ZnPc yields hot charges that localize and become less mobile as they thermalize. Excitation of high-lying Franck Condon states in C60 followed by hole-transfer to ZnPc similarly produces hot charge carriers that self-localize; charge transfer clearly precedes carrier cooling. This picture is contrasted to charge transfer in α-6T/C60, where hole transfer takes place from a thermalized state and produces equilibrium carriers that do not show characteristic signs of cooling and self-localization. These results illustrate the value of terahertz spectroscopic methods for probing charge transfer reactions.

  8. Probing the structural dynamics of the SNARE recycling machine based on coarse-grained modeling.

    Science.gov (United States)

    Zheng, Wenjun

    2016-08-01

    Membrane fusion in eukaryotes is driven by the formation of a four-helix bundle by three SNARE proteins. To recycle the SNARE proteins, they must be disassembled by the ATPase NSF and four SNAP proteins which together form a 20S supercomplex. Recently, the first high-resolution structures of the NSF (in both ATP and ADP state) and 20S (in four distinct states termed I, II, IIIa, and IIIb) were solved by cryo-electron microscopy (cryo-EM), which have paved the way for structure-driven studies of the SNARE recycling mechanism. To probe the structural dynamics of SNARE disassembly at amino-acid level of details, a systematic coarse-grained modeling based on an elastic network model and related analyses were performed. Our normal mode analysis of NSF, SNARE, and 20S predicted key modes of collective motions that partially account for the observed structural changes, and illuminated how the SNARE complex can be effectively destabilized by untwisting and bending motions of the SNARE complex driven by the amino-terminal domains of NSF in state II. Our flexibility analysis identified regions with high/low flexibility that coincide with key functional sites (such as the NSF-SNAPs-SNARE binding sites). A subset of hotspot residues that control the above collective motions, which will make promising targets for future mutagenesis studies were also identified. Finally, the conformational changes in 20S as induced by the transition of NSF from ATP to ADP state were modeled, and a concerted untwisting motion of SNARE/SNAPs and a sideway flip of two amino-terminal domains were observed. In sum, the findings have offered new structural and dynamic details relevant to the SNARE disassembly mechanism, and will guide future functional studies of the SNARE recycling machinery. Proteins 2016; 84:1055-1066. © 2016 Wiley Periodicals, Inc.

  9. Spin tune mapping as a novel tool to probe the spin dynamics in storage rings

    Directory of Open Access Journals (Sweden)

    2017-07-01

    Full Text Available Precision experiments, such as the search for electric dipole moments of charged particles using storage rings, demand for an understanding of the spin dynamics with unprecedented accuracy. The ultimate aim is to measure the electric dipole moments with a sensitivity up to 15 orders in magnitude better than the magnetic dipole moment of the stored particles. This formidable task requires an understanding of the background to the signal of the electric dipole from rotations of the spins in the spurious magnetic fields of a storage ring. One of the observables, especially sensitive to the imperfection magnetic fields in the ring is the angular orientation of stable spin axis. Up to now, the stable spin axis has never been determined experimentally, and in addition, the JEDI collaboration for the first time succeeded to quantify the background signals that stem from false rotations of the magnetic dipole moments in the horizontal and longitudinal imperfection magnetic fields of the storage ring. To this end, we developed a new method based on the spin tune response of a machine to artificially applied longitudinal magnetic fields. This novel technique, called spin tune mapping, emerges as a very powerful tool to probe the spin dynamics in storage rings. The technique was experimentally tested in 2014 using polarized deuterons stored in the cooler synchrotron COSY, and for the first time, the angular orientation of the stable spin axis at two different locations in the ring has been determined to an unprecedented accuracy of better than 2.8  μ  rad.

  10. Evolution and selection of river networks: statics, dynamics, and complexity.

    Science.gov (United States)

    Rinaldo, Andrea; Rigon, Riccardo; Banavar, Jayanth R; Maritan, Amos; Rodriguez-Iturbe, Ignacio

    2014-02-18

    Moving from the exact result that drainage network configurations minimizing total energy dissipation are stationary solutions of the general equation describing landscape evolution, we review the static properties and the dynamic origins of the scale-invariant structure of optimal river patterns. Optimal channel networks (OCNs) are feasible optimal configurations of a spanning network mimicking landscape evolution and network selection through imperfect searches for dynamically accessible states. OCNs are spanning loopless configurations, however, only under precise physical requirements that arise under the constraints imposed by river dynamics--every spanning tree is exactly a local minimum of total energy dissipation. It is remarkable that dynamically accessible configurations, the local optima, stabilize into diverse metastable forms that are nevertheless characterized by universal statistical features. Such universal features explain very well the statistics of, and the linkages among, the scaling features measured for fluvial landforms across a broad range of scales regardless of geology, exposed lithology, vegetation, or climate, and differ significantly from those of the ground state, known exactly. Results are provided on the emergence of criticality through adaptative evolution and on the yet-unexplored range of applications of the OCN concept.

  11. Ultrafast Hydration Dynamics Probed by Tryptophan at Protein Surface and Protein-DNA Interface

    Science.gov (United States)

    Qin, Yangzhong

    As we all live in a special water planet Earth, the significance of water to life has been universally recognized. The reason why water is so important to life has intrigued many researchers. This dissertation will focus on the ultrafast dynamics of protein surface water and protein-DNA interfacial water which have direct importance to the protein structure and function. Using tryptophan as an intrinsic fluorescence probe, combined with site-directed mutagenesis and ultrafast fluorescence up-conversion spectroscopy, we can achieve single residue spatial resolution and femtosecond temporal resolution. We can also precisely determine the local hydration water dynamics by monitoring the Stokes shift of tryptophan one at a time. Previously, the protein surface hydration has been extensively studied by our group. In this thesis, we will provide more details on the methods we are using to extract the hydration dynamics, and also validate our methods from both experimental and theoretical perspectives. To further interrogate the interfacial water hydration dynamics relative to the protein surface hydration, we studied two DNA polymerases: DNA Polymerase IV (Dpo4) and DNA Polymerase Beta (Pol beta). Both proteins show typical surface hydration pattern with three distinct time components including: (i) the ultrafast sub-picosecond component reflects the bulk type water motion; (ii) a few picoseconds component shows the inner water relaxation mainly corresponding to the local libration and reorientation; (iii) the tens to hundred picoseconds component represents the water-protein coupled motion involving the whole water network reorganization. Dpo4, a loosely DNA binding protein, exhibits very flexible interfacial water which resembles its surface water yet with a significantly reduced ultrafast component. Such dynamic interfacial water not only maintains interfacial flexibility, but also contributes to the low fidelity of the protein. In contrast to the Dpo4, pol beta

  12. Probing the interaction of nanoparticles with mucin for drug delivery applications using dynamic light scattering.

    Science.gov (United States)

    Griffiths, Peter Charles; Cattoz, Beatrice; Ibrahim, Mervat Shafik; Anuonye, Josephine Chibuzor

    2015-11-01

    Drug delivery via the eye, nose, gastrointestinal tract and lung is of great interest as they represent patient-compliant and facile methods to administer drugs. However, for a drug to reach the systemic circulation it must penetrate the "mucus barrier". An understanding of the characteristics of the mucus barrier is therefore important in the design of mucus penetrating drug delivery vehicles e.g. nanoparticles. Here, a range of nanoparticles - silica, aluminium coated silica, poly (lactic-co-glycolic acid) (PLGA) and PEGylated PLGA - each with known but different physicochemical characteristics were examined in the presence of mucin to identify those characteristics that engender nanoparticle/mucin interactions and thus, to define "design rules" for mucus penetrating (nano)particles (MPP), at least in terms of the surface characteristics of charge and hydrophilicity. Dynamic light scattering (DLS) and rheology have been used to assess the interaction between such nanoparticles and mucin. It was found that negatively charged and hydrophilic nanoparticles do not exhibit an interaction with mucin whereas positively charged and hydrophobic nanoparticles show a strong interaction. Surface grafted poly (ethylene glycol) (PEG) chains significantly reduced this interaction. This study clearly demonstrates that the established colloid science techniques of DLS and rheology are very powerful screening tools to probe nanoparticle/mucin interactions.

  13. Full data acquisition in Kelvin Probe Force Microscopy: Mapping dynamic electric phenomena in real space

    Science.gov (United States)

    Collins, Liam; Belianinov, Alex; Somnath, Suhas; Balke, Nina; Kalinin, Sergei V.; Jesse, Stephen

    2016-08-01

    Kelvin probe force microscopy (KPFM) has provided deep insights into the local electronic, ionic and electrochemical functionalities in a broad range of materials and devices. In classical KPFM, which utilizes heterodyne detection and closed loop bias feedback, the cantilever response is down-sampled to a single measurement of the contact potential difference (CPD) per pixel. This level of detail, however, is insufficient for materials and devices involving bias and time dependent electrochemical events; or at solid-liquid interfaces, where non-linear or lossy dielectrics are present. Here, we demonstrate direct recovery of the bias dependence of the electrostatic force at high temporal resolution using General acquisition Mode (G-Mode) KPFM. G-Mode KPFM utilizes high speed detection, compression, and storage of the raw cantilever deflection signal in its entirety at high sampling rates. We show how G-Mode KPFM can be used to capture nanoscale CPD and capacitance information with a temporal resolution much faster than the cantilever bandwidth, determined by the modulation frequency of the AC voltage. In this way, G-Mode KPFM offers a new paradigm to study dynamic electric phenomena in electroactive interfaces as well as a promising route to extend KPFM to the solid-liquid interface.

  14. Probing nuclear dynamics in jet production with a global event shape

    CERN Document Server

    Kang, Zhong-Bo; Mantry, Sonny; Qiu, Jian-Wei

    2013-01-01

    We study single jet production in electron-nucleus collisions e^- + N_A -> J + X, using the 1-jettiness (\\tau_1) global event shape. It inclusively quantifies the pattern of radiation in the final state, gives enhanced sensitivity to soft radiation at wide angles from the nuclear beam and final-state jet, and facilitates the resummation of large Sudakov logarithms associated with the veto on additional jets. Through their effect on the observed pattern of radiation, 1-jettiness can be a useful probe of nuclear PDFs and power corrections from dynamical effects in the nuclear medium. This formalism allows for the standard jet shape analysis while simultaneously providing sensitivity to soft radiation at wide angles from the jet. We use a factorization framework for cross-sections differential in $\\tau_1$ and the transverse momentum (P_{J_T}) and rapidity (y) of the jet, in the region \\tau_1<< P_{J_T}. The restriction $\\tau_1 << P_{J_T}$ allows only soft radiation between the nuclear beam and jet dir...

  15. Dynamic Viral Glycoprotein Machines: Approaches for Probing Transient States That Drive Membrane Fusion

    Directory of Open Access Journals (Sweden)

    Natalie K. Garcia

    2016-01-01

    Full Text Available The fusion glycoproteins that decorate the surface of enveloped viruses undergo dramatic conformational changes in the course of engaging with target cells through receptor interactions and during cell entry. These refolding events ultimately drive the fusion of viral and cellular membranes leading to delivery of the genetic cargo. While well-established methods for structure determination such as X-ray crystallography have provided detailed structures of fusion proteins in the pre- and post-fusion fusion states, to understand mechanistically how these fusion glycoproteins perform their structural calisthenics and drive membrane fusion requires new analytical approaches that enable dynamic intermediate states to be probed. Methods including structural mass spectrometry, small-angle X-ray scattering, and electron microscopy have begun to provide new insight into pathways of conformational change and fusion protein function. In combination, the approaches provide a significantly richer portrait of viral fusion glycoprotein structural variation and fusion activation as well as inhibition by neutralizing agents. Here recent studies that highlight the utility of these complementary approaches will be reviewed with a focus on the well-characterized influenza virus hemagglutinin fusion glycoprotein system.

  16. Pulsed field probe of real time magnetization dynamics in magnetic nanoparticle systems

    Science.gov (United States)

    Foulkes, T.; Syed, M.; Taplin, T.

    2015-05-01

    Magnetic nanoparticles (MNPs) are extensively used in biotechnology. These applications rely on magnetic properties that are a keen function of MNP size, distribution, and shape. Various magneto-optical techniques, including Faraday Rotation (FR), Cotton-Mouton Effect, etc., have been employed to characterize magnetic properties of MNPs. Generally, these measurements employ AC or DC fields. In this work, we describe the results from a FR setup that uses pulsed magnetic fields and an analysis technique that makes use of the entire pulse shape to investigate size distribution and shape anisotropy. The setup employs a light source, polarizing components, and a detector that are used to measure the rotation of light from a sample that is subjected to a pulsed magnetic field. This magnetic field "snapshot" is recorded alongside the intensity pulse of the sample's response. This side by side comparison yields useful information about the real time magnetization dynamics of the system being probed. The setup is highly flexible with variable control of pulse length and peak magnitude. Examining the raw data for the response of bare Fe3O4 and hybrid Au and Fe3O4 nanorods reveals interesting information about Brownian relaxation and the hydrodynamic size of these nanorods. This analysis exploits the self-referencing nature of this measurement to highlight the impact of an applied field on creating a field induced transparency for a longitudinal measurement. Possible sources for this behavior include shape anisotropy and field assisted aggregate formation.

  17. Probing initial-stages of ALD growth with dynamic in situ spectroscopic ellipsometry

    Science.gov (United States)

    Muneshwar, Triratna; Cadien, Ken

    2015-02-01

    The initial stages of ALD surface reactions are probed using dynamic in situ spectroscopic ellipsometry (d-iSE) technique during plasma-enhanced ALD of zirconium nitride (ZrN) thin films in spectral range of 0.73-6.4 eV. The measured change in the ellipsometry parameter Δ, with every precursor (TDMAZr) and reactant (forming gas plasma) exposure is interpreted as the combined effect of film growth and change in surface chemistry during ALD. We present application of Bruggeman's effective-medium approximation (B-EMA) in the analysis of d-iSE data to determine fractional surface coverage (θ) of ALD grown film at the end of every deposition cycle. During the deposition of first few ZrN monolayers, d-iSE datasets are analyzed on the basis of surface diffusion enhanced ALD growth, where the surface adsorbed precursor molecules can diffuse over substrate surface to occupy energetically favorable surface sites. The determined surface coverage of ZrN films highlights the effects of substrate enhanced ALD growth.

  18. Probing the surface profile and friction behavior of heterogeneous polymers: a molecular dynamics study

    Science.gov (United States)

    Dai, L.; Sorkin, V.; Zhang, Y. W.

    2017-04-01

    We perform molecular dynamics simulations to investigate molecular structure alternation and friction behavior of heterogeneous polymer (perfluoropolyether) surfaces using a nanoscale probing tip (tetrahedral amorphous carbon). It is found that depending on the magnitude of the applied normal force, three regimes exist: the shallow depth-sensing (SDS), deep depth-sensing (DDS), and transitional depth-sensing (TDS) regimes; TDS is between SDS and DDS. In SDS, the tip is floating on the polymer surface and there is insignificant permanent alternation in the polymer structure due to largely recoverable atomic deformations, and the surface roughness profile can be accurately measured. In DDS, the tip is plowing through the polymer surface and there is significant permanent alternation in the molecular structure. In this regime, the lateral friction force rises sharply and fluctuates violently when overcoming surface pile-ups. In SDS, the friction can be described by a modified Amonton’s law including the adhesion effect; meanwhile, in DDS, the adhesion effect is negligible but the friction coefficient is significantly higher. The underlying reason for the difference in these regimes rests upon different contributions by the repulsion and attraction forces between the tip and polymer surfaces to the friction force. Our findings here reveal important insights into lateral depth-sensing on heterogeneous polymer surfaces and may help improve the precision of depth-sensing devices.

  19. Dynamical transitions in the evolution of learning algorithms by selection

    CERN Document Server

    Neirotti, J P; Neirotti, Juan Pablo; Caticha, Nestor

    2002-01-01

    We study the evolution of artificial learning systems by means of selection. Genetic programming is used to generate a sequence of populations of algorithms which can be used by neural networks for supervised learning of a rule that generates examples. In opposition to concentrating on final results, which would be the natural aim while designing good learning algorithms, we study the evolution process and pay particular attention to the temporal order of appearance of functional structures responsible for the improvements in the learning process, as measured by the generalization capabilities of the resulting algorithms. The effect of such appearances can be described as dynamical phase transitions. The concepts of phenotypic and genotypic entropies, which serve to describe the distribution of fitness in the population and the distribution of symbols respectively, are used to monitor the dynamics. In different runs the phase transitions might be present or not, with the system finding out good solutions, or ...

  20. Selected Topics in Nonlinear Dynamics and Theoretical Electrical Engineering

    CERN Document Server

    Halang, Wolfgang; Mathis, Wolfgang; Chedjou, Jean; Li, Zhong

    2013-01-01

    This book contains a collection of recent advanced contributions in the field of nonlinear dynamics and synchronization, including selected applications in the area of theoretical electrical engineering. The present book is divided into twenty-one chapters grouped in five parts. The first part focuses on theoretical issues related to chaos and synchronization and their potential applications in mechanics, transportation, communication and security. The second part handles dynamic systems modelling and simulation with special applications to real physical systems and phenomena. The third part discusses some fundamentals of electromagnetics (EM) and addresses the modelling and simulation in some real physical electromagnetic scenarios. The fourth part mainly addresses stability concerns. Finally, the last part assembles some sample applications in the area of optimization, data mining, pattern recognition and image processing.

  1. Selected topics in nonlinear dynamics and theoretical electrical engineering

    CERN Document Server

    Halang, Wolfgang; Mathis, Wolfgang; Chedjou, Jean; Li, Zhong

    2013-01-01

    This book contains a collection of recent advanced contributions in the field of nonlinear dynamics and synchronization, including selected applications in the area of theoretical electrical engineering. The present book is divided into twenty-one chapters grouped in five parts. The first part focuses on theoretical issues related to chaos and synchronization and their potential applications in mechanics, transportation, communication and security. The second part handles dynamic systems modelling and simulation with special applications to real physical systems and phenomena. The third part discusses some fundamentals of electromagnetics (EM) and addresses the modelling and simulation in some real physical electromagnetic scenarios. The fourth part mainly addresses stability concerns. Finally, the last part assembles some sample applications in the area of optimization, data mining, pattern recognition and image processing.

  2. A Selective Imidazoline-2-thione-Bearing Two-Photon Fluorescent Probe for Hypochlorous Acid in Mitochondria.

    Science.gov (United States)

    Xu, Qingling; Heo, Cheol Ho; Kim, Jin A; Lee, Hye Sue; Hu, Ying; Kim, Dayoung; Swamy, Kunemadihalli Mathada Kotraiah; Kim, Gyoungmi; Nam, Sang-Jip; Kim, Hwan Myung; Yoon, Juyoung

    2016-06-21

    Hypochlorite (OCl(-)) plays a key role in the immune system and is involved in various diseases. Accordingly, direct detection of endogenous OCl(-) at the subcellular level is important for understanding inflammation and cellular apoptosis. In the current study, a two-photon fluorescent off/on probe (PNIS) bearing imidazoline-2-thione as an OCl(-) recognition unit and triphenylphosphine (TPP) as a mitochondrial-targeting group was synthesized and examined for its ability to image mitochondrial OCl(-) in situ. This probe, based on the specific reaction between imidazoline-2-thione and OCl(-), displayed a selective fluorescent off/on response to OCl(-) with the various reactive oxygen species in a physiological medium. PNIS was successfully applied to image of endogenously produced mitochondrial OCl(-) in live RAW 264.7 cells via two-photon microscopy.

  3. Probing the dynamics of identified neurons with a data-driven modeling approach.

    Directory of Open Access Journals (Sweden)

    Thomas Nowotny

    Full Text Available In controlling animal behavior the nervous system has to perform within the operational limits set by the requirements of each specific behavior. The implications for the corresponding range of suitable network, single neuron, and ion channel properties have remained elusive. In this article we approach the question of how well-constrained properties of neuronal systems may be on the neuronal level. We used large data sets of the activity of isolated invertebrate identified cells and built an accurate conductance-based model for this cell type using customized automated parameter estimation techniques. By direct inspection of the data we found that the variability of the neurons is larger when they are isolated from the circuit than when in the intact system. Furthermore, the responses of the neurons to perturbations appear to be more consistent than their autonomous behavior under stationary conditions. In the developed model, the constraints on different parameters that enforce appropriate model dynamics vary widely from some very tightly controlled parameters to others that are almost arbitrary. The model also allows predictions for the effect of blocking selected ionic currents and to prove that the origin of irregular dynamics in the neuron model is proper chaoticity and that this chaoticity is typical in an appropriate sense. Our results indicate that data driven models are useful tools for the in-depth analysis of neuronal dynamics. The better consistency of responses to perturbations, in the real neurons as well as in the model, suggests a paradigm shift away from measuring autonomous dynamics alone towards protocols of controlled perturbations. Our predictions for the impact of channel blockers on the neuronal dynamics and the proof of chaoticity underscore the wide scope of our approach.

  4. Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics.

    Directory of Open Access Journals (Sweden)

    Anshuman Dixit

    Full Text Available Deciphering functional mechanisms of the Hsp90 chaperone machinery is an important objective in cancer biology aiming to facilitate discovery of targeted anti-cancer therapies. Despite significant advances in understanding structure and function of molecular chaperones, organizing molecular principles that control the relationship between conformational diversity and functional mechanisms of the Hsp90 activity lack a sufficient quantitative characterization. We combined molecular dynamics simulations, principal component analysis, the energy landscape model and structure-functional analysis of Hsp90 regulatory interactions to systematically investigate functional dynamics of the molecular chaperone. This approach has identified a network of conserved regions common to the Hsp90 chaperones that could play a universal role in coordinating functional dynamics, principal collective motions and allosteric signaling of Hsp90. We have found that these functional motifs may be utilized by the molecular chaperone machinery to act collectively as central regulators of Hsp90 dynamics and activity, including the inter-domain communications, control of ATP hydrolysis, and protein client binding. These findings have provided support to a long-standing assertion that allosteric regulation and catalysis may have emerged via common evolutionary routes. The interaction networks regulating functional motions of Hsp90 may be determined by the inherent structural architecture of the molecular chaperone. At the same time, the thermodynamics-based "conformational selection" of functional states is likely to be activated based on the nature of the binding partner. This mechanistic model of Hsp90 dynamics and function is consistent with the notion that allosteric networks orchestrating cooperative protein motions can be formed by evolutionary conserved and sparsely connected residue clusters. Hence, allosteric signaling through a small network of distantly connected

  5. Determining habitat quality for species that demonstrate dynamic habitat selection

    Science.gov (United States)

    Beerens, James; Frederick, Peter C; Noonburg, Erik G; Gawlik, Dale E.

    2015-01-01

    Determining habitat quality for wildlife populations requires relating a species' habitat to its survival and reproduction. Within a season, species occurrence and density can be disconnected from measures of habitat quality when resources are highly seasonal, unpredictable over time, and patchy. Here we establish an explicit link among dynamic selection of changing resources, spatio-temporal species distributions, and fitness for predictive abundance and occurrence models that are used for short-term water management and long-term restoration planning. We used the wading bird distribution and evaluation models (WADEM) that estimate (1) daily changes in selection across resource gradients, (2) landscape abundance of flocks and individuals, (3) conspecific foraging aggregation, and (4) resource unit occurrence (at fixed 400 m cells) to quantify habitat quality and its consequences on reproduction for wetland indicator species. We linked maximum annual numbers of nests detected across the study area and nesting success of Great Egrets (Ardea alba), White Ibises (Eudocimus albus), and Wood Storks (Mycteria americana) over a 20-year period to estimated daily dynamics of food resources produced by WADEM over a 7490 km2 area. For all species, increases in predicted species abundance in March and high abundance in April were strongly linked to breeding responses. Great Egret nesting effort and success were higher when birds also showed greater conspecific foraging aggregation. Synthesis and applications: This study provides the first empirical evidence that dynamic habitat selection processes and distributions of wading birds over environmental gradients are linked with reproductive measures over periods of decades. Further, predictor variables at a variety of temporal (daily-multiannual) resolutions and spatial (400 m to regional) scales effectively explained variation in ecological processes that change habitat quality. The process used here allows managers to develop

  6. Identifying potential selective fluorescent probes for cancer-associated protein carbonic anhydrase IX using a computational approach.

    Science.gov (United States)

    Kamstra, Rhiannon L; Floriano, Wely B

    2014-11-01

    Carbonic anhydrase IX (CAIX) is a biomarker for tumor hypoxia. Fluorescent inhibitors of CAIX have been used to study hypoxic tumor cell lines. However, these inhibitor-based fluorescent probes may have a therapeutic effect that is not appropriate for monitoring treatment efficacy. In the search for novel fluorescent probes that are not based on known inhibitors, a database of 20,860 fluorescent compounds was virtually screened against CAIX using hierarchical virtual ligand screening (HierVLS). The screening database contained 14,862 compounds tagged with the ATTO680 fluorophore plus an additional 5998 intrinsically fluorescent compounds. Overall ranking of compounds to identify hit molecular probe candidates utilized a principal component analysis (PCA) approach. Four potential binding sites, including the catalytic site, were identified within the structure of the protein and targeted for virtual screening. Available sequence information for 23 carbonic anhydrase isoforms was used to prioritize the four sites based on the estimated "uniqueness" of each site in CAIX relative to the other isoforms. A database of 32 known inhibitors and 478 decoy compounds was used to validate the methodology. A receiver-operating characteristic (ROC) analysis using the first principal component (PC1) as predictive score for the validation database yielded an area under the curve (AUC) of 0.92. AUC is interpreted as the probability that a binder will have a better score than a non-binder. The use of first component analysis of binding energies for multiple sites is a novel approach for hit selection. The very high prediction power for this approach increases confidence in the outcome from the fluorescent library screening. Ten of the top scoring candidates for isoform-selective putative binding sites are suggested for future testing as fluorescent molecular probe candidates.

  7. Investigation of ligand selectivity in CYP3A7 by molecular dynamics simulations.

    Science.gov (United States)

    Fan, Jing-Rong; Zheng, Qing-Chuan; Cui, Ying-Lu; Li, Wei-Kang; Zhang, Hong-Xing

    2015-01-01

    Cytochrome P450 (CYP) 3A7 plays a crucial role in the biotransformation of the metabolized endogenous and exogenous steroids. To compare the metabolic capabilities of CYP3A7-ligands complexes, three endogenous ligands were selected, namely dehydroepiandrosterone (DHEA), estrone, and estradiol. In this study, a three-dimensional model of CYP3A7 was constructed by homology modeling using the crystal structure of CYP3A4 as the template and refined by molecular dynamics simulation (MD). The docking method was adopted, combined with MD simulation and the molecular mechanics generalized born surface area method, to probe the ligand selectivity of CYP3A7. These results demonstrate that DHEA has the highest binding affinity, and the results of the binding free energy were in accordance with the experimental conclusion that estrone is better than estradiol. Moreover, several key residues responsible for substrate specificity were identified on the enzyme. Arg372 may be the most important residue due to the low interaction energies and the existence of hydrogen bond with DHEA throughout simulation. In addition, a cluster of Phe residues provides a hydrophobic environment to stabilize ligands. This study provides insights into the structural features of CYP3A7, which could contribute to further understanding of related protein structures and dynamics.

  8. Pump-probe reflectivity study of ultrafast dynamics of strongly correlated 5f electrons inUO2

    Energy Technology Data Exchange (ETDEWEB)

    Au, Yongqiang Q [Los Alamos National Laboratory; Taylor, Antoinette J [Los Alamos National Laboratory; Durakiewicz, Tomasz [Los Alamos National Laboratory; Rodriguez, George [Los Alamos National Laboratory

    2010-01-01

    5f electrons in the Mott insulator UO{sub 2} produce intriguing electronic states and dynamics, such as strong correlation and f-f excitations. We have performed femtosecond pump-probe reflectivity measurements on a single crystal UO{sub 2} at temperatures 5-300 K to study the ultrafast dynamics of photoexcited 5f electrons. The laser pulses at 400 nm pump 5 f electrons across the Mott gap, while those at 800 nm probe the pump-induced change of reflectivity. We find temperature-dependent excitation and relaxation processes and long-lived acoustic phonons, and extract picosecond risetimes and microsecond relaxation times at low temperatures. The observed slow relaxation is ascribed to the decay of Hubbard excitons formed by U{sup 3+}-U{sup 5+} pairs.

  9. Nickel(II) dithiocarbamate complexes containing sulforhodamine B as fluorescent probes for selective detection of nitrogen dioxide.

    Science.gov (United States)

    Yan, Yan; Krishnakumar, Saarangan; Yu, Huan; Ramishetti, Srinivas; Deng, Lih-Wen; Wang, Suhua; Huang, Leaf; Huang, Dejian

    2013-04-10

    We synthesized complexes of Ni(II) with dithiocarbamate ligands derived from the ortho and para isomers of sulforhodamine B fluorophores and demonstrated they are highly selective in reactions with nitrogen dioxide (NO2). Compared with the para isomer, the ortho isomer showed a much greater fluorescence increase upon reaction with NO2, which led to oxidation and decomplexation of the dithiocarbamate ligand from Ni(II). We applied this probe for visual detection of 1 ppm NO2 in the gas phase and fluorescence imaging of NO2 in macrophage cells treated with a nitrogen dioxide donor.

  10. Green synthesis of carbon nanodots as an effective fluorescent probe for sensitive and selective detection of mercury(II) ions

    Energy Technology Data Exchange (ETDEWEB)

    Lu Wenbo; Qin Xiaoyun [China West Normal University, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, School of Chemistry and Chemical Industry (China); Asiri, Abdullah M.; Al-Youbi, Abdulrahman O. [King Abdulaziz University, Chemistry Department, Faculty of Science (Saudi Arabia); Sun Xuping, E-mail: sunxp@ciac.jl.cn [China West Normal University, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, School of Chemistry and Chemical Industry (China)

    2013-01-15

    The present communication reports on the use of sweet potatoes as carbon source for green synthesis of fluorescent carbon nanodots (CNDs) ranging from 1 to 3 nm. We further demonstrate the use of such CNDs as a very effective fluorescent probe for label-free, sensitive, and selective detection of Hg{sup 2+} with a detection limit as low as 1 nM. The feasibility of the CNDs for analysis of Hg{sup 2+} in a real water sample is also demonstrated successfully.Graphical Abstract.

  11. Local Environment and Interactions of Liquid and Solid Interfaces Revealed by Spectral Line Shape of Surface Selective Nonlinear Vibrational Probe

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Shun-Li; Fu, Li; Chase, Zizwe A.; Gan, Wei; Wang, Hong-Fei

    2016-11-10

    Vibrational spectral lineshape contains important detailed information of molecular vibration and reports its specific interactions and couplings to its local environment. In this work, recently developed sub-1 cm-1 high-resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS) was used to measure the -C≡N stretch vibration in the 4-n-octyl-4’-cyanobiphenyl (8CB) Langmuir or Langmuir-Blodgett (LB) monolayer as a unique vibrational probe, and the spectral lineshape analysis revealed the local environment and interactions at the air/water, air/glass, air/calcium fluoride and air/-quartz interfaces for the first time. The 8CB Langmuir or LB film is uniform and the vibrational spectral lineshape of its -C≡N group has been well characterized, making it a good choice as the surface vibrational probe. Lineshape analysis of the 8CB -C≡N stretch SFG vibrational spectra suggests the coherent vibrational dynamics and the structural and dynamic inhomogeneity of the -C≡N group at each interface are uniquely different. In addition, it is also found that there are significantly different roles for water molecules in the LB films on different substrate surfaces. These results demonstrated the novel capabilities of the surface nonlinear spectroscopy in characterization and in understanding the specific structures and chemical interactions at the liquid and solid interfaces in general.

  12. Element Selective Probe of the Ultra-Fast Magnetic Response to an Element Selective Excitation in Fe-Ni Compounds Using a Two-Color FEL Source

    Directory of Open Access Journals (Sweden)

    Eugenio Ferrari

    2017-01-01

    Full Text Available The potential of the two-color mode implemented at the FERMI free-electron laser (FEL source for pumping and probing selectively different atomic species has been demonstrated by time-resolved scattering experiments with permalloy (FeNi alloy and NiFe2O4 samples. We monitored the ultra-fast demagnetization of Ni induced by the pump FEL pulse, by tuning the linearly-polarized FEL probe pulse to the Ni-3p resonance and measuring the scattered intensity in the transverse magneto-optical Kerr effect geometry. The measurements were performed by varying the intensity of the FEL pump pulse, tuning its wavelength to and off of the Fe-3p resonance, and by spanning the FEL probe pulse delays across the 300–900 fs range. The obtained results have evidenced that for the case of NiFe2O4, there is a sensible difference in the magnetic response at the Ni site when the pump pulse causes electronic excitations at the Fe site.

  13. Probing spin-vibronic dynamics using femtosecond X-ray spectroscopy

    DEFF Research Database (Denmark)

    Penfold, T. J.; Pápai, Mátyás Imre; Rozgonyi, T.;

    2016-01-01

    Ultrafast pump-probe spectroscopy within the X-ray regime is now possible owing to the development of X-ray Free Electrons Lasers (X-FELs) and is opening new opportunities for the direct probing of femtosecond evolution of the nuclei, the electronic and spin degrees of freedom. In this contributi...

  14. Selective detection of endogenous H2S in living cells and the mouse hippocampus using a ratiometric fluorescent probe

    Science.gov (United States)

    Zhang, Ling; Meng, Wen-Qi; Lu, Liang; Xue, Yun-Sheng; Li, Cheng; Zou, Fang; Liu, Yi; Zhao, Jing

    2014-07-01

    As one of three gasotransmitters, the fundamental signalling roles of hydrogen sulphide are receiving increasing attention. New tools for the accurate detection of hydrogen sulphide in cells and tissues are in demand to probe its biological functions. We report the p-nitrobenzyl-based ratiometric fluorescent probe RHP-2, which features a low detection limit, high selectivity and good photostability. The emission intensity ratios had a good linear relationship with the sulphide concentrations in PBS buffer and bovine serum. Our probe was applied to the ratiometric determination and imaging of endogenous H2S in living cells. Furthermore, RHP-2 was used as an effective tool to measure endogenous H2S in the mouse hippocampus. We observed a significant reduction in sulphide concentrations and downregulated expression of cystathionine β-synthetase (CBS) mRNA and CBS protein in the mouse hippocampus in a chronic unpredictable mild stress (CUMS)-induced depression model. These data suggested that decreased concentrations of endogenous H2S may be involved in the pathogenesis of chronic stress depression.

  15. Dynamics of a probe null string in the gravitational field of a closed null string radially collapsing in the plane

    Science.gov (United States)

    Lelyakov, A. P.; Karpenko, A. S.

    2017-01-01

    We consider the dynamics of a probe null string in the gravitational field of a closed ( "thick") null string radially collapsing in a plane. Analysis of the obtained solutions suggests that there might exist several properties of a null-string gas interesting from the cosmological standpoint, such as acceleration of expansion or contraction, a granular structure of the gas, the emergence of stable polarized states, and a domain structure.

  16. Probing nuclear dynamics in jet production with a global event shape

    Science.gov (United States)

    Kang, Zhong-Bo; Liu, Xiaohui; Mantry, Sonny; Qiu, Jian-Wei

    2013-10-01

    We study single jet production in electron-nucleus collisions e-+NA→J+X, using the 1-jettiness (τ1) global event shape. It inclusively quantifies the pattern of radiation in the final state, gives enhanced sensitivity to soft radiation at wide angles from the nuclear beam and final-state jet, and facilitates the resummation of large Sudakov logarithms associated with the veto on additional jets. Through their effect on the observed pattern of radiation, 1-jettiness can be a useful probe of nuclear parton distribution functions and power corrections from dynamical effects in the nuclear medium. This formalism allows for the standard jet shape analysis while simultaneously providing sensitivity to soft radiation at wide angles from the jet. We use a factorization framework for cross-sections differential in τ1 and the transverse momentum (PJT) and rapidity (y) of the jet, in the region τ1≪PJT. The restriction τ1≪PJT allows only soft radiation between the nuclear beam and jet directions, thereby acting as a veto on additional jets. This region is also insensitive to the details of the jet algorithm, allowing for better theoretical control over resummation, while providing enhanced sensitivity to nuclear medium effects. We give numerical results at leading twist, with resummation at the next-to-next-to-leading logarithmic level of accuracy, for a variety of nuclear targets. Such studies would be ideal for the electron-ion collider and the LHeC proposals for a future electron-ion collider, where a range of nuclear targets are planned.

  17. Probing photoluminescence dynamics of colloidal CdSe/ZnS core/shell nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Kaur, Gurvir; Tripathi, S.K., E-mail: surya@pu.ac.in

    2014-11-15

    The paper presents the synthesis of thiol capped CdSe/ZnS core/shell nanoparticles with CdSe core and ZnS shell. The thickness of the ZnS shell has been controlled by the regulating the amount of Zn/S precursors for reaction. The steady and transient photoluminescence properties substantiate the growth of ZnS shell over the CdSe cores. High resolution transmission electron microscope and the X-ray diffraction patterns reveal nanocrystalline particles of an average size 3.4 nm packed in wurtzite lattice. Photoluminescence excitation spectra as well as the excitation–emission matrix of CdSe and CdSe/ZnS evidence the growth of ZnS for Type I hetero-junction without interfering the energy states of core. By this method, ZnS layer of 8.84 Å is optimum for fluorescence enhancement of the core/shell quantum dots. The multiexponential fluorescence decay of the quantum dots represents independent radiative recombinations with overlapped energies. It is revealed that the average fluorescence lifetimes of quantum dots decreased with increase in ZnS shell, which is due to the enhanced contribution from initially populated excitonic recombination and the reduction in the surface trap states with shell growth. - Highlights: • Synthesis of MAA capped CdSe/ZnS core/shell QDs with different shell thicknesses. • Shell thickness has been controlled by the amount of shell precursors added. • ZnS shell significantly enhanced the fluorescence quantum yield of QDs. • Superposition of quantum confinement energy model employed for shell thickness. • Probed the fluorescence dynamics of QDs by time resolved fluorescence spectroscopy.

  18. Dynamic high pressure measurements using a Fiber Bragg Grating probe and an arrayed waveguide grating spectrometer

    Science.gov (United States)

    Barbarin, Y.; Lefrançois, A.; Magne, S.; Woirin, K.; Sinatti, F.; Osmont, A.; Luc, J.

    2016-08-01

    High pressure shock profiles are monitored using a long Fiber Bragg Grating (FBG). Such thin probe, with a diameter of typically 150 μm, can be inserted directly into targets for shock plate experiments. The shocked FBG's portion is stressed under compression, which increases its optical group index and shortens its grating period. Placed along the 2D symmetrical axis of the cylindrical target, the second effect is stronger and the reflected spectrum shifts towards the shorter wavelengths. The dynamic evolution of FBG spectra is recorded with a customized Arrayed Waveguide Grating (AWG) spectrometer covering the C+L band. The AWG provides 40 channels of 200-GHz spacing with a special flattop design. The output channels are fiber-connected to photoreceivers (bandwidth: DC - 400 MHz or 10 kHz - 2 GHz). The experimental setup was a symmetric impact, completed in a 110-mm diameter single-stage gas gun with Aluminum (6061T6) impactors and targets. The FBG's central wavelength was 1605 nm to cover the pressure range of 0 - 8 GPa. The FBG was 50-mm long as well as the target's thickness. The 20-mm thick impactor maintains a shock within the target over a distance of 30 mm. For the impact at 522 m/s, the sustained pressure of 3.6 GPa, which resulted in a Bragg shift of (26.2 +/- 1.5) nm, is measured and retrieved with respectively thin-film gauges and the hydrodynamic code Ouranos. The shock sensitivity of the FBG is about 7 nm/GPa, but it decreases with the pressure level. The overall spectra evolution is in good agreement with the numerical simulations.

  19. Scanning probe microscopy studies on the adsorption of selected molecular dyes on titania

    Directory of Open Access Journals (Sweden)

    Jakub S. Prauzner-Bechcicki

    2016-11-01

    Full Text Available Titanium dioxide, or titania, sensitized with organic dyes is a very attractive platform for photovoltaic applications. In this context, the knowledge of properties of the titania–sensitizer junction is essential for designing efficient devices. Consequently, studies on the adsorption of organic dyes on titania surfaces and on the influence of the adsorption geometry on the energy level alignment between the substrate and an organic adsorbate are necessary. The method of choice for investigating the local environment of a single dye molecule is high-resolution scanning probe microscopy. Microscopic results combined with the outcome of common spectroscopic methods provide a better understanding of the mechanism taking place at the titania–sensitizer interface. In the following paper, we review the recent scanning probe microscopic research of a certain group of molecular assemblies on rutile titania surfaces as it pertains to dye-sensitized solar cell applications. We focus on experiments on adsorption of three types of prototypical dye molecules, i.e., perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA, phtalocyanines and porphyrins. Two interesting heteromolecular systems comprising molecules that are aligned with the given review are discussed as well.

  20. Dynamics of trapped atoms around an optical nanofiber probed through polarimetry

    Science.gov (United States)

    Solano, Pablo; Fatemi, Fredrik K.; Orozco, Luis A.; Rolston, S. L.

    2017-06-01

    The evanescent field outside an optical nanofiber (ONF) can create optical traps for neutral atoms. We present a non-destructive method to characterize such trapping potentials. An off-resonance linearly polarized probe beam that propagates through the ONF experiences a slow axis of polarization produced by trapped atoms on opposite sides along the ONF. The transverse atomic motion is imprinted onto the probe polarization through the changing atomic index of of refraction. By applying a transient impulse, we measure a time-dependent polarization rotation of the probe beam that provides both a rapid and non-destructive measurement of the optical trapping frequencies.

  1. Glucagon-Secreting Alpha Cell Selective Two-Photon Fluorescent Probe TP-α: For Live Pancreatic Islet Imaging.

    Science.gov (United States)

    Agrawalla, Bikram Keshari; Chandran, Yogeswari; Phue, Wut-Hmone; Lee, Sung-Chan; Jeong, Yun-Mi; Wan, Si Yan Diana; Kang, Nam-Young; Chang, Young-Tae

    2015-04-29

    Two-photon (TP) microscopy has an advantage for live tissue imaging which allows a deeper tissue penetration up to 1 mm comparing to one-photon (OP) microscopy. While there are several OP fluorescence probes in use for pancreatic islet imaging, TP imaging of selective cells in live islet still remains a challenge. Herein, we report the discovery of first TP live pancreatic islet imaging probe; TP-α (Two Photon-alpha) which can selectively stain glucagon secreting alpha cells. Through fluorescent image based screening using three pancreatic cell lines, we discovered TP-α from a TP fluorescent dye library TPG (TP-Green). In vitro fluorescence test showed that TP-α have direct interaction and appear glucagon with a significant fluorescence increase, but not with insulin or other hormones/analytes. Finally, TP-α was successfully applied for 3D imaging of live islets by staining alpha cell directly. The newly developed TP-α can be a practical tool to evaluate and identify live alpha cells in terms of localization, distribution and availability in the intact islets.

  2. Label-free selective sensing of mercury(II) via reduced aggregation of the perylene fluorescent probe.

    Science.gov (United States)

    Wang, Bin; Wang, Fangyuan; Jiao, Huping; Yang, Xiangyu; Yu, Cong

    2010-08-01

    In the present work, we report a fluorescence turn-on approach for the sensitive and selective detection of Hg(2+). A cationic perylene derivative (compound 1) was used as the fluorescence probe, and a thymine-rich oligonucleotide (oligo-M) was employed for the specific interaction with Hg(2+). Compound 1 shows strong tendency to self-aggregate into linear chain structures in aqueous media because of the pi-pi stacking interactions of its planar aromatic ring structure. The compound 1 free monomer is strongly fluorescent, whereas its aggregates are not fluorescent. When oligo-M and compound 1 were mixed, oligo-M induced strong compound 1 aggregation and resulted in significant fluorescence quenching. In the presence of Hg(2+), the specific interactions between oligo-M and Hg(2+) induced hairpin structure formation of oligo-M and thus weakened its binding to compound 1 aggregates. As a result, free probe monomers were released, and increased fluorescence was observed. The fluorescence intensity increase was in direct proportion to the concentration of Hg(2+) added. Our method provides a simple, fast, and efficient means for Hg(2+) quantification, it is highly sensitive with a limit of detection of 1 nM, and is also highly selective against other common metal ions.

  3. Indole-based cyanine as a nuclear RNA-selective two-photon fluorescent probe for live cell imaging.

    Science.gov (United States)

    Guo, Lei; Chan, Miu Shan; Xu, Di; Tam, Dick Yan; Bolze, Frédéric; Lo, Pik Kwan; Wong, Man Shing

    2015-05-15

    We have demonstrated that the subcellular targeting properties of the indole-based cyanines can be tuned by the functional substituent attached onto the indole moiety in which the first example of a highly RNA-selective and two-photon active fluorescent light-up probe for high contrast and brightness TPEF images of rRNA in the nucleolus of live cells has been developed. It is important to find that this cyanine binds much stronger toward RNA than DNA in a buffer solution as well as selectively stains and targets to rRNA in the nucleolus. Remarkably, the TPEF brightness (Φσmax) is dramatically increased with 11-fold enhancement in the presence of rRNA, leading to the record high Φσmax of 228 GM for RNA. This probe not only shows good biocompatibility and superior photostability but also offers general applicability to various live cell lines including HeLa, HepG2, MCF-7, and KB cells and excellent counterstaining compatibility with commercially available DNA or protein trackers.

  4. Probing Silica-Biomolecule Interactions by Solid-State NMR and Molecular Dynamics Simulations.

    Science.gov (United States)

    Brückner, Stephan Ingmar; Donets, Sergii; Dianat, Arezoo; Bobeth, Manfred; Gutiérrez, Rafael; Cuniberti, Gianaurelio; Brunner, Eike

    2016-11-08

    Understanding the molecular interactions between inorganic phases such as silica and organic material is fundamental for chromatographic applications, for tailoring silica-enzyme interactions, and for elucidating the mechanisms of biomineralization. The formation, structure, and properties of the organic/inorganic interface is crucial in this context. Here, we investigate the interaction of selectively (13)C-labeled choline with (29)Si-labeled monosilicic acid/silica at the molecular level. Silica/choline nanocomposites were analyzed by solid-state NMR spectroscopy in combination with extended molecular dynamics (MD) simulations to understand the silica/organic interface. Cross-polarization magic angle spinning (CP MAS)-based NMR experiments like (1)H-(13)C CP-REDOR (rotational-echo double resonance), (1)H-(13)C HETCOR (heteronuclear correlation), and (1)H-(29)Si-(1)H double CP are employed to determine spatial parameters. The measurement of (29)Si-(13)C internuclear distances for selectively (13)C-labeled choline provides an experimental parameter that allows the direct verification of MD simulations. Atomistic modeling using classical MD methodologies is performed using the INTERFACE force field. The modeling results are in excellent agreement with the experimental data and reveal the relevant molecular conformations as well as the nature and interplay of the interactions between the choline cation and the silica surface. Electrostatic interactions and hydrogen bonding are both important and depend strongly on the hydration level as well as the charge state of the silica surface.

  5. The selective dynamical downscaling method for extreme-wind atlases

    DEFF Research Database (Denmark)

    Larsén, Xiaoli Guo; Badger, Jake; Hahmann, Andrea N.

    2012-01-01

    and (iii) post-processing. The post-processing generalizes the winds from the mesoscale modelling to standard conditions, i.e. 10-m height over a homogeneous surface with roughness length of 5 cm. The generalized winds are then used to calculate the 50-year wind using the annual maximum method for each......A selective dynamical downscaling method is developed to obtain extreme-wind atlases for large areas. The method is general, efficient and flexible. The method consists of three steps: (i) identifying storm episodes for a particular area, (ii) downscaling of the storms using mesoscale modelling...... mesoscale grid point. The generalization of the mesoscale winds through the post-processing provides a framework for data validation and for applying further the mesoscale extreme winds at specific places using microscale modelling. The results are compared with measurements from two areas with different...

  6. Monitoring live human mesenchymal stromal cell differentiation and subsequent selection using fluorescent RNA-based probes

    DEFF Research Database (Denmark)

    Li, Bojun; Menzel, Ursula; Loebel, Claudia

    2016-01-01

    Investigating mesenchymal stromal cell differentiation requires time and multiple samples due to destructive endpoint assays. Osteogenesis of human bone marrow derived mesenchymal stromal cells (hBMSCs) has been widely studied for bone tissue engineering. Recent studies show that the osteogenic...... differentiation of hBMSCs can be assessed by quantifying the ratio of two important transcription factors (Runx2/Sox9). We demonstrate a method to observe mRNA expression of two genes in individual live cells using fluorescent probes specific for Runx2 and Sox9 mRNA. The changes of mRNA expression in cells can...... and isolating differentiating cells at early time points, prospective analysis of differentiation is also possible, which will lead to a greater understanding of MSC differentiation....

  7. A Fluorescence Turn-On Probe for Thiols with a Tunable Dynamic Range.

    Science.gov (United States)

    Li, Qian; Guo, Rui; Lin, Weiying

    2016-05-01

    We designed and synthesized a novel probe Cou-Rho-SA-Cu (II) for detection of thiols based on a coumarin-rhodamine FRET system. The compound Cou-Rho-SA exhibited strong blue fluorescence as the rhodamine moiety of the compound Cou-Rho-SA was in a ring-closing form and no FRET process occurred. The probe Cou-Rho-SA-Cu (II) was prepared by addition of Cu(2+) to the solution of Cou-Rho-SA. In the absence of GSH, the complex Cou-Rho-SA-Cu (II) showed almost no fluorescence owing to the FRET process and the paramagnetic nature of Cu(2+) . However, upon addition of GSH, the rhodamine moiety of the probe Cou-Rho-SA-Cu (II) recovered to its ring-closing form, and the FRET process was prohibited to show the blue fluorescence again. Moreover, via tuning the Cu(2+) concentrations, the probe could detect the different levels of GSH.

  8. A dynamic sandwich assay on magnetic beads for selective detection of single-nucleotide mutations at room temperature.

    Science.gov (United States)

    Wang, Junxiu; Xiong, Guoliang; Ma, Liang; Wang, Shihui; Zhou, Xu; Wang, Lei; Xiao, Lehui; Su, Xin; Yu, Changyuan

    2017-08-15

    Single-nucleotide mutation (SNM) has proven to be associated with a variety of human diseases. Development of reliable methods for the detection of SNM is crucial for molecular diagnosis and personalized medicine. The sandwich assays are widely used tools for detecting nucleic acid biomarkers due to their low cost and rapid signaling. However, the poor hybridization specificity of signal probe at room temperature hampers the discrimination of mutant and wild type. Here, we demonstrate a dynamic sandwich assay on magnetic beads for SNM detection based on the transient binding between signal probe and target. By taking the advantage of mismatch sensitive thermodynamics of transient DNA binding, the dynamic sandwich assay exhibits high discrimination factor for mutant with a broad range of salt concentration at room temperature. The beads used in this assay serve as a tool for separation, and might be helpful to enhance SNM selectivity. Flexible design of signal probe and facile magnetic separation allow multiple-mode downstream analysis including colorimetric detection and isothermal amplification. With this method, BRAF mutations in the genomic DNA extracted from cancer cell lines were tested, allowing sensitive detection of SNM at very low abundances (0.1-0.5% mutant/wild type). Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy

    Science.gov (United States)

    Balke, Nina; Jesse, Stephen; Carmichael, Ben; Baris Okatan, M.; Kravchenko, Ivan I.; Kalinin, Sergei V.; Tselev, Alexander

    2017-02-01

    Atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. In combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm-1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.

  10. Slingshot Dynamics for Self Replicating Probes and the Effect on Exploration Timescales

    CERN Document Server

    Nicholson, Arwen

    2013-01-01

    Interstellar probes can carry out slingshot manoeuvres around the stars they visit, gaining a boost in velocity by extracting energy from the star's motion around the Galactic Centre. These maneouvres carry little to no extra energy cost, and in previous work it has been shown that a single Voyager-like probe exploring the galaxy does so 100 times faster when carrying out these slingshots than when navigating purely by powered flight (Forgan et al. 2012). We expand on these results by repeating the experiment with self-replicating probes. The probes explore a box of stars representative of the local Solar neighbourhood, to investigate how self-replication affects exploration timescales when compared with a single non-replicating probe. We explore three different scenarios of probe behaviour: i) standard powered flight to the nearest unvisited star (no slingshot techniques used), ii) flight to the nearest unvisited star using slingshot techniques, and iii) flight to the next unvisited star that will give the m...

  11. Rational design of reversible fluorescent probes for live-cell imaging and quantification of fast glutathione dynamics

    Science.gov (United States)

    Umezawa, Keitaro; Yoshida, Masafumi; Kamiya, Mako; Yamasoba, Tatsuya; Urano, Yasuteru

    2017-03-01

    Alterations in glutathione (GSH) homeostasis are associated with a variety of diseases and cellular functions, and therefore, real-time live-cell imaging and quantification of GSH dynamics are important for understanding pathophysiological processes. However, existing fluorescent probes are unsuitable for these purposes due to their irreversible fluorogenic mechanisms or slow reaction rates. In this work, we have successfully overcome these problems by establishing a design strategy inspired by Mayr's work on nucleophilic reaction kinetics. The synthesized probes exhibit concentration-dependent, reversible and rapid absorption/fluorescence changes (t1/2 = 620 ms at [GSH] = 1 mM), as well as appropriate Kd values (1-10 mM: within the range of intracellular GSH concentrations). We also developed FRET-based ratiometric probes, and demonstrated that they are useful for quantifying GSH concentration in various cell types and also for real-time live-cell imaging of GSH dynamics with temporal resolution of seconds.

  12. Mapping and controlling ultrafast dynamics of highly excited H2 molecules by VUV-IR pump-probe schemes

    Science.gov (United States)

    Sturm, F. P.; Tong, X. M.; Palacios, A.; Wright, T. W.; Zalyubovskaya, I.; Ray, D.; Shivaram, N.; Martín, F.; Belkacem, A.; Ranitovic, P.; Weber, Th.

    2017-01-01

    We used ultrashort femtosecond vacuum ultraviolet (VUV) and infrared (IR) pulses in a pump-probe scheme to map the dynamics and nonequilibrium dissociation channels of excited neutral H2 molecules. A nuclear wave packet is created in the B Σ+1u state of the neutral H2 molecule by absorption of the ninth harmonic of the driving infrared laser field. Due to the large stretching amplitude of the molecule excited in the B Σ+1u electronic state, the effective H2+ ionization potential changes significantly as the nuclear wave packet vibrates in the bound, highly electronically and vibrationally excited B potential-energy curve. We probed such dynamics by ionizing the excited neutral molecule using time-delayed VUV-or-IR radiation. We identified the nonequilibrium dissociation channels by utilizing three-dimensional momentum imaging of the ion fragments. We found that different dissociation channels can be controlled, to some extent, by changing the IR laser intensity and by choosing the wavelength of the probe laser light. Furthermore, we concluded that even in a benchmark molecular system such as H2*, the interpretation of the nonequilibrium multiphoton and multicolor ionization processes is still a challenging task, requiring intricate theoretical analysis.

  13. Spin probe dynamics in relation to free volume in crystalline organics by means of ESR and PALS: n-Hexadecane

    Energy Technology Data Exchange (ETDEWEB)

    Bartoš, J., E-mail: Jozef.Bartos@savba.sk [Institute of SAS, Department of Structure and Physical Properties, Dúbravská cesta 9, 845 41 Bratislava (Slovakia); Švajdlenková, H. [Institute of SAS, Department of Structure and Physical Properties, Dúbravská cesta 9, 845 41 Bratislava (Slovakia); Zaleski, R. [Institute of Physics, Maria Curie-Sklodowska University, Pl. Marii Curie-Sklodowskiej 1, PL-20-031 Lublin (Poland); Edelmann, M. [Leibniz Institute of Polymer Research Dresden, Hohe Strasse 6, D-01069 Dresden (Germany); Lukešová, M. [Institute of SAS, Department of Structure and Physical Properties, Dúbravská cesta 9, 845 41 Bratislava (Slovakia)

    2013-12-01

    We report on a combined study of the guest dynamics and free volume in n-hexadecane (n-HXD) using two external microscopic probes: stable free radical 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) and ortho-positronium (o-Ps) by means of ESR or PALS, respectively. Dynamic behavior of the molecular TEMPO probe and annihilation properties of the atomistic o-Ps one as a function of temperature are compared. Two coincidencies between the crossover effects at the characteristic ESR and PALS temperatures T{sub 50G} and T{sub b1}{sup cr} below and T{sub X2}{sup fast} and T{sub m}{sup PALS} at the melting point T{sub m}{sup DSC} of n-HXD from macroscopic DSC scan were found. First, the slow to fast regime transition is ascribed to the spin probe TEMPO localization in the expanding interlamellar gap due to the induced enhanced end-chain mobility. Second, the high-temperature crossover within the fast regime is directly connected to the collective chain movements at the melting which takes place under the similar free volume fluctuation condition as revealed recently for a series of amorphous small molecular and polymer glass-formers.

  14. A Class of Multiresponsive Colorimetric and Fluorescent pH Probes via Three Different Reaction Mechanisms of Salen Complexes: A Selective and Accurate pH Measurement.

    Science.gov (United States)

    Cheng, Jinghui; Gou, Fei; Zhang, Xiaohong; Shen, Guangyu; Zhou, Xiangge; Xiang, Haifeng

    2016-09-19

    We report a class of multiresponsive colorimetric and fluorescent pH probes based on three different reaction mechanisms including cation exchange, protonation, and hydrolysis reaction of K(I), Ca(II), Zn(II), Cu(II), Al(III), and Pd(II) Salen complexes. Compared with traditional pure organic pH probes, these complex-based pH probes exhibited a much better selectivity due to the shielding function of the filled-in metal ion in the complex. Their pH sensing performances were affected by the ligand structure and the central metal ion. This work is the first report of "off-on-on'-off" colorimetric and fluorescent pH probes that possess three different reaction mechanisms and should inspire the design of multiple-responsive probes for important analytes in biological systems.

  15. Global analysis of fluorescence decays to probe the internal dynamics of fluorescently labeled macromolecules.

    Science.gov (United States)

    Duhamel, Jean

    2014-03-11

    The aim of this review is to introduce the reader first to the mathematical complexity associated with the analysis of fluorescence decays acquired with solutions of macromolecules labeled with a fluorophore and its quencher that are capable of interacting with each other via photophysical processes within the macromolecular volume, second to the experimental and mathematical approaches that have been proposed over the years to handle this mathematical complexity, and third to the information that one can expect to retrieve with respect to the internal dynamics of such fluorescently labeled macromolecules. In my view, the ideal fluorophore-quencher pair to use in studying the internal dynamics of fluorescently labeled macromolecules would involve a long-lived fluorophore, a fluorophore and a quencher that do not undergo energy migration, and a photophysical process that results in a change in fluorophore emission upon contact between the excited fluorophore and quencher. Pyrene, with its ability to form an excimer on contact between excited-state and ground-state species, happens to possess all of these properties. Although the concepts described in this review apply to any fluorophore and quencher pair sharing pyrene's exceptional photophysical properties, this review focuses on the study of pyrene-labeled macromolecules that have been characterized in great detail over the past 40 years and presents the main models that are being used today to analyze the fluorescence decays of pyrene-labeled macromolecules reliably. These models are based on Birks' scheme, the DMD model, the fluorescence blob model, and the model free analysis. The review also provides a step-by-step protocol that should enable the noneducated user to achieve a successful decay analysis exempt of artifacts. Finally, some examples of studies of pyrene-labeled macromolecules are also presented to illustrate the different types of information that can be retrieved from these fluorescence decay

  16. Dynamics of tropomyosin in muscle fibers as monitored by saturation transfer EPR of bi-functional probe.

    Directory of Open Access Journals (Sweden)

    Roni F Rayes

    Full Text Available The dynamics of four regions of tropomyosin was assessed using saturation transfer electron paramagnetic resonance in the muscle fiber. In order to fully immobilize the spin probe on the surface of tropomyosin, a bi-functional spin label was attached to i,i+4 positions via cysteine mutagenesis. The dynamics of bi-functionally labeled tropomyosin mutants decreased by three orders of magnitude when reconstituted into "ghost muscle fibers". The rates of motion varied along the length of tropomyosin with the C-terminus position 268/272 being one order of magnitude slower then N-terminal domain or the center of the molecule. Introduction of troponin decreases the dynamics of all four sites in the muscle fiber, but there was no significant effect upon addition of calcium or myosin subfragment-1.

  17. Isatin functionalized nanoporous SBA-15 as a selective fluorescent probe for the detection of Hg(II) in water.

    Science.gov (United States)

    Lashgari, Negar; Badiei, Alireza; Mohammadi Ziarani, Ghodsi; Faridbod, Farnoush

    2017-03-07

    A highly ordered mesoporous silica material functionalized with isatin (SBA-Pr-IS) was designed and synthesized. Characterization techniques including XRD, TGA, BET, SEM, and FT-IR were employed to characterize the pore structure, textural properties, microscopic morphology, and molecular composition of grafted organic moieties of SBA-Pr-IS. The successful attachment of the organic moiety (0.34 mmol g(-1)) without the SBA-15 structure collapsing after the modification steps was confirmed. Fluorescence characterization of SBA-Pr-IS was examined upon addition of a wide variety of cations in aqueous medium and it showed high sensitivity toward Hg(2+) ions. During testing in an ion competition experiment, it was observed that the fluorescence changes of the probe were remarkably specific for Hg(2+) ions. Furthermore, a good linearity between the fluorescence intensity of this material and the concentration of Hg(2+) ions was constructed with a suitable detection limit of 3.7 × 10(-6) M. Finally, the applicability of the proposed method was successfully evaluated for the determination of Hg(2+) ions in real samples. Therefore, SBA-Pr-IS can be used as an efficient fluorescence probe for Hg(2+) ions. Graphical Abstract A novel organic-inorganic hybrid material was designed and synthesized by functionalization of SBA-15 mesoporous silica material with isatin. The evaluation of the sensing ability of SBA-Pr-IS using fluorescence spectroscopy revealed that the SBA-Pr-IS was a selective fluorescent probe for Hg(2+) ion in water in the presence of a wide range of metal cations.

  18. Probing ultrafast dynamics in electronic structure of epitaxial Gd(0 0 0 1) on W(1 1 0)

    Energy Technology Data Exchange (ETDEWEB)

    Beaulieu, Nathan [Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette Cedex (France); Malinowski, Gregory [Laboratoire de Physique des Solides, Université Paris Sud, Orsay (France); Bendounan, Azzedine; Silly, Mathieu G.; Chauvet, Christian [Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette Cedex (France); Krizmancic, Damjan [Instituto Officina dei Materiali (IOM)-CNR Laboratorio TASC, in Area Science Park S.S.14, Km 163.5, I-34149 Trieste (Italy); Sirotti, Fausto [Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette Cedex (France)

    2013-08-15

    Highlights: •Study of the magnetism of epitaxial Gd(0 0 0 1)/W(1 1 0). •Study of Gd(0 0 0 1) band structure as a function of the temperature. •Study of the Gd magnetism dynamics probing the M5 edge. -- Abstract: The electronic and magnetic properties of Gd have been studied using time- and angle-resolved photoelectron spectroscopy employing laser pump and synchrotron radiation probe pulses. The static temperature evolution of the valence band and more precisely, the 5d6s exchange splitting is reported. Ultrafast demagnetization is measured using dichroic resonant Auger spectroscopy. Remarkably, a complete demagnetization is observed followed up by a non-monotonic recovery that could be associated to magnetization oscillations.

  19. Theoretical Investigation of Dynamic Properties of Magnetic Molecule Systems as Probed by NMR and Pulsed Fields Experiments

    Energy Technology Data Exchange (ETDEWEB)

    Rousochatzakis, Ioannis [Iowa State Univ., Ames, IA (United States)

    2005-12-17

    The field of molecular magnetism[l-6] has become a subject of intense theoretical and experimental interest and has rapidly evolved during the last years. This inter-disciplinary field concerns magnetic systems at the molecular or "nanoscopic" level, whose realization has become feasible due to recent advances in the field of chemical synthesis. The present theoretical work provides a first step towards exploiting the possibilities that are offered by probing magnetic molecules using external magnetic fields with high sweep rates. These probes, apart for providing information specific to magnetic molecules, offer the possibility of conducting a detailed study of the relaxational behavior of interacting spin systems as a result of their coupling with a "heat bath" and in particular the excitations of the host lattice. Development of a broad theoretical framework for dealing with relaxational phenomena induced by dynamical magnetic fields is indeed a worthy goal.

  20. Identification of Early Intermediates of Caspase Activation Using Selective Inhibitors and Activity-Based Probes

    NARCIS (Netherlands)

    Berger, Alicia B.; Witte, Martin D.; Denault, Jean-Bernard; Sadaghiani, Amir Masoud; Sexton, Kelly M.B.; Salvesen, Guy S.; Bogyo, Matthew

    2006-01-01

    Caspases are cysteine proteases that are key effectors in apoptotic cell death. Currently, there is a lack of tools that can be used to monitor the regulation of specific caspases in the context of distinct apoptotic programs. We describe the development of highly selective inhibitors and active sit

  1. Dynamic PET and Optical Imaging and Compartment Modeling using a Dual-labeled Cyclic RGD Peptide Probe

    Directory of Open Access Journals (Sweden)

    Lei Zhu, Ning Guo, Quanzheng Li, Ying Ma, Orit Jacboson, Seulki Lee, Hak Soo Choi, James R. Mansfield, Gang Niu, Xiaoyuan Chen

    2012-01-01

    Full Text Available Purpose: The aim of this study is to determine if dynamic optical imaging could provide comparable kinetic parameters to that of dynamic PET imaging by a near-infrared dye/64Cu dual-labeled cyclic RGD peptide.Methods: The integrin αvβ3 binding RGD peptide was conjugated with a macrocyclic chelator 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA for copper labeling and PET imaging and a near-infrared dye ZW-1 for optical imaging. The in vitro biological activity of RGD-C(DOTA-ZW-1 was characterized by cell staining and receptor binding assay. Sixty-min dynamic PET and optical imaging were acquired on a MDA-MB-435 tumor model. Singular value decomposition (SVD method was applied to compute the dynamic optical signal from the two-dimensional optical projection images. Compartment models were used to quantitatively analyze and compare the dynamic optical and PET data.Results: The dual-labeled probe 64Cu-RGD-C(DOTA-ZW-1 showed integrin specific binding in vitro and in vivo. The binding potential (Bp derived from dynamic optical imaging (1.762 ± 0.020 is comparable to that from dynamic PET (1.752 ± 0.026.Conclusion: The signal un-mixing process using SVD improved the accuracy of kinetic modeling of 2D dynamic optical data. Our results demonstrate that 2D dynamic optical imaging with SVD analysis could achieve comparable quantitative results as dynamic PET imaging in preclinical xenograft models.

  2. Supersandwich cytosensor for selective and ultrasensitive detection of cancer cells using aptamer-DNA concatamer-quantum dots probes.

    Science.gov (United States)

    Liu, Hongying; Xu, Shouming; He, Zhimei; Deng, Anping; Zhu, Jun-Jie

    2013-03-19

    In this work, a signal amplification supersandwich strategy was developed for highly selective and sensitive detection of cancer cells using aptamer-DNA concatamer-quantum dots (QDs) probes. First of all, electrode materials denoted as MWCNTs@PDA@AuNPs were fabricated by multiwall carbon nanotubes (MWCNTs), gold nanoparticles (AuNPs), and polydopamine (PDA) using a layer-by-layer technique. Then, the prepared bases as matrices were applied to bind concanavalin A (Con A), resulting in high stability, bioactivity, and capability for cell capture. Meanwhile, aptamer-DNA concatamer-QDs were designed via DNA hybridization followed by covalent assembling, which incorporated the specific recognition of the aptamer with the signal amplification of the DNA concatamer and QDs. With aptamer-DNA concatamer-QDs as recognizing probes, the model cancer cells (CCRF-CEM cells) were detected using a MWCNTs@PDA@AuNPs modified electrode with trapped Con A by means of fluorescence and electrochemical methods. The proposed supersandwich cytosensor showed high sensitivity with the detection limit of 50 cells mL(-1). More importantly, it could distinguish cancer cells from normal cells, which indicated the promising applications of our method in clinical diagnosis and treatment of cancers.

  3. Label-free silicon quantum dots as fluorescent probe for selective and sensitive detection of copper ions.

    Science.gov (United States)

    Zhao, Jiangna; Deng, Jianhui; Yi, Yinhui; Li, Haitai; Zhang, Youyu; Yao, Shouzhuo

    2014-07-01

    In this work, label-free silicon quantum dots (SiQDs) were used as a novel fluorescence probe for the sensitive and selective detection of Cu(2+). The fluorescence of the SiQDs was effectively quenched by H2O2 from the reaction of ascorbic acid with O2, and hydroxyl radicals from Fenton reaction between H2O2 and Cu(+). The fluorescence intensity of SiQDs was quenched about 25% in 15 min after the addition of H2O2 (1mM). While the SiQDs was incubated with AA (1mM) and Cu(2+) (1 µM) under the same conditions, the fluorescence intensity of SiQDs decreased about 55%. Obviously, the recycling of Cu(2+) in the test system may lead to a dramatical decrease in the fluorescence of SiQDs. Under the optimized experimental conditions, the rate of fluorescence quenching of SiQDs was linearly dependent on the Cu(2+) concentration ranging from 25 to 600 nM with the limit of detection as low as 8 nM, which was much lower than that of existing methods. Moreover, the probe was successfully applied to the determination of Cu(2+) in different environmental water samples and human hair.

  4. A highly selective ratiometric fluorescent pH probe based on a PAMAM wavelength-shifting bichromophoric system

    Science.gov (United States)

    Alamry, Khalid A.; Georgiev, Nikolai I.; El-Daly, Samy Abdullah; Taib, Layla A.; Bojinov, Vladimir B.

    2015-01-01

    A novel PAMAM wavelength-shifting bichromophoric system has been successfully developed. Novel compound was configured as a light harvesting antenna where the system surface is labeled with yellow-green emitting 4-(N,N-dimethylamino)ethylamino-1,8-naphthalimide "donor" units capable of absorbing light and efficiently transferring the energy to a focal Rhodamine 6G "acceptor". The periphery of the system was designed on the "fluorophore-spacer-receptor" format, capable of acting as a molecular fluorescence photoinduced electron transfer based probe. Due to the both effects, photoinduced electron transfer in the periphery of the system and pH dependent rhodamine core absorption, novel antenna is able to act as a selective ratiometric pH fluorescence probe in aqueous medium. Thus, the distinguishing features of the fluorescence resonance energy transfer systems were successfully combined with the properties of classical ring-opening charge transfer systems, which may be beneficially for monitoring pH variations in complex samples.

  5. Selection of Color-Changing and Intensity-Increasing Fluorogenic Probe as Protein-Specific Indicator Obtained via the 10BASE(d)-T.

    Science.gov (United States)

    Taki, Masumi; Inoue, Hiroaki; Mochizuki, Kazuto; Yang, Jay; Ito, Yuji

    2016-01-19

    To obtain a molecular probe for specific protein detection, we have synthesized fluorogenic probe library of vast diversity on bacteriophage T7 via the gp10 based-thioetherificaion (10BASE(d)-T). A remarkable color-changing and turning-on probe was selected from the library, and its physicochemical properties upon target-specific binding were obtained. Combination analyses of fluorescence emission titration, isothermal titration calorimetry (ITC), and quantitative saturation-transfer difference (STD) NMR measurements, followed by in silico docking simulation, rationalized the most plausible geometry of the ligand-protein interaction.

  6. Probing excited states dynamics in CO cations using few-cycle IR and EUV laser pulses

    Energy Technology Data Exchange (ETDEWEB)

    Alnaser, A S [Department of Physics, American University in Sharjah, Sharjah (United Arab Emirates); Bocharova, I; Singh, K P; Wei, C; Cocke, C L; Litvinyuk, I V [J. R. Macdonald Laboratory, Physics Department, Kansas State University (United States); Kling, M, E-mail: aalnaser@aus.ed [Max-Planck Institute for Quantum Optics, Garching (Germany)

    2009-11-01

    We have used few-cycle IR and EUV laser pulses in pump-probe arrangement to trace out the dissociation pathways in CO when exploded by strong laser fields. We present two preliminary sets of data of different pump pulses. In these sets, different excited state of CO cations are populated using (< 10 fs) IR, and EUV pulses respectively. We followed the time evolution of these states using the time-resolved Coulomb explosion imaging technique. We compare the time evolution of IR- and EUV-induced excited states by measuring the KER of the fragment ions as a function of the time delay between the pump and the IR probe pulse.

  7. Brain dynamics of meal size selection in humans.

    Science.gov (United States)

    Toepel, Ulrike; Bielser, Marie-Laure; Forde, Ciaran; Martin, Nathalie; Voirin, Alexandre; le Coutre, Johannes; Murray, Micah M; Hudry, Julie

    2015-06-01

    Although neuroimaging research has evidenced specific responses to visual food stimuli based on their nutritional quality (e.g., energy density, fat content), brain processes underlying portion size selection remain largely unexplored. We identified spatio-temporal brain dynamics in response to meal images varying in portion size during a task of ideal portion selection for prospective lunch intake and expected satiety. Brain responses to meal portions judged by the participants as 'too small', 'ideal' and 'too big' were measured by means of electro-encephalographic (EEG) recordings in 21 normal-weight women. During an early stage of meal viewing (105-145 ms), data showed an incremental increase of the head-surface global electric field strength (quantified via global field power; GFP) as portion judgments ranged from 'too small' to 'too big'. Estimations of neural source activity revealed that brain regions underlying this effect were located in the insula, middle frontal gyrus and middle temporal gyrus, and are similar to those reported in previous studies investigating responses to changes in food nutritional content. In contrast, during a later stage (230-270 ms), GFP was maximal for the 'ideal' relative to the 'non-ideal' portion sizes. Greater neural source activity to 'ideal' vs. 'non-ideal' portion sizes was observed in the inferior parietal lobule, superior temporal gyrus and mid-posterior cingulate gyrus. Collectively, our results provide evidence that several brain regions involved in attention and adaptive behavior track 'ideal' meal portion sizes as early as 230 ms during visual encounter. That is, responses do not show an increase paralleling the amount of food viewed (and, in extension, the amount of reward), but are shaped by regulatory mechanisms.

  8. A highly stable dynamic fluorescent metal-organic framework for selective sensing of nitroaromatic explosives.

    Science.gov (United States)

    Gong, Yun-Nan; Jiang, Long; Lu, Tong-Bu

    2013-12-07

    A dynamic fluorescent metal-organic framework has been constructed using triphenylene-2,6,10-tricarboxylate and Tb(3+) as building blocks, which exhibits guest-responsive structural dynamism and selective sensing of nitroaromatic explosives.

  9. Structure, dynamics and selectivity in the sulfotransferase family.

    Science.gov (United States)

    Leyh, Thomas S; Cook, Ian; Wang, Ting

    2013-11-01

    Combined structure, function and molecular dynamics studies of human cytosolic sulfotransferases (SULT1A1 and 2A1) have revealed that these enzymes contain a ≈ 30-residue active-site cap whose structure responds to substrates and mediates their interactions. The binding of 3'-phosphoadenosine 5'-phosphosulfate (PAPS) gates access to the active site by a remodeling of the cap that constricts the pore through which acceptors must pass to enter the active site. While the PAPS-bound enzyme spends the majority (≈ 95%) of its time in the constricted state, the pore isomerizes between the open and closed states when the nucleotide (PAPS) is bound. The dimensions of the open and closed pores place widely different steric constraints on substrate selectivity. Nature appears to have crafted these enzymes with two specificity settings - a closed-pore setting that admits a set of closely related structures, and an open setting that allows a far wider spectrum of acceptor geometries. The specificities of these settings seem well matched to the metabolic demands for homeostatic and defensive SULT functions. The departure of nucleotide requires that the cap open. This isomerization dependent release can explain both the product bursts and substrate inhibition seen in many SULTs. Here, the experimental underpinnings of the cap-mechanism are reviewed, and the advantages of such a mechanism are considered in the context of the cellular and metabolic environment in which these enzymes operate.

  10. Degeneracy-driven self-structuring dynamics in selective repertoires.

    Science.gov (United States)

    Atamas, Sergei P; Bell, Jonathan

    2009-08-01

    Numerous biological interactions, such as interactions between T cell receptors or antibodies with antigens, interactions between enzymes and substrates, or interactions between predators and prey are often not strictly specific. In such less specific, or "sloppy," systems, referred to here as degenerate systems, a given unit of a diverse resource (antigens, enzymatic substrates, prey) is at risk of being recognized and consumed by multiple consumers (lymphocytes, enzymes, predators). In this study, we model generalized degenerate consumer-resource systems of Lotka-Volterra and Verhulst types. In the degenerate systems of Lotka-Volterra, there is a continuum of types of consumer and resource based on variation of a single trait (characteristic, or preference). The consumers experience competition for a continuum of resource types. This non-local interaction system is modeled with partial differential-integral equations and shows spontaneous self-structuring of the consumer population that depends on the degree of interaction degeneracy between resource and consumer, but does not mirror the distribution of resource. We also show that the classical Verhulst (i.e. logistic) single population model can be generalized to a degenerate model, which shows qualitative behavior similar to that in the degenerate Lotka-Volterra model. These results provide better insight into the dynamics of selective systems in biology, suggesting that adaptation of degenerate repertoires is not a simple "mirroring" of the environment by the "fittest" elements of population.

  11. A Dynamical Study of Optically Selected Distant Clusters

    CERN Document Server

    Bower, R G; Couch, W J; Ellis, Richard S; Böhringer, H; Bower, Richard G.; Couch, Warrick J.

    1997-01-01

    We present a programme of spectroscopic observations of galaxies in a sample of optically-selected clusters taken from the catalogue of Couch et al (1991). Previous ROSAT observations of these clusters have shown them to have lower X-ray luminosities, given their optical richness, than might be expected on the basis of local samples. In the present paper we extend this work by determining velocity dispersions of a subsample of the clusters. We confirm the dynamical reality of all but one of the original sample, and find velocity dispersions comparable with present-day clusters of equivalent comoving space density. Thus, in the context of the $L_X-\\sigma$ relation for present-day clusters, there is evidence for a higher velocity dispersion at fixed X-ray luminosity. A key question is whether the high velocity dispersions are indicative of the gravitational potential. If they are, the X-ray luminosities measured in Bower et al., 1994 (Paper I), would then imply an implausibly low efficiency of X-ray generation....

  12. Ultrafast pump-probe study of the excited-state charge-transfer dynamics in blue copper rusticyanin.

    Science.gov (United States)

    Bizzarri, Anna Rita; Brida, Daniele; Santini, Simona; Cerullo, Giulio; Cannistraro, Salvatore

    2012-04-12

    We have used femtosecond pump-probe spectroscopy to investigate the excited-state dynamics of the anticancer blue copper protein rusticyanin, by exciting its ligand to metal charge-transfer band with 25 fs pump pulses centered at 585 nm. The charge-transfer excited state decays exponentially to the ground state with a time constant of about 230 fs, and its recovery is modulated by coherent oscillations. The Fourier transform of the oscillatory component of the signal provides most of the vibrational modes obtained by means of conventional resonance Raman studies, in addition to the low frequency modes below 80 cm(-1) believed to reflect collective motions of biological relevance.

  13. Highly Sensitive Fluorescence Probe Based on Functional SBA-15 for Selective Detection of Hg2+

    Directory of Open Access Journals (Sweden)

    Wang Xiaoyu

    2010-01-01

    Full Text Available Abstract An inorganic–organic hybrid fluorescence chemosensor (DA/SBA-15 was prepared by covalent immobilization of a dansylamide derivative into the channels of mesoporous silica material SBA-15 via (3-aminopropyltriethoxysilane (APTES groups. The primary hexagonally ordered mesoporous structure of SBA-15 was preserved after the grafting procedure. Fluorescence characterization shows that the obtained inorganic–organic hybrid composite is highly selective and sensitive to Hg2+ detection, suggesting the possibility for real-time qualitative or quantitative detection of Hg2+ and the convenience for potential application in toxicology and environmental science.

  14. Simulation of psychophysical stimulus selection procedures for dynamic threshold tracking

    NARCIS (Netherlands)

    Doll, Robert; Yang, H.; Meijer, Hil Gaétan Ellart; Buitenweg, Jan R.

    2011-01-01

    Stimulus selection procedures are of importance for adequate psychophysical nociceptive threshold estimation. Various stimulus selection procedures were analyzed by means of simulations. Precision, bias, efficiency, and time constants of the various stimulus selection procedures were determined in a

  15. Experimental and Theoretical Probing of Molecular Dynamics at Catalytic and Ionic Liquid Interfaces

    Science.gov (United States)

    2014-04-01

    diffraction at grazing incidence. Subsequently the HH beam is focused on the sample surface inside of the UHV chamber by cylindrical and toroidal ...probe beams onto the sample surface (cf. Figure 1). The UHV surface science chamber contains specific tools for surface preparation and...Light Source. Experimental evidence for di- and tri-alkylimidazolium cations and nitrile- containing anions indicates thermal decomposition occurs

  16. Dynamic recurrent Elman neural network based on immune clonal selection algorithm

    Science.gov (United States)

    Wang, Limin; Han, Xuming; Li, Ming; Sun, Haibo; Li, Qingzhao

    2012-04-01

    Owing to the immune clonal selection algorithm introduced into dynamic threshold strategy has better advantage on optimizing multi-parameters, therefore a novel approach that the immune clonal selection algorithm introduced into dynamic threshold strategy, is used to optimize the dynamic recursion Elman neural network is proposed in the paper. The concrete structure of the recursion neural network, the connect weight and the initial values of the contact units etc. are done by evolving training and learning automatically. Thus it could realize to construct and design for dynamic recursion Elman neural networks. It could provide a new effective approach for immune clonal selection algorithm optimizing dynamic recursion neural networks.

  17. Probing cosmology with weak lensing selected clusters I: Halo approach and all-sky simulations

    CERN Document Server

    Shirasaki, Masato; Yoshida, Naoki

    2015-01-01

    Weak gravitational lensing enables us to search clusters without the conventional assumption on the relation between visible and dark matter. We explore a variety of statistics of clusters selected with cosmic shear measurement by utilizing both analytic models and large numerical simulations. We first develop a halo model to predict the abundance and the clustering of weak lensing selected clusters. Observational effects such as galaxy shape noise are included in our model. We then generate realistic mock weak lensing catalogs to test the accuracy of our analytic model. To this end, we perform full-sky ray-tracing simulations that allow us to have multiple realizations of a large continuous area. We model the masked regions on the sky using the actual positions of bright stars, and generate 200 mock weak lensing catalogs with sky coverage of $\\sim$1000 squared degrees. We utilize the large set of mock catalogs to evaluate the covariance matrices between the local and non-local statistics. We show that our th...

  18. Re-engineering of CYP2C9 to probe acid-base substrate selectivity.

    Science.gov (United States)

    Tai, Guoying; Dickmann, Leslie J; Matovic, Nicholas; DeVoss, James J; Gillam, Elizabeth M J; Rettie, Allan E

    2008-10-01

    A common feature of many CYP2C9 ligands is their weak acidity. As revealed by crystallography, the structural basis for this behavior involves a charge-pairing interaction between an anionic moiety on the substrate and an active site R108 residue. In the present study we attempted to re-engineer CYP2C9 to better accept basic ligands by charge reversal at this key residue. We expressed and purified the R108E and R108E/D293N mutants and compared their ability with that of native CYP2C9 to interact with (S)-warfarin, diclofenac, pyrene, propranolol, and ibuprofen amine. As expected, the R108E mutant maintained all the native enzyme's pyrene 1-hydroxylation activity, but catalytic activity toward diclofenac and (S)-warfarin was abrogated. In contrast, the double mutant displayed much less selectivity in its behavior toward these control ligands. Neither of the mutants displayed significant enhancement of propranolol metabolism, and all three preparations exhibited a type II (inhibitor) rather than type I (substrate) spectrum with ibuprofen amine, although binding became progressively weaker with the single and double mutants. Collectively, these data underscore the importance of the amino acid at position 108 in the acid substrate selectivity of CYP2C9, highlight the accommodating nature of the CYP2C9 active site, and provide a cautionary note regarding facile re-engineering of these complex cytochrome P450 active sites.

  19. Pure zinc sulfide quantum dot as highly selective luminescent probe for determination of hazardous cyanide ion.

    Science.gov (United States)

    Shamsipur, Mojtaba; Rajabi, Hamid Reza

    2014-03-01

    A rapid and simple fluorescence method is presented for selective and sensitive determination of hazardous cyanide ion in aqueous solution based on functionalized zinc sulfide (ZnS) quantum dot (QD) as luminescent prob. The ultra-small ZnS QDs were synthesized using a chemical co-precipitation method in the presence of 2-mercaptoethanol (ME) as an efficient capping agent. The prepared pure ZnS QDs was applied as an optical sensor for determination of cyanide ions in aqueous solutions. ZnS nanoparticles have exhibited a strong fluorescent emission at about 424 nm. The fluorescence intensity of QDs is linearly proportional to the cyanide ion concentration in the range 2.44×10(-6) to 2.59×10(-5)M with a detection limit of 1.70×10(-7)M at pH11. The designed fluorescent sensor possesses remarkable selectivity for cyanide ion over other anions such as Cl(-), Br(-), F(-), I(-), IO3(-), ClO4(-), BrO3(-), CO3(2-), NO2(-), NO3(-), SO4(2-), S2O4(2-), C2O4(2-), SCN(-), N3(-), citrate and tartarate with negligible influences on the cyanide detection by fluorescence spectroscopy. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. First selection, then influence : Developmental differences in friendship dynamics regarding academic achievement

    NARCIS (Netherlands)

    Gremmen, Mariola Claudia; Dijkstra, Jan Kornelis; Steglich, Christian; Veenstra, René

    This study concerns peer selection and influence dynamics in early adolescents' friendships regarding academic achievement. Using longitudinal social network analysis (RSiena), both selection and influence processes were investigated for students' average grades and their cluster-specific grades

  1. A dihydrazone based fluorescent probe for selective determination of Al{sup 3+} ions

    Energy Technology Data Exchange (ETDEWEB)

    Pratap Singh, Divya; Singh, Vinod P., E-mail: singvp@yahoo.co.in

    2014-11-15

    A highly selective fluorescent sensor N,N′-bis((2-hydroxynaphthalen-1-yl)methylene) oxalohydrazide (H{sub 2}ohn) for the determination of Al{sup 3+} ions was synthesized and characterized by different physico-chemical and spectroscopic techniques. The single crystal structure of H{sub 2}ohn receptor has also been reported. The H{sub 2}ohn shows an enhanced fluorescence in the presence of Al{sup 3+} ions in ethanol–water (2:3 v/v) solution. Other cations viz. Na{sup +}, K{sup +}, Mg{sup 2+}, Ca{sup 2+}, Mn{sup 2+}, Fe{sup 3+}, Co{sup 2+}, Ni{sup 2+}, Cu{sup 2+}, Zn{sup 2+}, Pb{sup 2+}, Cd{sup 2+} and Hg{sup 2+} show no appreciable change in fluorescence intensity. The binding mode of H{sub 2}ohn receptor with Al{sup 3+} was studied by UV–visible, fluorescence and {sup 1}H NMR titrations. The receptor acts as a dibasic hexadentate ligand and interacts with two Al{sup 3+} ions with a high binding constant K{sub B}=2.62×10{sup 11} M{sup −2}. The lowest detection limit for Al{sup 3+} complex of H{sub 2}ohn was determined to be 8.56×10{sup −10} M. The structures of H{sub 2}ohn and its Al(III) complex were also optimized by DFT calculations. - Highlights: • A dihydrazone based fluorescent sensor is synthesized. • Characterized by IR, NMR, UV−visible and mass spectral analysis. • The receptor serves as a selective fluorescent sensor for Al{sup 3+} over other cations. • The sensing property is monitored by UV−visible, fluorescence and NMR spectroscopy. • A high binding constant of the receptor with Al{sup 3+} is reported here.

  2. In vivo quantitative visualization of hypochlorous acid in the liver using a novel selective two-photon fluorescent probe

    Science.gov (United States)

    Wang, Haolu; Jayachandran, Aparna; Gravot, Germain; Liang, Xiaowen; Thorling, Camilla A.; Zhang, Run; Liu, Xin; Roberts, Michael S.

    2016-11-01

    Hypochlorous acid (HOCl) plays a vital role in physiological events and diseases. During hepatic ischemia-reperfusion (I/R) injury, HOCl is generated by neutrophils and diffuses into hepatocytes, causing oxidant stress-mediated injury. Although many probes have been developed to detect HOCl, most were difficult to be distinguished from endogenous fluorophores in intravital imaging and only can be employed under one-photon microscopy. A novel iridium(III) complex-based ferrocene dual-signaling chemosensor (Ir-Fc) was designed and synthesized. Ir-Fc exhibited a strong positive fluorescent response only in the presence of HOCl, whereas negligible fluorescent signals were observed upon the additions of other reactive oxygen/nitrogen species and metal ions. There was a good linear relationship between probe responsive fluorescent intensity and HOCl concentration. Ir-Fc was then intravenously injected into BALB/c mice at the final concentration of 50 μM and the mouse livers were imaged using multiphoton microscopy (MPM). In the I/R liver, reduced autofluorescence was detected by MPM, indicating the hepatocyte necrosis. Remarkable enhancement of red fluorescence was observed in hepatocytes with decreased autofluorescence, indicating the reaction of Ir-Fc with endogenous HOCl molecules. The cellular concentration of HOCl was first calculated based on the intensity of MPM images. No obvious toxic effects were observed in histological examination of major organs after Ir-Fc injection. In summary, Ir-Fc has low cytotoxicity, high specificity to HOCl, and rapid "off-on" fluorescence. It is suitable for dynamic quantitatively monitoring HOCl generation using MPM at the cellular level. This technique can be readily extended to examination of liver diseases and injury.

  3. Dynamics of a Room Temperature Ionic Liquid in Supported Ionic Liquid Membranes vs the Bulk Liquid: 2D IR and Polarized IR Pump-Probe Experiments.

    Science.gov (United States)

    Shin, Jae Yoon; Yamada, Steven A; Fayer, Michael D

    2017-01-11

    Supported ionic liquid membranes (SILMs) are membranes that have ionic liquids impregnated in their pores. SILMs have been proposed for advanced carbon capture materials. Two-dimensional infrared (2D IR) and polarization selective IR pump-probe (PSPP) techniques were used to investigate the dynamics of reorientation and spectral diffusion of the linear triatomic anion, SeCN(-), in poly(ether sulfone) (PES) membranes and room-temperature ionic liquid (RTIL), 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EmimNTf2). The dynamics in the bulk EmimNTf2 were compared to its dynamics in the SILM samples. Two PES membranes, PES200 and PES30, have pores with average sizes, ∼300 nm and ∼100 nm, respectively. Despite the relatively large pore sizes, the measurements reveal that the reorientation of SeCN(-) and the RTIL structural fluctuations are substantially slower in the SILMs than in the bulk liquid. The complete orientational randomization, slows from 136 ps in the bulk to 513 ps in the PES30. 2D IR measurements yield three time scales for structural spectral diffusion (SSD), that is, the time evolution of the liquid structure. The slowest decay constant increases from 140 ps in the bulk to 504 ps in the PES200 and increases further to 1660 ps in the PES30. The results suggest that changes at the interface propagate out and influence the RTIL structural dynamics even more than a hundred nanometers from the polymer surface. The differences between the IL dynamics in the bulk and in the membranes suggest that studies of bulk RTIL properties may be poor guides to their use in SILMs in carbon capture applications.

  4. On the mutual relationships between spin probe mobility, free volume and relaxation dynamics in organic glass-formers: Glycerol

    Science.gov (United States)

    Bartoš, J.; Švajdlenková, H.

    2017-02-01

    The rotation dynamics of the spin probe TEMPO in glycerol from ESR is compared with the ortho-positronium (o-Ps) annihilation from PALS and interpreted using the relaxation dynamics from BDS. Rotation time scale within the slow motion regime exhibits two Arrhenius regions with the characteristic ESR temperature, TX1τ, close to the characteristic PALS temperature, Tb1L, which is related to the secondary β process above Tg. Next, a slow to fast motion regime transition at the characteristic ESR temperature, Tcτ, close to the characteristic PALS temperature, Tb2L, followed by non-Arrhenius fast motion regime region is fully coupled with the primary α process.

  5. Probing ultrafast spin dynamics through a magnon resonance in the antiferromagnetic multiferroic HoMnO3

    Science.gov (United States)

    Bowlan, P.; Trugman, S. A.; Bowlan, J.; Zhu, J.-X.; Hur, N. J.; Taylor, A. J.; Yarotski, D. A.; Prasankumar, R. P.

    2016-09-01

    We demonstrate an approach for directly tracking antiferromagnetic (AFM) spin dynamics by measuring ultrafast changes in a magnon resonance. We test this idea on the multiferroic HoMnO3 by optically photoexciting electrons, after which changes in the spin order are probed with a THz pulse tuned to a magnon resonance. This reveals a photoinduced change in the magnon line shape that builds up over 5-12 picoseconds, which we show to be the spin-lattice thermalization time, indicating that electrons heat the spins via phonons. We compare our results to previous studies of spin-lattice thermalization in ferromagnetic manganites, giving insight into fundamental differences between the two systems. Our work sheds light on the microscopic mechanism governing spin-phonon interactions in AFMs and demonstrates a powerful approach for directly monitoring ultrafast spin dynamics.

  6. Using NV centers to probe magnetization dynamics in normal metal/magnetic insulator hybrid system at the nanoscale

    Science.gov (United States)

    Zhang, Huiliang; Ku, Mark J. H.; Han, Minyong; Casola, Francesco; van der Sar, Toeno; Yacoby, Amir; Walsworth, Ronald L.

    2016-05-01

    Understanding magnetization dynamics induced by electric current is of great interest for both fundamental and practical reasons. Great endeavor has been dedicated to spin-orbit torques (SOT) in metallic structures, while quantitative study of analogous phenomena in magnetic insulators remains challenging where transport measurements are not feasible. Recently we have developed techniques using nitrogen vacancy (NV) centers in diamond to probe few-nanometre-scale correlated-electron magnetic excitations (i.e., spin waves). Here we demonstrate how this powerful tool can be implemented to study magnetization dynamics inside ferromagnetic insulator, Yttrium iron garnet (YIG) with spin injection from electrical current through normal metal (Platinum in our case). Particularly our work will focus on NV magnetic detection, imaging, and spectroscopy of coherent auto-oscillations in Pt/YIG microdisc. Magnetic fluctuations and local temperature measurements, both with nearby NV centers, will also be interesting topics relevant to SOT physics in Pt/YIG hybrid system.

  7. Probing the dynamic structure factor of a neutral Fermi superfluid along the BCS-BEC crossover using atomic impurity qubits

    Science.gov (United States)

    Mitchison, Mark T.; Johnson, Tomi H.; Jaksch, Dieter

    2016-12-01

    We study an impurity atom trapped by an anharmonic potential, immersed within a cold atomic Fermi gas with attractive interactions that realizes the crossover from a Bardeen-Cooper-Schrieffer superfluid to a Bose-Einstein condensate. Considering the qubit comprising the lowest two vibrational energy eigenstates of the impurity, we demonstrate that its dynamics probes the equilibrium density fluctuations encoded in the dynamic structure factor of the superfluid. Observing the impurity's evolution is thus shown to facilitate nondestructive measurements of the superfluid order parameter and the contact between collective and single-particle excitation spectra. Our setup constitutes a model of an open quantum system interacting with a thermal reservoir, the latter supporting both bosonic and fermionic excitations that are also coupled to each other.

  8. Extended pump-probe Faraday rotation spectroscopy of the submicrosecond electron spin dynamics in n -type GaAs

    Science.gov (United States)

    Belykh, V. V.; Evers, E.; Yakovlev, D. R.; Fobbe, F.; Greilich, A.; Bayer, M.

    2016-12-01

    We develop an extended pump-probe Faraday rotation technique to study submicrosecond electron spin dynamics with picosecond time resolution in a wide range of magnetic fields. The electron spin dephasing time T2* and the longitudinal spin relaxation time T1, both approaching 250 ns in weak fields, are measured thereby in n -type bulk GaAs. By tailoring the pump pulse train through increasing the contained number of pulses, the buildup of resonant spin amplification is demonstrated for the electron spin polarization. The spin precession amplitude in high magnetic fields applied in the Voigt geometry shows a nonmonotonic dynamics deviating strongly from a monoexponential decay and revealing slow beatings. The beatings indicate a two spin component behavior with a g -factor difference of Δ g ˜4 ×10-4 , much smaller than the Δ g expected for free and donor-bound electrons. This g -factor variation indicates efficient, but incomplete spin exchange averaging.

  9. Microfabricated solid-state ion-selective electrode probe for measuring potassium in the living rodent brain: Compatibility with DC-EEG recordings to study spreading depression

    NARCIS (Netherlands)

    Odijk, M.; Wouden, van der E.J.; Olthuis, W.; Ferrari, M.D.; Tolner, E.A.; Maagdenberg, van den A.M.J.M.; Berg, van den A.

    2014-01-01

    There is considerable need in neuroscience research to reliably measure concentrations of extracellular ions in the living brain as the dynamics of ion levels increasingly is considered to play a key role in the pathophysiology of many brain disorders. Unfortunately, most probes currently used for d

  10. A sensitive and selective fluorescent probe for cysteine based on a new response-assisted electrostatic attraction strategy: the role of spatial charge configuration.

    Science.gov (United States)

    Zhou, Xin; Jin, Xuejun; Sun, Guangyan; Wu, Xue

    2013-06-10

    A new strategy for fast fluorescent detection of cysteine (Cys), based on a response-assisted electrostatic attraction, is demonstrated. By utilizing this strategy, we designed and synthesized three fluorescent probes for the specific detection of Cys under actual physiological conditions. The probe m-CP, a coumarin fluorophore conjugated with a substituted methyl pyridinium group through an unsaturated ketone unit, showed highly selective and sensitive detection for cysteine (Cys) over homocysteine (Hcy) and glutathione (GSH). The kinetic analysis indicated that the sensing process was highly accelerated (a response time less than 1 min) by the response-assisted electrostatic attraction. More importantly, control experiments with isomeric probes first demonstrated that the spatial charge configuration of the probe played an important role in Cys-preferred selectivity and kinetic rate acceleration. Furthermore, the practical utility of the probe m-CP in the fluorescent labeling of Cys residues within proteins was demonstrated. Finally, these probes were employed in living cell imaging with HeLa cells, in which it displayed satisfactory cell permeability and enabled us to distinguish active thiols in the cytoplasm, nucleus, and mitochondria. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Multimodal use of new coumarin-based fluorescent chemosensors: towards highly selective optical sensors for Hg(2+) probing.

    Science.gov (United States)

    Bazzicalupi, Carla; Caltagirone, Claudia; Cao, Zenfeng; Chen, Qibin; Di Natale, Corrado; Garau, Alessandra; Lippolis, Vito; Lvova, Larisa; Liu, Honglai; Lundström, Ingemar; Mostallino, M Cristina; Nieddu, Mattia; Paolesse, Roberto; Prodi, Luca; Sgarzi, Massimo; Zaccheroni, Nelsi

    2013-10-18

    Despite several types of fluorescent sensing molecules have been proposed and examined to signal Hg(2+) ion binding, the development of fluorescence-based devices for in-field Hg(2+) detection and screening in environmental and industrial samples is still a challenging task. Herein, we report the synthesis and characterization of three new coumarin-based fluorescent chemosensors featuring mixed thia/aza macrocyclic framework as receptors units, that is, ligands L1-L3. These probes revealed an OFF-ON selective response to the presence of Hg(2+) ions in MeCN/H2 O 4:1 (v/v), which allowed imaging of this metal ion in Cos-7 cells in vitro. Once included in silica core-polyethylene glycol (PEG) shell nanoparticles or supported on polyvinyl chloride (PVC)-based polymeric membranes, ligands L1-L3 can also selectively sense Hg(2+) ions in pure water. In particular we have developed an optical sensing array tacking advantage of the fluorescent properties of ligand L3 and based on the computer screen photo assisted technique (CSPT). In the device ligand L3 is dispersed into PVC membranes and it quantitatively responds to Hg(2+) ions in natural water samples.

  12. Dynamics of GaAs photocarriers probed with pulsed infrared synchrotron radiation

    CERN Document Server

    Carr, G L

    2003-01-01

    Synchrotron radiation is a source of high brightness, pulsed infrared light that is well suited to the study of materials by pump-probe spectroscopy. A synchronized laser produces pump pulses and synchrotron infrared pulses serve as the probe. This method has been used for a number of time-resolved investigations, including a study of the frequency-dependent conductivity of photocarrier relaxation in GaAs. For this material, a Drude model gives a good description of the photoconductivity, but requires that the average carrier scattering rate change from electron like to hole like during the decay process (a few nanoseconds). This behavior suggests the rapid trapping of electrons, as may occur near a surface with defect states.

  13. A METHOD FOR SELECTING SOFTWARE FOR DYNAMIC EVENT ANALYSIS I: PROBLEM SELECTION

    Energy Technology Data Exchange (ETDEWEB)

    J. M. Lacy; S. R. Novascone; W. D. Richins; T. K. Larson

    2007-08-01

    New nuclear power reactor designs will require resistance to a variety of possible malevolent attacks, as well as traditional dynamic accident scenarios. The design/analysis team may be faced with a broad range of phenomena including air and ground blasts, high-velocity penetrators or shaped charges, and vehicle or aircraft impacts. With a host of software tools available to address these high-energy events, the analysis team must evaluate and select the software most appropriate for their particular set of problems. The accuracy of the selected software should then be validated with respect to the phenomena governing the interaction of the threat and structure. In this paper, we present a method for systematically comparing current high-energy physics codes for specific applications in new reactor design. Several codes are available for the study of blast, impact, and other shock phenomena. Historically, these packages were developed to study specific phenomena such as explosives performance, penetrator/target interaction, or accidental impacts. As developers generalize the capabilities of their software, legacy biases and assumptions can remain that could affect the applicability of the code to other processes and phenomena. R&D institutions generally adopt one or two software packages and use them almost exclusively, performing benchmarks on a single-problem basis. At the Idaho National Laboratory (INL), new comparative information was desired to permit researchers to select the best code for a particular application by matching its characteristics to the physics, materials, and rate scale (or scales) representing the problem at hand. A study was undertaken to investigate the comparative characteristics of a group of shock and high-strain rate physics codes including ABAQUS, LS-DYNA, CTH, ALEGRA, ALE-3D, and RADIOSS. A series of benchmark problems were identified to exercise the features and capabilities of the subject software. To be useful, benchmark problems

  14. Selective coupling of HE{sub 11} and TM{sub 01} modes into microfabricated fully metal-coated quartz probes

    Energy Technology Data Exchange (ETDEWEB)

    Tortora, P. [Institute of Microtechnology, University of Neuchatel, Rue A.L. Breguet 2, CH-2000 Neuchatel (Switzerland)]. E-mail: piero.tortora@unine.ch; Descrovi, E. [Institute of Microtechnology, University of Neuchatel, Rue A.L. Breguet 2, CH-2000 Neuchatel (Switzerland)]. E-mail: emiliano.descrovi@polito.it; Aeschimann, L. [Institute of Microtechnology, University of Neuchatel, Rue A.L. Breguet 2, CH-2000 Neuchatel (Switzerland); Vaccaro, L. [Institute of Microtechnology, University of Neuchatel, Rue A.L. Breguet 2, CH-2000 Neuchatel (Switzerland); Herzig, H.-P. [Institute of Microtechnology, University of Neuchatel, Rue A.L. Breguet 2, CH-2000 Neuchatel (Switzerland); Daendliker, R. [Institute of Microtechnology, University of Neuchatel, Rue A.L. Breguet 2, CH-2000 Neuchatel (Switzerland)

    2007-02-15

    We report computational and experimental investigations on injection and transmission of light in microfabricated fully Aluminum-coated quartz probes. In particular, we show that a selective coupling of either the HE{sub 11} or the TM{sub 01} mode can be carried out by injecting focused linearly or radially polarized beams into the probe. Optical fields, emitted by the probe after a controlled injection, are characterized in intensity and phase with the help of an interferometric technique. With the help of near-field measurement, we finally demonstrate that a longitudinally polarized spot localized at the tip apex is actually produced when the TM{sub 01} mode is coupled into the probe.

  15. 4-(11)C-Methoxy N-(2-Diethylaminoethyl) Benzamide: A Novel Probe to Selectively Target Melanoma.

    Science.gov (United States)

    Garg, Pradeep K; Nazih, Rachid; Wu, Yanjun; Singh, Ravi; Garg, Sudha

    2017-05-01

    We report the synthesis and preclinical evaluation of a (11)C-labeled probe to target melanoma using PET. Methods: The target compound 4-(11)C-methoxy N-(2-diethylaminoethyl) benzamide (4-(11)C-MBZA) was prepared via the (11)C-methylation of 4-hydroxy N-(2-diethylaminoethyl) benzamide (4-HBZA). The in vitro binding was performed using B16F1 (melanoma cells), MCF-10A (breast epithelial cells), and MDA-MB 231 (breast cancer cells). The internalization studies were conducted using B16F1 cells. In vivo biodistribution and small-animal PET imaging were performed in mice bearing B16F1 melanoma tumor xenografts. Results: The target compound 4-(11)C-MBZA was prepared in 46% ± 7% radiochemical yields by reacting (11)C-methyltriflate with 4-HBZA followed by high-performance liquid chromatography purification. The specific activity of this compound was 853 ± 29.6 GBq/μmol (23 ± 0.8 Ci/μmol). The binding of 4-(11)C-MBZA to B16F1, MCF-10A, and MDA-MB-231 cells was 6.41% ± 1.28%, 1.51% ± 0.17%, and 0.30% ± 0.17%, respectively. Internalization studies using B16F1 melanoma cells show 60.7% of the cell-bound activity was internalized. Results from biodistribution studies show a rapid and high uptake of radioactivity in the tumor, with uptake levels reaching 5.85 ± 0.79 and 8.13 ± 1.46 percentage injected dose per gram at 10 and 60 min, respectively. Low uptake in normal tissues in conjunction with high tumor uptake resulted in high tumor-to-tissue ratios. On small-animal PET images, the tumor was clearly delineated soon after 4-(11)C-MBZA injection and tumor uptake reached 4.2 percentage injected dose per gram by 20 min. These preclinical evaluations show a high propensity of 4-(11)C-MBZA toward melanoma tumor. Conclusion: We successfully developed 4-(11)C-MBZA as a PET imaging probe, displaying properties advantageous over those for its (18)F analogs. These preclinical evaluation results demonstrate the clinical potential of this probe to selectively target melanoma.

  16. Structural dynamics in water probed by heterodyne-detected photon echo

    NARCIS (Netherlands)

    Yeremenko, S; Pshenichnikov, MS; Wiersma, DA; Miller, DR; Murnane, MM; Scherer, NF; Weiner, AM

    2003-01-01

    Results of heterodyne-detected photon echo experiments on the OH stretching mode of HDO molecule in heavy water and acetonitrile are reported and discussed. Two vibrational dynamical processes with time constants of 130 A and 900 fs were identified. The former is attributed to bond breaking dynamics

  17. Fast, broadband, and high-dynamic range 3-D field strength probe

    NARCIS (Netherlands)

    Leferink, Frank

    2013-01-01

    Electromagnetic fields are conventionally measured using diode detectors or thermocouple detectors. The diode is limited in dynamic range. The dynamic range is important when considering modern pulsed wireless systems with a high peak-average ratio or crest factor. The thermocouple is too slow to me

  18. Dynamic metabolic flux analysis--tools for probing transient states of metabolic networks.

    Science.gov (United States)

    Antoniewicz, Maciek R

    2013-12-01

    Computational approaches for analyzing dynamic states of metabolic networks provide a practical framework for design, control, and optimization of biotechnological processes. In recent years, two promising modeling approaches have emerged for characterizing transients in cellular metabolism, dynamic metabolic flux analysis (DMFA), and dynamic flux balance analysis (DFBA). Both approaches combine metabolic network analysis based on pseudo steady-state (PSS) assumption for intracellular metabolism with dynamic models for extracellular environment. One strategy to capture dynamics is by combining network analysis with a kinetic model. Predictive models are thus established that can be used to optimize bioprocessing conditions and identify useful genetic manipulations. Alternatively, by combining network analysis with methods for analyzing extracellular time-series data, transients in intracellular metabolic fluxes can be determined and applied for process monitoring and control.

  19. An NBD derivative of the selective rat toxicant norbormide as a new probe for living cell imaging.

    Directory of Open Access Journals (Sweden)

    Claudio D'amore

    2016-09-01

    Full Text Available Norbormide (NRB is a unique compound that acts directly on rat vascular myocytes to trigger a contractile process, through an as yet unknown mechanism, which results in the selective contraction of rat peripheral arteries. To gain insight into the mechanisms involved in NRB rat-selective activity, we investigated the subcellular distribution of NRB-AF12, a nitrobenzodiazole (NBD-derivative of NRB, in living NRB-sensitive and NRB-insensitive cells. In both cell types, NRB-AF12 localised to the endoplasmic reticulum (ER, Golgi apparatus, mitochondria, lysosomes and endosomes; however, in NRB-sensitive cells, the fluorescence also extended to the plasma membrane. NRB-AF12 was rapidly internalised into the cells, could easily be washed out and then reloaded back into the same cells, all with a high degree of reproducibility. Cells exposed for 24 h to NRB-AF12 did not show apparent signs of toxicity, even at concentrations of the dye (10 µM much higher than those required for fluorescence labelling (500 ηM. The distribution pattern of NRB-AF12 fluorescence was near identical to that of ER-Tracker® (Er-Tr, a fluorescent derivative of glibenclamide, a known KATP channel blocker. Displacement tests did not demonstrate, but at the same time did not rule out the possibility of a common target for ER-Tr, NRB-AF12, NRB and glibenclamide. On the basis of these results we hypothesize a common target site for NRB-AF12 and ER-Tr, and a similar target profile for norbormide and glibenclamide, and propose NRB-AF12 as an alternative fluorescence probe to ER-Tracker. Furthermore, NRB-based fluorescence derivatives could be designed to selectively label single cellular structures.

  20. A sensing mechanism for the detection of carbon nanotubes using selective photoluminescent probes based on ionic complexes with organic dyes

    Institute of Scientific and Technical Information of China (English)

    Petro Lutsyk; Raz Arif; Jan Hruby; Anatolii Bukivskyi; Olexander Vinijchuk; Mykola Shandura; Viktor Yakubovskyi

    2016-01-01

    The multifunctional properties of carbon nanotubes (CNTs) make them a powerful platform for unprecedented innovations in a variety of practical applications.As a result of the surging growth of nanotechnology,nanotubes present a potential problem as an environmental pollutant,and as such,an efficient method for their rapid detection must be established.Here,we propose a novel type of ionic sensor complex for detecting CNTs-an organic dye that responds sensitively and selectively to CNTs with a photoluminescent signal.The complexes are formed through Coulomb attractions between dye molecules with uncompensated charges and CNTs covered with an ionic surfactant in water.We demonstrate that the photoluminescent excitation of the dye can be transferred to the nanotubes,resulting in selective and strong amplification (up to a factor of 6) of the light emission from the excitonic levels of CNTs in the near-infrared spectral range,as experimentally observed via excitation-emission photoluminescence (PL) mapping.The chirality of the nanotubes and the type of ionic surfactant used to disperse the nanotubes both strongly affect the amplification;thus,the complexation provides sensing selectivity towards specific CNTs.Additionally,neither similar uncharged dyes nor CNTs covered with neutral surfactant form such complexes.As model organic molecules,we use a family of pelymethine dyes with an easily tailorable molecular structure and,consequently,tunable absorbance and PL characteristics.This provides us with a versatile tool for the controllable photonic and electronic engineering of an efficient probe for CNT detection.

  1. An NBD Derivative of the Selective Rat Toxicant Norbormide as a New Probe for Living Cell Imaging

    Science.gov (United States)

    D'Amore, Claudio; Orso, Genny; Fusi, Fabio; Pagano, Mario A.; Miotto, Giovanni; Forgiarini, Alessia; De Martin, Sara; Castellani, Giulia; Ribaudo, Giovanni; Rennison, David; Brimble, Margaret A.; Hopkins, Brian; Ferrarese, Alessandro; Bova, Sergio

    2016-01-01

    Norbormide (NRB) is a unique compound that acts directly on rat vascular myocytes to trigger a contractile process, through an as yet unknown mechanism, which results in the selective contraction of rat peripheral arteries. To gain insight into the mechanisms involved in NRB rat-selective activity, we investigated the subcellular distribution of NRB-AF12, a nitrobenzoxadiazole (NBD)-derivative of NRB, in living NRB-sensitive and NRB-insensitive cells. In both cell types, NRB-AF12 localized to the endoplasmic reticulum (ER), Golgi apparatus, mitochondria, lysosomes, and endosomes; however, in NRB-sensitive cells, the fluorescence also extended to the plasma membrane. NRB-AF12 was rapidly internalized into the cells, could easily be washed out and then reloaded back into the same cells, all with a high degree of reproducibility. Cells exposed for 24 h to NRB-AF12 did not show apparent signs of toxicity, even at concentrations of the dye (10 μM) much higher than those required for fluorescence labeling (500 ηM). The distribution pattern of NRB-AF12 fluorescence was near identical to that of ER-Tracker® (Er-Tr), a fluorescent derivative of glibenclamide, a known KATP channel blocker. Displacement tests did not demonstrate, but at the same time did not rule out the possibility of a common target for ER-Tr, NRB-AF12, NRB, and glibenclamide. On the basis of these results we hypothesize a common target site for NRB-AF12 and ER-Tr, and a similar target profile for NRB and glibenclamide, and propose NRB-AF12 as an alternative fluorescence probe to ER-Tracker. Furthermore, NRB-based fluorescence derivatives could be designed to selectively label single cellular structures. PMID:27721792

  2. Diffusion-assisted selective dynamical recoupling: A new approach to measure background gradients in magnetic resonance

    Science.gov (United States)

    Álvarez, Gonzalo A.; Shemesh, Noam; Frydman, Lucio

    2014-02-01

    Dynamical decoupling, a generalization of the original NMR spin-echo sequence, is becoming increasingly relevant as a tool for reducing decoherence in quantum systems. Such sequences apply non-equidistant refocusing pulses for optimizing the coupling between systems, and environmental fluctuations characterized by a given noise spectrum. One such sequence, dubbed Selective Dynamical Recoupling (SDR) [P. E. S. Smith, G. Bensky, G. A. Álvarez, G. Kurizki, and L. Frydman, Proc. Natl. Acad. Sci. 109, 5958 (2012)], allows one to coherently reintroduce diffusion decoherence effects driven by fluctuations arising from restricted molecular diffusion [G. A. Álvarez, N. Shemesh, and L. Frydman, Phys. Rev. Lett. 111, 080404 (2013)]. The fully-refocused, constant-time, and constant-number-of-pulses nature of SDR also allows one to filter out "intrinsic" T1 and T2 weightings, as well as pulse errors acting as additional sources of decoherence. This article explores such features when the fluctuations are now driven by unrestricted molecular diffusion. In particular, we show that diffusion-driven SDR can be exploited to investigate the decoherence arising from the frequency fluctuations imposed by internal gradients. As a result, SDR presents a unique way of probing and characterizing these internal magnetic fields, given an a priori known free diffusion coefficient. This has important implications in studies of structured systems, including porous media and live tissues, where the internal gradients may serve as fingerprints for the system's composition or structure. The principles of this method, along with full analytical solutions for the unrestricted diffusion-driven modulation of the SDR signal, are presented. The potential of this approach is demonstrated with the generation of a novel source of MRI contrast, based on the background gradients active in an ex vivo mouse brain. Additional features and limitations of this new method are discussed.

  3. Time-frequency analysis of neonatal cranial ultrasonic movies for selective detection of pulsatile tissues by avoiding probe-motion artifact

    Science.gov (United States)

    Fukuzawa, Masayuki; Tabata, Yuki; Izuwaki, Yusuke; Nakamori, Nobuyuki; Kitsunezuka, Yoshiki

    2015-03-01

    In order to detect the pulsatile tissues in neonatal cranial ultrasonic movies by avoiding probe-motion artifact, a time-frequency analysis has been performed in several movie fragments at typical three scenes: (a) a brain-lost, (b) a brain-captured and probe-stabilized, and (c) a brain-captured and probe-swayed ones. The pulsatile tissue, which is a key point of pediatric diagnosis, had successfully detected with an algorithm based on Fourier transform but it had required us to extract the probe-stabilized scene manually by visual observation of the movie. A spatial mean square of echo intensity Etot and a total AC power Ptot over a fan-shape of field of view were evaluated according to a power spectrum of a time-variation of 64 samples of echo intensity at each pixel in each movie fragment split from actual B-mode ultrasonic movies taken at coronal sections of a neonate. The results revealed that (1) significant low Etot was found at the brain-lost scene rather than that at the other scenes, and (2) lower Ptot was found at the probe-stabilized scene rather than the probe-swayed ones. This fact strongly suggests that the Etot and Ptot are promising features for automatic extraction of probe-stabilized scenes. It must lead to detect the pulsatile tissues selectively by avoiding probe-motion artifact and to realize systematic analysis of the whole of our extensive movie archives, which is useful not only for retrospective study of ischemic diseases but also for bedside diagnosis to stabilize the freehand ultrasonic probe.

  4. Large Scale Explorative Oligonucleotide Probe Selection for Thousands of Genetic Groups on a Computing Grid: Application to Phylogenetic Probe Design Using a Curated Small Subunit Ribosomal RNA Gene Database

    Directory of Open Access Journals (Sweden)

    Faouzi Jaziri

    2014-01-01

    Full Text Available Phylogenetic Oligonucleotide Arrays (POAs were recently adapted for studying the huge microbial communities in a flexible and easy-to-use way. POA coupled with the use of explorative probes to detect the unknown part is now one of the most powerful approaches for a better understanding of microbial community functioning. However, the selection of probes remains a very difficult task. The rapid growth of environmental databases has led to an exponential increase of data to be managed for an efficient design. Consequently, the use of high performance computing facilities is mandatory. In this paper, we present an efficient parallelization method to select known and explorative oligonucleotide probes at large scale using computing grids. We implemented a software that generates and monitors thousands of jobs over the European Computing Grid Infrastructure (EGI. We also developed a new algorithm for the construction of a high-quality curated phylogenetic database to avoid erroneous design due to bad sequence affiliation. We present here the performance and statistics of our method on real biological datasets based on a phylogenetic prokaryotic database at the genus level and a complete design of about 20,000 probes for 2,069 genera of prokaryotes.

  5. Vibrational frequency fluctuations of ionic vibrational probe in water: Theoretical study with molecular dynamics simulation

    Science.gov (United States)

    Okuda, Masaki; Higashi, Masahiro; Ohta, Kaoru; Saito, Shinji; Tominaga, Keisuke

    2017-09-01

    The vibrational dynamics of SCN- in H2O are theoretically investigated by molecular dynamics simulations. Based on the vibrational solvatochromism theory, we calculate the frequency-frequency time correlation function of the SCN anti-symmetric stretching mode, which is characterized by time constants of 0.13 and 1.41 ps. We find that the frequency fluctuation is almost determined by the electrostatic interaction from the water molecules in the first-hydration shell. The collective dynamics of the water molecules in the first-hydration shell is found to be similar to that of bulk water, though the hydrogen bond between the ion and water molecule is very strong.

  6. Single shot, temporally and spatially resolved measurements of fast electron dynamics using a chirped optical probe

    Science.gov (United States)

    Green, J. S.; Murphy, C. D.; Booth, N.; Dance, R. J.; Gray, R. J.; MacLellan, D. A.; McKenna, P.; Rusby, D.; Wilson, L.

    2014-03-01

    A new approach to rear surface optical probing is presented that permits multiple, time-resolved 2D measurements to be made during a single, ultra-intense ( > 1018 W cm-2) laser-plasma interaction. The diagnostic is capable of resolving rapid changes in target reflectivity which can be used to infer valuable information on fast electron transport and plasma formation at the target rear surface. Initial results from the Astra-Gemini laser are presented, with rapid radial sheath expansion together with detailed filamentary features being observed to evolve during single shots.

  7. Fusion–fission dynamics studies using mass distribution as a probe

    Indian Academy of Sciences (India)

    T K Ghosh; A Chaudhuri; K Banerjee; S Bhattacharya; C Bhattacharya; S Kundu; G Mukherjee; R Pandey; T K Rana; P Roy; T Roy; V Srivastava; P Bhattacharya

    2015-08-01

    Study of quasifission reaction mechanism and shell effects in compound nuclei has important implications on the synthesis of superheavy elements (SHE). Using the major accelerator facilities available in India, quasifission reaction mechanism and shell effects in compound nuclei were studied extensively. Fission fragment mass distribution was used as a probe. Two factors, viz., nuclear orientation and direction of mass flow of the initial dinuclear system after capture were seen to determine the extent of quasifission. From the measurement of fragment mass distribution in -induced reaction on actinide targets, it was possible to constrain the excitation energy at which nuclear shell effect washed out.

  8. Dynamics of the EAG1 K(+) channel selectivity filter assessed by molecular dynamics simulations.

    Science.gov (United States)

    Bernsteiner, Harald; Bründl, Michael; Stary-Weinzinger, Anna

    2017-02-26

    EAG1 channels belong to the KCNH family of voltage gated potassium channels. They are expressed in several brain regions and increased expression is linked to certain cancer types. Recent cryo-EM structure determination finally revealed the structure of these channels in atomic detail, allowing computational investigations. In this study, we performed molecular dynamics simulations to investigate the ion binding sites and the dynamical behavior of the selectivity filter. Our simulations suggest that sites S2 and S4 form stable ion binding sites, while ions placed at sites S1 and S3 rapidly switched to sites S2 and S4. Further, ions tended to dissociate away from S0 within less than 20 ns, due to increased filter flexibility. This was followed by water influx from the extracellular side, leading to a widening of the filter in this region, and likely non-conductive filter configurations. Simulations with the inactivation-enhancing mutant Y464A or Na(+) ions lead to trapped water molecules behind the SF, suggesting that these simulations captured early conformational changes linked to C-type inactivation.

  9. Probing heterogeneous dynamics from spatial density correlation in glass-forming liquids

    Science.gov (United States)

    Li, Yan-Wei; Zhu, You-Liang; Sun, Zhao-Yan

    2016-12-01

    We numerically investigate the connection between spatial density correlation and dynamical heterogeneity in glass-forming liquids. We demonstrate that the cluster size defined by the spatial aggregation of densely packed particles (DPPs) can better capture the difference between the dynamics of the Lennard-Jones glass model and the Weeks-Chandler-Andersen truncation model than the commonly used pair correlation functions. More interestingly, we compare the mobility of DPPs and loosely packed particles, and we find that high local density correlates well with slow dynamics in systems with relatively hard repulsive interactions but links to mobile ones in the system with soft repulsive interactions at one relaxation time scale. Our results show clear evidence that the above model dependence behavior stems from the hopping motion of DPPs at the end of the caging stage due to the compressive nature of soft repulsive spheres, which activates the dynamics of DPPs in the α relaxation stage.

  10. Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes.

    Science.gov (United States)

    Sergé, Arnauld; Bertaux, Nicolas; Rigneault, Hervé; Marguet, Didier

    2008-08-01

    Although the highly dynamic and mosaic organization of the plasma membrane is well-recognized, depicting a resolved, global view of this organization remains challenging. We present an analytical single-particle tracking (SPT) method and tool, multiple-target tracing (MTT), that takes advantage of the high spatial resolution provided by single-fluorophore sensitivity. MTT can be used to generate dynamic maps at high densities of tracked particles, thereby providing global representation of molecular dynamics in cell membranes. Deflation by subtracting detected peaks allows detection of lower-intensity peaks. We exhaustively detected particles using MTT, with performance reaching theoretical limits, and then reconnected trajectories integrating the statistical information from past trajectories. We demonstrate the potential of this method by applying it to the epidermal growth factor receptor (EGFR) labeled with quantum dots (Qdots), in the plasma membrane of live cells. We anticipate the use of MTT to explore molecular dynamics and interactions at the cell membrane.

  11. Dynamical transition in molecular glasses and proteins observed by spin relaxation of nitroxide spin probes and labels

    Science.gov (United States)

    Golysheva, Elena A.; Shevelev, Georgiy Yu.; Dzuba, Sergei A.

    2017-08-01

    In glassy substances and biological media, dynamical transitions are observed in neutron scattering that manifests itself as deviations of the translational mean-squared displacement, , of hydrogen atoms from harmonic dynamics. In biological media, the deviation occurs at two temperature intervals, at ˜100-150 K and at ˜170-230 K, and it is attributed to the motion of methyl groups in the former case and to the transition from harmonic to anharmonic or diffusive motions in the latter case. In this work, electron spin echo (ESE) spectroscopy—a pulsed version of electron paramagnetic resonance—is applied to study the spin relaxation of nitroxide spin probes and labels introduced in molecular glass former o-terphenyl and in protein lysozyme. The anisotropic contribution to the rate of the two-pulse ESE decay, ΔW, is induced by spin relaxation appearing because of restricted orientational stochastic molecular motion; it is proportional to τc, where is the mean-squared angle of reorientation of the nitroxide molecule around the equilibrium position and τc is the correlation time of reorientation. The ESE time window allows us to study motions with τc τc temperature dependence shows a transition near 240 K, which is in agreement with the literature data on . For spin probes of essentially different size, the obtained data were found to be close, which evidences that motion is cooperative, involving a nanocluster of several neighboring molecules. For the dry lysozyme, the τc values below 260 K were found to linearly depend on the temperature in the same way as it was observed in neutron scattering for . As spin relaxation is influenced only by stochastic motion, the harmonic motions seen in ESE must be overdamped. In the hydrated lysozyme, ESE data show transitions near 130 K for all nitroxides, near 160 K for the probe located in the hydration layer, and near 180 K for the label in the protein interior. For this system, the two latter transitions are not

  12. Ultrafast pump-probe microscopy reveals the mechanism of selective fs laser structuring of transparent thin films for maskless micropatterning

    Science.gov (United States)

    Rapp, Stephan; Rosenberger, Janosch; Domke, Matthias; Heise, Gerhard; Huber, Heinz P.; Schmidt, Michael

    2014-01-01

    Maskless patterning of biocompatible Ta2O5/Pt/glass sensor chips can be realized by ultra-short laser pulse ablation. At a fluence of 0.2 J/cm2, the thin Ta2O5 film is selectively lifted-off by indirectly-induced ablation at laser wavelenghts where the Ta2O5 is transparent and the Pt absorbing. This enables precise and very fast structuring. Here, 660 fs laser pulses at a center wavelength of 1053 nm are applied. The driving physical effects of this ablation mechanism are revealed by pump-probe microscopy. This technique allows the observation of the whole ablation process ranging temporally from femtoseconds to microseconds. An ultrafast heat-expansion in the absorbing Pt, initiating a shock-wave to the Ta2O5 within the first 10 ps, bulges the Ta2O5 film after some nanoseconds. Bulging velocities of 750 m/s are determined corresponding to an extreme acceleration of about 1010 g. Exceeding the stress limit in the Ta2O5 causes film disintegration after 50 ns. A model, describing essential reaction steps, is developed. This model is also applicable to other industrial important layer systems, where thin transparent films have to be removed.

  13. Next-generation repeat-free FISH probes for DNA amplification in glioblastoma in vivo: Improving patient selection to MDM2-targeted inhibitors.

    Science.gov (United States)

    Brunelli, Matteo; Eccher, Albino; Cima, Luca; Trippini, Tobia; Pedron, Serena; Chilosi, Marco; Barbareschi, Mattia; Scarpa, Aldo; Pinna, Giampietro; Cabrini, Giulio; Pilotto, Sara; Carbognin, Luisa; Bria, Emilio; Tortora, Giampaolo; Fioravanzo, Adele; Schiavo, Nicola; Meglio, Mario; Sava, Teodoro; Belli, Laura; Martignoni, Guido; Ghimenton, Claudio

    2017-01-01

    A next-generation FISH probe mapping to the MDM2 locus-specific region has recently been designed. The level of MDM2 gene amplification (high versus low) may allow selection of patients for cancer treatment with MDM2 inhibitors and may predict their responsiveness. We investigated the spectrum of MDM2 gene alterations using the new probes in vivo after visualizing single neoplastic cells in situ from a series of glioblastomas. Signals from next-generation repeat-free FISH interphase probes were identified in tissue microarrays that included 3 spots for each of the 48 cases. The murine double minutes (MDM2)-specific DNA probe and the satellite enumeration probe for chromosome 12 were used. Three cases (6%) showed more than 25 signals (high gene amplification), and 7 (15%) showed 3-10 signals (gains); among these, 4 cases (8%) had an equal number of MDM2 and centromeric signals on chromosome 12 (polyploidy). Genomic heterogeneity was observed only in 3 cases with low gene amplification. In our series, 6% of glioblastomas exhibited high MDM2 amplification (in vivo) with a pattern related to the known double minutes/chromothripsis phenomenon (in situ), and only cases with low amplification showed genomic heterogeneity. We concluded that the rate of MDM2 gene amplification can be a useful predictive biomarker to improve patient selection.

  14. Traffic dynamics in empirical probe vehicle data studied with three-phase theory: Spatiotemporal reconstruction of traffic phases and generation of jam warning messages

    Science.gov (United States)

    Kerner, Boris S.; Rehborn, Hubert; Schäfer, Ralf-Peter; Klenov, Sergey L.; Palmer, Jochen; Lorkowski, Stefan; Witte, Nikolaus

    2013-01-01

    Empirical and theoretical analyses of the spatiotemporal dynamics of traffic flow reconstructed from randomly distributed probe vehicle data are presented. For the empirical analysis, probe vehicle data generated by TomTom’s navigation devices in the commercial TomTom’s HD-traffic service as well as road detector data measured at the same road section are used. A stochastic microscopic (car-following) three-phase model is further developed for simulations of a real empirical complex spatiotemporal traffic dynamics measured over a three-lane long road stretch with several different bottlenecks. Physical features and limitations of simulations of real spatiotemporal traffic dynamics are revealed. Phase transition points between free flow (F), synchronized flow (S), and wide moving jam (J) are identified along trajectories of empirical and simulated probe vehicles randomly distributed in traffic flow. As predicted by three-phase theory, the empirical probe vehicle data shows that traffic breakdown is an F→S transition and wide moving jams emerge only in synchronized flow, i.e., due to S→J transitions. Through the use of the simulations, it has been found that already about 2% of probe vehicle data allows us to reconstruct traffic dynamics in space and time with an accuracy that is high enough for most applications like the generation of jam warning messages studied in the article.

  15. Nonlinear ultrafast dynamics of high temperature YBa2Cu3O7–δ superconductors probed with THz pump / THz probe spectroscopy

    Directory of Open Access Journals (Sweden)

    Chen H. T.

    2013-03-01

    Full Text Available High power THz pulses induce near transparency in superconductive YBCO thin films below the critical temperature. THz pump/THz probe measurements reveal a decay of the induced transparency on the time scale of a few picoseconds.

  16. A Dual-Colour Architecture for Pump-Probe Spectroscopy of Ultrafast Magnetization Dynamics in the Sub-10-femtosecond Range

    Science.gov (United States)

    Gonçalves, C. S.; Silva, A. S.; Navas, D.; Miranda, M.; Silva, F.; Crespo, H.; Schmool, D. S.

    2016-03-01

    Current time-resolution-limited dynamic measurements clearly show the need for improved techniques to access processes on the sub-10-femtosecond timescale. To access this regime, we have designed and constructed a state-of-the-art time-resolved magneto-optic Kerr effect apparatus, based on a new dual-color scheme, for the measurement of ultrafast demagnetization and precessional dynamics in magnetic materials. This system can operate well below the current temporal ranges reported in the literature, which typically lie in the region of around 50 fs and above. We have used a dual-colour scheme, based on ultra broadband hollow-core fibre and chirped mirror pulse compression techniques, to obtain unprecedented sub-8-fs pump and probe pulse durations at the sample plane. To demonstrate the capabilities of this system for ultrafast demagnetization and precessional dynamics studies, we have performed measurements in a ferrimagnetic GdFeCo thin film. Our study has shown that the magnetization shows a sudden drop within the first picosecond after the pump pulse, a fast recovery (remagnetization) within a few picoseconds, followed by a clear oscillation or precession during a slower magnetization recovery. Moreover, we have experimentally confirmed for the first time that a sub-10-fs pulse is able to efficiently excite a magnetic system such as GdFeCo.

  17. Excited-state dynamics of bacteriorhodopsin probed by broadband femtosecond fluorescence spectroscopy.

    Science.gov (United States)

    Schmidt, B; Sobotta, C; Heinz, B; Laimgruber, S; Braun, M; Gilch, P

    2005-01-07

    The impact of varying excitation densities (approximately 0.3 to approximately 40 photons per molecule) on the ultrafast fluorescence dynamics of bacteriorhodopsin has been studied in a wide spectral range (630-900 nm). For low excitation densities, the fluorescence dynamics can be approximated biexponentially with time constants of <0.15 and approximately 0.45 ps. The spectrum associated with the fastest time constant peaks at 650 nm, while the 0.45 ps component is most prominent at 750 nm. Superimposed on these kinetics is a shift of the fluorescence maximum with time (dynamic Stokes shift). Higher excitation densities alter the time constants and their amplitudes. These changes are assigned to multi-photon absorptions.

  18. 2D IR spectroscopy of histidine: probing side-chain structure and dynamics via backbone amide vibrations.

    Science.gov (United States)

    Ghosh, Ayanjeet; Tucker, Matthew J; Gai, Feng

    2014-07-17

    It is well known that histidine is involved in many biological functions due to the structural versatility of its side chain. However, probing the conformational transitions of histidine in proteins, especially those occurring on an ultrafast time scale, is difficult. Herein we show, using a histidine dipeptide as a model, that it is possible to probe the tautomer and protonation status of a histidine residue by measuring the two-dimensional infrared (2D IR) spectrum of its amide I vibrational transition. Specifically, for the histidine dipeptide studied, the amide unit of the histidine gives rise to three spectrally resolvable amide I features at approximately 1630, 1644, and 1656 cm(-1), respectively, which, based on measurements at different pH values and frequency calculations, are assigned to a τ tautomer (1630 cm(-1) component) and a π tautomer with a hydrated (1644 cm(-1) component) or dehydrated (1656 cm(-1) component) amide. Because of the intrinsic ultrafast time resolution of 2D IR spectroscopy, we believe that the current approach, when combined with the isotope editing techniques, will be useful in revealing the structural dynamics of key histidine residues in proteins that are important for function.

  19. Molecular dynamics simulations and Kelvin probe force microscopy to study of cholesterol-induced electrostatic nanodomains in complex lipid mixtures

    Science.gov (United States)

    Drolle, E.; Bennett, W. F. D.; Hammond, K.; Lyman, E.; Karttunen, M.; Leonenko, Z.

    The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To probe these nanodomains in soft matter is a challenging task both experimentally and theoretically. This work addresses the effects of cholesterol, lipid composition, lipid charge, and lipid phase on the monolayer structure and the electrical surface potential distribution. Atomic Force Microscopy (AFM) was used to resolve topographical nanodomains and Kelvin Probe Force Microscopy (KPFM) to resolve electrical surface potential of these nanodomains in lipid monolayers. Model monolayers composed of dipalmitoylphosphatidylcholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(3-lysyl(1-glycerol))] (DOPG), sphingomyelin, and cholesterol were studied. It is shown that cholesterol changes nanoscale domain formation, affecting both topography and electrical surface potential. The molecular basis for differences in electrical surface potential was addressed with atomistic molecular dynamics (MD). MD simulations qualitatively match the experimental results, with 100s of mV difference in electrostatic potential between liquid-disordered bilayer (Ld, less cholesterol and lower chain order) and a liquid-ordered bilayer (Lo, more cholesterol and higher chain order). Importantly, the difference in electrostatic properties between Lo and Ld phases suggests a new mechanism by which membrane composition couples to membrane function.

  20. Size-dependent ligand layer dynamics in semiconductor nanocrystals probed by anisotropy measurements.

    Science.gov (United States)

    Hadar, Ido; Abir, Tsafrir; Halivni, Shira; Faust, Adam; Banin, Uri

    2015-10-12

    Colloidal semiconductor nanocrystals (NC) have reached a high level of synthetic control allowing the tuning of their properties, and their use in various applications. However, the surface of NCs and in particular their size-dependent capping organic ligand behavior, which play an important role in the NC synthesis, dispersibility, and optoelectronic properties, is still not well understood. We study the size-dependent properties of the ligand shell on the surface of NCs, by embedding surface bound dyes as a probe within the ligand shell. The reorientation times for these dyes show a linear dependence on the NC surface curvature indicating size-dependent change in viscosity, which is related to a change in the density of the ligand layer because of the geometry of the surface, a unique feature of NCs. Understanding the properties of the ligand shell will allow rational design of the surface to achieve the desired properties, providing an additional important knob for tuning their functionality.

  1. Probing lattice dynamics in silicon with laser-wakefield accelerated electrons

    Science.gov (United States)

    Nees, John; He, Z.-H.; Thomas, A. G. R.; Krushelnick, Karl; Scott, S.; Legally, M.; Beaurepaire, B.; Gallé, G.; Faure, J.

    2016-10-01

    Laser wakefield acceleration is the key technology in a new breed of electron and photon beam sources that operate in the ultrafast domain. We show that the spatial and temporal properties of wakefield-generated electron beams can be manipulated to enable them interrogate ultrafast lattice dynamics in freestanding single-crystal silicon membranes, while maintaining spatial resolution on the atomic scale. In particular, picosecond resolution of Si lattice dynamics is obtained by recording streaked electron diffraction peaks using static magnetic fields. We will also discuss the role of wave front control in establishing optimal beam characteristics and the significance of single-shot measurements. Michigan support from NSF PHY-1535628.

  2. Wavelet transforms to probe long- and short-range forces by thermally excited dynamic force spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Malegori, Giovanna; Ferrini, Gabriele, E-mail: gabriele@dmf.unicatt.it [Dipartimento di Matematica e Fisica, Universita Cattolica, I-25121 Brescia (Italy)

    2011-05-13

    The use of wavelet transforms in thermally excited dynamic force spectroscopy allows us to gain insight into the fundamental thermodynamical properties of a cantilever's Brownian motion as well as giving a meaningful and intuitive representation of the cantilever dynamics in time and frequency caused by the interaction with long- and short-range forces. The possibility of carrying out measurements across the jump-to-contact transition without interruption, providing information on both van der Waals forces and short-range adhesion surface forces, is remarkable.

  3. Dynamic Probing of Nanoparticle Stability In Vivo: A Liposomal Model Assessed Using In Situ Microdialysis and Optical Imaging

    Directory of Open Access Journals (Sweden)

    Chien-Chung Jeng

    2011-01-01

    Full Text Available Nanoparticle-mediated drug delivery and controlled release has been a vigorous research area in contemporary nanomedicine. The in vivo stability of nanoparticle delivered on site is a prerequisite for the design of drug-controlled release by any means. In this study, the first methodology comprised of microdialysis and optical imaging to assess the liposome stability in vivo is reported. Macroscopically, we demonstrated the DPPG liposomes with negative surface charge fast accumulated in the rat liver upon their i.v. administration using optical imaging. Microscopically, the concurrent analysis of fluorescent molecules leaching from the liposomes, in situ sampled using microdialysis probe, provides the dynamic information of stability of DPPG liposomes locus in quo. The current combination of in situ microdialysis and optical imaging possesses a great potential for use as a platform technology to evaluate the nanoparticle stability and the bioavailability of drug payload released on targeted site in vivo.

  4. A multi-property fluorescent probe for the investigation of polymer dynamics near the glass transition

    NARCIS (Netherlands)

    Siekierzycka, J.R.; Hippius, C.; Würthner, F.; Williams, R.M.; Brouwer, A.M.

    2014-01-01

    In addition to the commonly observed single molecule fluorescence intensity fluctuations due to molecular reorientation dynamics, a perylene bisimide-calixarene compound (1) shows additional on-off fluctuations due to its ability to undergo intramolecular excited state electron transfer (PET). This

  5. The dynamics of the local group as a probe of Dark Energy and Modified Gravity

    Science.gov (United States)

    Carlesi, Edoardo; Mota, David F.; Winther, Hans A.

    2017-01-01

    In this work we study the dynamics of the Local Group (LG) within the context of cosmological models beyond General Relativity (GR). Using observable kinematic quantities to identify candidate pairs we build up samples of simulated LG-like objects drawing from f(R), symmetron, DGP and quintessence N-body simulations together with their ΛCDM counterparts featuring the same initial random phase realisations. The variables and intervals used to define LG-like objects are referred to as Local Group model; different models are used throughout this work and adapted to study their dynamical and kinematic properties. The aim is to determine how well the observed LG-dynamics can be reproduced within cosmological theories beyond GR, We compute kinematic properties of samples drawn from alternative theories and ΛCDM and compare them to actual observations of the LG mass, velocity and position. As a consequence of the additional pull, pairwise tangential and radial velocities are enhanced in modified gravity and coupled dark energy with respect to ΛCDM inducing significant changes to the total angular momentum and energy of the LG. For example, in models such as f(R) and the symmetron this increase can be as large as 60%, peaking well outside of the 95% confidence region allowed by the data. This shows how simple considerations about the LG dynamics can lead to clear small-scale observational signatures for alternative scenarios, without the need of expensive high-resolution simulations.

  6. Bending Dynamics of Fluctuating Biopolymers Probed by Automated High-Resolution Filament Tracking

    Science.gov (United States)

    Brangwynne, Clifford P.; Koenderink, Gijsje H.; Barry, Ed; Dogic, Zvonimir; MacKintosh, Frederick C.; Weitz, David A.

    2007-01-01

    Microscope images of fluctuating biopolymers contain a wealth of information about their underlying mechanics and dynamics. However, successful extraction of this information requires precise localization of filament position and shape from thousands of noisy images. Here, we present careful measurements of the bending dynamics of filamentous (F-)actin and microtubules at thermal equilibrium with high spatial and temporal resolution using a new, simple but robust, automated image analysis algorithm with subpixel accuracy. We find that slender actin filaments have a persistence length of ∼17 μm, and display a q−4-dependent relaxation spectrum, as expected from viscous drag. Microtubules have a persistence length of several millimeters; interestingly, there is a small correlation between total microtubule length and rigidity, with shorter filaments appearing softer. However, we show that this correlation can arise, in principle, from intrinsic measurement noise that must be carefully considered. The dynamic behavior of the bending of microtubules also appears more complex than that of F-actin, reflecting their higher-order structure. These results emphasize both the power and limitations of light microscopy techniques for studying the mechanics and dynamics of biopolymers. PMID:17416612

  7. Glass Dynamics Probed by the Long-Lived Stimulated Photon Echo

    NARCIS (Netherlands)

    Meijers, Hans C.; Wiersma, Douwe A.

    1992-01-01

    The dynamics in an ethanol glass at 1.5 K has been investigated from picoseconds to milliseconds by two-dimensional stimulated-photon-echo measurements on zinc porphin. In this time frame the distribution of relaxation rates exhibits a 1/R dependence except for a gap stretching from about 1 kHz to 1

  8. Real-time Dynamics of Surface Photoreactions Probed with Ultrashort XUV Pulses

    Science.gov (United States)

    Li, Xinlong; Zhao, Peng; Corder, Christopher; Polanco, Austin; Reber, Melanie; Chen, Yuning; Muraca, Amanda; Kershis, Matthew; White, Michael; Allison, Thomas

    2015-05-01

    High harmonic generation (HHG) and time-resolved photoelectron spectroscopy (TRPES) are well-established technique, broadly applicable for studying electronic and nuclear dynamics in real time. However, conventional HHG is typically limited to low repetition rates (titania surfaces which contain noble metal nanoparticles. AFOSR. Stony Brook University.

  9. Ultrafast supercontinuum fiber-laser based pump-probe scanning MOKE microscope for the investigation of electron spin dynamics in semiconductors at cryogenic temperatures with picosecond time and micrometer spatial resolution

    CERN Document Server

    Henn, T; Ossau, W; Molenkamp, L W; Biermann, K; Santos, P V

    2013-01-01

    We describe a two-color pump-probe scanning magneto-optical Kerr effect (MOKE) microscope which we have developed to investigate electron spin phenomena in semiconductors at cryogenic temperatures with picosecond time and micrometer spatial resolution. The key innovation of our microscope is the usage of an ultrafast `white light' supercontinuum fiber-laser source which provides access to the whole visible and near-infrared spectral range. Our Kerr microscope allows for the independent selection of the excitation and detection energy while avoiding the necessity to synchronize the pulse trains of two separate picosecond laser systems. The ability to independently tune the pump and probe wavelength enables the investigation of the influence of excitation energy on the optically induced electron spin dynamics in semiconductors. We demonstrate picosecond real-space imaging of the diffusive expansion of optically excited electron spin packets in a (110) GaAs quantum well sample to illustrate the capabilities of t...

  10. Interfacial coarsening dynamics in epitaxial growth with slope selection

    Science.gov (United States)

    Moldovan; Golubovic

    2000-06-01

    We investigate interfacial dynamics of molecular-beam epitaxy (MBE) growth in the presence of instabilities inducing formation of pyramids. We introduce a kinetic scaling theory which provides an analytic understanding of the coarsening dynamics laws observed in numerous experiments and simulations of the MBE. We address MBE growth on crystalline surfaces with different symmetries in order to explain experimentally observed differences between the growth on (111) and (001) surfaces and understand the coarsening exponents measured on these surfaces. We supplement our kinetic scaling theory by numerical simulations which document that the edges of the pyramids, forming a network across the growing interface, are essential for qualitative understanding of the coarsening dynamics of molecular-beam epitaxy.

  11. Supplier Selection in Dynamic Environment using Analytic Hierarchy Process

    Directory of Open Access Journals (Sweden)

    Prince Agarwal

    2014-08-01

    Full Text Available In today’s highly competitive business environment, the rapidly changing customer demands and with the advent of enterprise wide information systems, the managers are bound to think beyond the conventional business processes and devise new ways to squeeze out costs and improve the performance without compromising on the quality at the same time. Supplier evaluation and selection is one such area which determines the success of any manufacturing firm. Supplier selection is the problem wherein the company decides which vendor to select to have that strategic and operational advantage of meeting the customers’ varying demands and fight the fierce competition. This paper presents a simple model based on Analytic Hierarchy Process (AHP to help decision makers in supplier evaluation and selection, taking into account the firm’s requirements. The article is intended to help new scholars and researchers understand the AHP model and see different facets in first sight.

  12. Mobile Game Probes

    DEFF Research Database (Denmark)

    Borup Lynggaard, Aviaja

    2006-01-01

    This paper will examine how probes can be useful for game designers in the preliminary phases of a design process. The work is based upon a case study concerning pervasive mobile phone games where Mobile Game Probes have emerged from the project. The new probes are aimed towards a specific target...... group and the goal is to specify the probes so they will cover the most relevant areas for our project. The Mobile Game Probes generated many interesting results and new issues occurred, since the probes came to be dynamic and favorable for the process in new ways....

  13. Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

    Directory of Open Access Journals (Sweden)

    Townsend Henrik J

    2005-11-01

    Full Text Available Abstract High-density oligonucleotide (oligo arrays are a powerful tool for transcript profiling. Arrays based on GeneChip® technology are amongst the most widely used, although GeneChip® arrays are currently available for only a small number of plant and animal species. Thus, we have developed a method to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species and tested the method by analysing the transcriptome of Brassica oleracea L., a species for which no GeneChip® array is available, using a GeneChip® array designed for Arabidopsis thaliana (L. Heynh. Genomic DNA from B. oleracea was labelled and hybridised to the ATH1-121501 GeneChip® array. Arabidopsis thaliana probe-pairs that hybridised to the B. oleracea genomic DNA on the basis of the perfect-match (PM probe signal were then selected for subsequent B. oleracea transcriptome analysis using a .cel file parser script to generate probe mask files. The transcriptional response of B. oleracea to a mineral nutrient (phosphorus; P stress was quantified using probe mask files generated for a wide range of gDNA hybridisation intensity thresholds. An example probe mask file generated with a gDNA hybridisation intensity threshold of 400 removed > 68 % of the available PM probes from the analysis but retained >96 % of available A. thaliana probe-sets. Ninety-nine of these genes were then identified as significantly regulated under P stress in B. oleracea, including the homologues of P stress responsive genes in A. thaliana. Increasing the gDNA hybridisation intensity thresholds up to 500 for probe-selection increased the sensitivity of the GeneChip® array to detect regulation of gene expression in B. oleracea under P stress by up to 13-fold. Our open-source software to create probe mask files is freely available http://affymetrix.arabidopsis.info/xspecies/ and may be used to facilitate transcriptomic analyses of a wide range of plant and animal

  14. Probing the Dynamical Behaviour of Surface Dipoles Through Energy Absorption Interferometry

    CERN Document Server

    Withington, Stafford

    2012-01-01

    Spatial interferometry, based on the measurement of total absorbed power, can be used to determine the state of coherence of the electromagnetic field to which any energy-absorbing structure is sensitive. The measured coherence tensor can be diagonalized to give the amplitude, phase, polarization patterns, and responsivities of the individual electromagnetic modes through which the structure can absorb energy. Because the electromagnetic modes are intimately related to dynamical modes of the system, information about collective excitations can be found. We present simulations, based on the Discrete Dipole Approximation (DDA), showing how the dynamical modes of systems of surface dipoles can be recovered. Interactions are taken into consideration, leading to long-range coherent phenomena, which are revealed by the method. The use of DDA enables the interferometric response of a wide variety of objects to be modeled, from patterned photonic films to biological macromolecules.

  15. How to Probe for Dynamical Structure in the Collapse of Entangled States Using Nuclear Magnetic Resonance

    CERN Document Server

    Fivel, D I

    1998-01-01

    The spin state of two magnetically inequivalent protons in contiguous atoms of a molecule becomes entangeled by the indirect spin-spin interaction (j-coupling). The degree of entanglement oscillates at the beat frequency resulting from the splitting of a degeneracy. This beating is manifest in NMR spectroscopy as an envelope of the transverse magnetization and should be visible in the free induction decay signal. The period (approximately 1 sec) is long enough for interference between the linear dynamics and collapse of the wave-function induced by a Stern-Gerlach inhomogeneity to significantly alter the shape of that envelope. Various dynamical collapse theories can be distinguished by their observably different predictions with respect to this alteration. Adverse effects of detuning due to the Stern-Gerlach inhomogeneity can be reduced to an acceptable level by having a sufficiently thin sample or a strong rf field.

  16. Dynamics of ferrocene in molecular sieves probed by Mossbauer spectroscopy and nuclear resonant scattering

    Energy Technology Data Exchange (ETDEWEB)

    Asthalter, T [Institut fuer Physikalische Chemie, Universitat Stuttgart, D-70569 Stuttgart (Germany); Sergueev, I [European Synchrotron Radiation Facility, F-38043 Grenoble (France); Buerck, U van; Wagner, F E [Experimentalphysik E13, Technische Universitaet Muenchen, D-85747 Garching (Germany); Haerter, P [Anorganische Chemie, Technische Universitaet Muenchen, D-85747 Garching (Germany); Kornatowski, J [Max-Planck-Institut fuer Kohlenforschung, D-45470 Muelheim (Germany); Klingelhoefer, S; Behrens, P, E-mail: t.asthalter@ipc.uni-stuttgart.d [Anorganische Chemie, Leibniz-Universitaet Hannover, D-30167 Hannover (Germany)

    2010-03-01

    A detailed study on the slow dynamics of ferrocene in the unidimensional channels of the molecular sieves SSZ-24 and AlPO{sub 4}-5 has been carried out, using Moessbauer spectroscopy (MS), nuclear forward scattering (NFS) and synchrotron radiation-based perturbed angular correlations (SRPAC). In both host systems, anisotropic rotational dynamics is observed above 100 K. For SSZ-24, this anisotropy persists even above the bulk melting temperature of ferrocene. Various theoretical models are exploited for the study of anisotropic discrete jump rotations for the first time. The experimental data can be described fairly well by a jump model that involves reorientations of the molecular axis on a cone mantle with an opening angle dependant on temperature.

  17. On the dynamic and static manifestation of molecular absorption in thin films probed by a microcantilever

    Energy Technology Data Exchange (ETDEWEB)

    Finot, Eric [Institut CARNOT de Bourgogne; Fabre, Arnaud [French Atomic Energy Commission (CEA), Centre de Valduc, Is-sur-Tille; Passian, Ali [ORNL; Thundat, Thomas [University of Alberta, Edmonton, Canada

    2014-03-01

    Mechanical resonators shaped like microcantilevers have been demonstrated as a platform for very sensitive detection of chemical and biological analytes. However, its use as an analytical tool will require fundamental understanding of the molecular absorption-induced effects in the static and dynamic sensor response. The effect of absorption-induced surface stress on the microcantilever response is here investigated using palladium hydride formation. It is shown that the resonance and deformation states of the cantilever monitored simultaneously exhibit excellent correlation with the phase of the hydride formation. However, the associated frequency shifts and quasistatic bending are observed to be independent during solid solution phase. Importantly, absorption-induced changes in the elastic parameters of the palladium film are found to play a dominant role in the static and dynamic response. The presented results help in discerning the parameters that control the cantilever response as well as the relationships between these parameters.

  18. A Probe into the Dynamic Change of Land Use in the Southern Loess Plateau

    Institute of Scientific and Technical Information of China (English)

    Bin; GUO; Li; ZHANG

    2013-01-01

    In order to reveal the characteristics of land use change in the south loess plateau,this paper tentatively divided Loess Plateau into North and South under the support of GIS,and then introduced land use spatial temporal dynamic model,analyzed land use dynamic change in provincial scale. The results showed: during the 25 years,construction land area increased from 3 555. 99 km2 to 4 794. 28 km2,unused land decreased by 0. 02 percentage points,forest land area increased from 51 011. 31 km2 to 51 066. 79 km2,waters increased of 0. 01 percentage points,farmland area decreased to 98 561. 57 km2 from 100 004. 79 km2,grassland area increased by 0.08 percentage points. Land use change important values in province scale on each were not identical,showed obvious regional differences.

  19. Hidden Markov Model of atomic quantum jump dynamics in an optically probed cavity

    DEFF Research Database (Denmark)

    Gammelmark, S.; Molmer, K.; Alt, W.

    2014-01-01

    We analyze the quantum jumps of an atom interacting with a cavity field. The strong atom- field interaction makes the cavity transmission depend on the time dependent atomic state, and we present a Hidden Markov Model description of the atomic state dynamics which is conditioned in a Bayesian......, the atomic state is determined in a Bayesian manner from the measurement data, and we present an iterative protocol, which determines both the atomic state and the model parameters. As a new element in the treatment of observed quantum systems, we employ a Bayesian approach that conditions the atomic state...... manner on the detected signal. We suggest that small variations in the observed signal may be due to spatial motion of the atom within the cavity, and we represent the atomic system by a number of hidden states to account for both the small variations and the internal state jump dynamics. In our theory...

  20. Hidden Markov Model of atomic quantum jump dynamics in an optically probed cavity

    DEFF Research Database (Denmark)

    Gammelmark, S.; Molmer, K.; Alt, W.

    2014-01-01

    manner on the detected signal. We suggest that small variations in the observed signal may be due to spatial motion of the atom within the cavity, and we represent the atomic system by a number of hidden states to account for both the small variations and the internal state jump dynamics. In our theory......We analyze the quantum jumps of an atom interacting with a cavity field. The strong atom- field interaction makes the cavity transmission depend on the time dependent atomic state, and we present a Hidden Markov Model description of the atomic state dynamics which is conditioned in a Bayesian......, the atomic state is determined in a Bayesian manner from the measurement data, and we present an iterative protocol, which determines both the atomic state and the model parameters. As a new element in the treatment of observed quantum systems, we employ a Bayesian approach that conditions the atomic state...

  1. k-space image correlation to probe the intracellular dynamics of gold nanoparticles

    Science.gov (United States)

    Bouzin, M.; Sironi, L.; Chirico, G.; D'Alfonso, L.; Inverso, D.; Pallavicini, P.; Collini, M.

    2016-04-01

    The collective action of dynein, kinesin and myosin molecular motors is responsible for the intracellular active transport of cargoes, vesicles and organelles along the semi-flexible oriented filaments of the cytoskeleton. The overall mobility of the cargoes upon binding and unbinding to motor proteins can be modeled as an intermittency between Brownian diffusion in the cell cytoplasm and active ballistic excursions along actin filaments or microtubules. Such an intermittent intracellular active transport, exhibited by star-shaped gold nanoparticles (GNSs, Gold Nanostars) upon internalization in HeLa cancer cells, is investigated here by combining live-cell time-lapse confocal reflectance microscopy and the spatio-temporal correlation, in the reciprocal Fourier space, of the acquired image sequences. At first, the analytical theoretical framework for the investigation of a two-state intermittent dynamics is presented for Fourier-space Image Correlation Spectroscopy (kICS). Then simulated kICS correlation functions are employed to evaluate the influence of, and sensitivity to, all the kinetic and dynamic parameters the model involves (the transition rates between the diffusive and the active transport states, the diffusion coefficient and drift velocity of the imaged particles). The optimal procedure for the analysis of the experimental data is outlined and finally exploited to derive whole-cell maps for the parameters underlying the GNSs super-diffusive dynamics. Applied here to the GNSs subcellular trafficking, the proposed kICS analysis can be adopted for the characterization of the intracellular (super-) diffusive dynamics of any fluorescent or scattering biological macromolecule.

  2. Eta bound states in nuclei: a probe of flavour-singlet dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Steven D. Bass; Anthony W. Thomas

    2005-07-01

    We argue that eta bound states in nuclei are sensitive to the singlet component in the eta. The bigger the singlet component, the more attraction and the greater the binding. Thus, measurements of eta bound states will yield new information about axial U(1) dynamics and glue in mesons. Eta - etaprime mixing plays an important role in understanding the value of the eta-nucleon scattering length.

  3. Probing the Impact of Local Structural Dynamics of Conformational Epitopes on Antibody Recognition.

    Science.gov (United States)

    Liang, Yu; Guttman, Miklos; Davenport, Thaddeus M; Hu, Shiu-Lok; Lee, Kelly K

    2016-04-19

    Antibody-antigen interactions are governed by recognition of specific residues and structural complementarity between the antigen epitope and antibody paratope. While X-ray crystallography has provided detailed insights into static conformations of antibody-antigen complexes, factors such as conformational flexibility and dynamics, which are not readily apparent in the structures, can also have an impact on the binding event. Here we investigate the contribution of dynamics in the HIV-1 gp120 glycoprotein to antibody recognition of conserved conformational epitopes, including the CD4- and coreceptor-binding sites, and an inner domain site that is targeted by ADCC-active antibodies. Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) was used to measure local structural dynamics across a panel of variable loop truncation mutants of HIV-1 gp120, including full-length gp120, ΔV3, ΔV1/V2, and extended core, which includes ΔV1/V2 and V3 loop truncations. CD4-bound full-length gp120 was also examined as a reference state. HDX-MS revealed a clear trend toward an increased level of order of the conserved subunit core resulting from loop truncation. Combined with biolayer interferometry and enzyme-linked immunosorbent assay measurements of antibody-antigen binding, we demonstrate that an increased level of ordering of the subunit core was associated with better recognition by an array of antibodies targeting complex conformational epitopes. These results provide detailed insight into the influence of structural dynamics on antibody-antigen interactions and suggest the importance of characterizing the structural stability of vaccine candidates to improve antibody recognition of complex epitopes.

  4. Selective and High Dynamic Range Assay Format for Multiplex Detection of Pathogenic Pseudomonas aeruginosa, Salmonella typhimurium, and Legionella pneumophila RNAs Using Surface Plasmon Resonance Imaging.

    Science.gov (United States)

    Melaine, F; Saad, M; Faucher, S; Tabrizian, M

    2017-07-18

    Due to its well-characterized and highly conserved structure, as well as its relative abundance in metabolically active cells, bacterial 16S rRNA sequence plays an important role in microbial identification. In this work, a biosensing strategy has been developed for simultaneous detection of 16S rRNA analytes of three pathogenic bacterial strains: Legionella pneumophila, Pseudomonas aeruginosa, and Salmonella typhimurium. Surface plasmon resonance imaging (SPRi) was used as a detection technique coupled with DNA probe sandwich assemblies and gold nanoparticles (GNPs) for signal amplification. The targets 16S rRNA were selectively captured at the interface of the biosensor by surface-bound DNA probes through a hybridization process. GNP-grafted DNA detection probes were then introduced and were hybridized with a defined 16S rRNA region on the long DNA-RNA sandwich assemblies, resulting in a significant increase of the SPR signal. The results demonstrated the successful implementation of this strategy for detecting 16S rRNA sequences in total RNA mixed samples extracted from the three pathogenic strains at a concentration down to 10 pg mL(-1) with a large dynamic range of 0.01-100 ng mL(-1) and high selectivity. Since no particular optimization of the probe design was applied, this method should be relatively easy to adapt for quantification of a wide range of bacteria in various liquids.

  5. Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics

    Science.gov (United States)

    Reppert, Mike; Tokmakoff, Andrei

    2016-05-01

    Two-dimensional infrared spectroscopy of amide I vibrations is increasingly being used to study the structure and dynamics of proteins and peptides. Amide I, a primarily carbonyl stretching vibration of the protein backbone, provides information on secondary structures as a result of vibrational couplings and on hydrogen-bonding contacts when isotope labeling is used to isolate specific sites. In parallel with experiments, computational models of amide I spectra that use atomistic structures from molecular dynamics simulations have evolved to calculate experimental spectra. Mixed quantum-classical models use spectroscopic maps to translate the structural information into a quantum-mechanical Hamiltonian for the spectroscopically observed vibrations. This allows one to model the spectroscopy of large proteins, disordered states, and protein conformational dynamics. With improvements in amide I models, quantitative modeling of time-dependent structural ensembles and of direct feedback between experiments and simulations is possible. We review the advances in developing these models, their theoretical basis, and current and future applications.

  6. Expansion dynamics of supercritical water probed by picosecond time-resolved photoelectron spectroscopy.

    Science.gov (United States)

    Gladytz, Thomas; Abel, Bernd; Siefermann, Katrin R

    2015-02-21

    Vibrational excitation of liquid water with femtosecond laser pulses can create extreme states of water. Yet, the dynamics directly after initial sub-picosecond delocalization of molecular vibrations remain largely unclear. We study the ultrafast expansion dynamics of an accordingly prepared supercritical water phase with a picosecond time resolution. Our experimental setup combines vacuum-compatible liquid micro-jet technology and a table top High Harmonic light source driven by a femtosecond laser system. An ultrashort laser pulse centered at a wavelength of 2900 nm excites the OH-stretch vibration of water molecules in the liquid. The deposited energy corresponds to a supercritical phase with a temperature of about 1000 K and a pressure of more than 1 GPa. We use a time-delayed extreme ultraviolet pulse centered at 38.6 eV, and obtained via High Harmonic generation (HHG), to record valence band photoelectron spectra of the expanding water sample. The series of photoelectron spectra is analyzed with noise-corrected target transform fitting (cTTF), a specifically developed multivariate method. Together with a simple fluid dynamics simulation, the following picture emerges: when a supercritical phase of water expands into vacuum, temperature and density of the first few nanometers of the expanding phase drop below the critical values within a few picoseconds. This results in a supersaturated phase, in which condensation seeds form and grow from small clusters to large clusters on a 100 picosecond timescale.

  7. Magnetic fluid hyperthermia probed by both calorimetric and dynamic hysteresis measurements

    Science.gov (United States)

    Guibert, Clément; Fresnais, Jérôme; Peyre, Véronique; Dupuis, Vincent

    2017-01-01

    In this paper, we report an investigation of magnetic fluid hyperthermia (MFH) using combined calorimetric and newly implemented dynamic hysteresis measurements for two sets of well characterized size-sorted maghemite nanoparticles (with diameters of about 10 nm and 20 nm) dispersed in water and in glycerol. Our primary goal was to assess the influence of viscosity on the heating efficiency of magnetic nanoparticles described in terms of specific loss power (SLP or specific absorption rate, SAR) and dynamic hysteresis. In particular, we aimed to investigate how this SLP depends on the transition from Néelian to Brownian behavior of nanoparticles expected to occur between 10 nm and 20 nm (for maghemite) and dependent on the viscosity. While we observed a good agreement between calorimetric and dynamic hysteresis measurements, we found that the SLP measured for the different systems do not depend noticeably on the viscosity of solvent. Calculations performed according to Rosensweig's linear model [1] allow us to quantitatively reproduce our results at low field intensities, provided we use a value for the magnetic anisotropy constant much smaller than the one commonly used in the literature. This raises the question of the temperature dependance of the magnetic anisotropy constant and its relevance for a quantitative description of MFH.

  8. DNA as a Model for Probing Polymer Entanglements: Circular Polymers and Non-Classical Dynamics

    Directory of Open Access Journals (Sweden)

    Kathryn Regan

    2016-09-01

    Full Text Available Double-stranded DNA offers a robust platform for investigating fundamental questions regarding the dynamics of entangled polymer solutions. The exceptional monodispersity and multiple naturally occurring topologies of DNA, as well as a wide range of tunable lengths and concentrations that encompass the entanglement regime, enable direct testing of molecular-level entanglement theories and corresponding scaling laws. DNA is also amenable to a wide range of techniques from passive to nonlinear measurements and from single-molecule to bulk macroscopic experiments. Over the past two decades, researchers have developed methods to directly visualize and manipulate single entangled DNA molecules in steady-state and stressed conditions using fluorescence microscopy, particle tracking and optical tweezers. Developments in microfluidics, microrheology and bulk rheology have also enabled characterization of the viscoelastic response of entangled DNA from molecular levels to macroscopic scales and over timescales that span from linear to nonlinear regimes. Experiments using DNA have uniquely elucidated the debated entanglement properties of circular polymers and blends of linear and circular polymers. Experiments have also revealed important lengthscale and timescale dependent entanglement dynamics not predicted by classical tube models, both validating and refuting new proposed extensions and alternatives to tube theory and motivating further theoretical work to describe the rich dynamics exhibited in entangled polymer systems.

  9. Probing ultrafast carrier dynamics, nonlinear absorption and refraction in core–shell silicon nanowires

    Indian Academy of Sciences (India)

    Sunil Kumar; M Khorasaninejad; M M Adachi; K S Karim; S S Saini; A K Sood

    2012-09-01

    We investigate the relaxation dynamics of photogenerated carriers in silicon nanowires consisting of a crystalline core and a surrounding amorphous shell, using femtosecond time resolved differential reflectivity and transmission spectroscopy at 3.15 eV and 1.57 eV photon energies. The complex behaviour of the differential transmission and reflectivity transients is the mixed contributions from the crystalline core and the amorphous silicon on the nanowire surface and the substrate where competing effects of state-filling and photoinduced absorption govern the carrier dynamics. Faster relaxation rates are observed on increasing the photogenerated carrier density. Independent experimental results on crystalline silicon-on-sapphire (SOS) help us in separating the contributions from the carrier dynamics in crystalline core and the amorphous regions in the nanowire samples. Further, single-beam z-scan nonlinear transmission experiments at 1.57 eV in both open- and close-aperture configurations yield two-photon absorption coefficient (∼3 cm/GW) and nonlinear refraction coefficient (−2.5 × 10−4 cm2 /GW).

  10. Einstein Probe - a small mission to monitor and explore the dynamic X-ray Universe

    CERN Document Server

    Yuan, Weimin; Feng, H; Zhang, S N; Ling, Z X; Zhao, D; Deng, J; Qiu, Y; Osborne, J P; O'Brien, P; Willingale, R; Lapington, J; Fraser, G W

    2015-01-01

    Einstein Probe is a small mission dedicated to time-domain high-energy astrophysics. Its primary goals are to discover high-energy transients and to monitor variable objects in the $0.5-4~$keV X-rays, at higher sensitivity by one order of magnitude than those of the ones currently in orbit. Its wide-field imaging capability, featuring a large instantaneous field-of-view ($60^\\circ \\times60^\\circ$, $\\sim1.1$sr), is achieved by using established technology of micro-pore (MPO) lobster-eye optics, thereby offering unprecedentedly high sensitivity and large Grasp. To complement this powerful monitoring ability, it also carries a narrow-field, sensitive follow-up X-ray telescope based on the same MPO technology to perform follow-up observations of newly-discovered transients. Public transient alerts will be downlinked rapidly, so as to trigger multi-wavelength follow-up observations from the world-wide community. Over three of its 97-minute orbits almost the entire night sky will be sampled, with cadences ranging f...

  11. Probing BL Lac and Cluster Evolution via a Wide-angle, Deep X-ray Selected Sample

    Science.gov (United States)

    Perlman, E.; Jones, L.; White, N.; Angelini, L.; Giommi, P.; McHardy, I.; Wegner, G.

    1994-12-01

    The WARPS survey (Wide-Angle ROSAT Pointed Survey) has been constructed from the archive of all public ROSAT PSPC observations, and is a subset of the WGACAT catalog. WARPS will include a complete sample of >= 100 BL Lacs at F_x >= 10(-13) erg s(-1) cm(-2) . A second selection technique will identify ~ 100 clusters at 0.15 = 0.304 +/- 0.062 for XBLs but = 0.60 +/- 0.05 for RBLs. Models of the X-ray luminosity function (XLF) are also poorly constrained. WARPS will allow us to compute an accurate XLF, decreasing the error bars above by over a factor of two. We will also test for low-luminosity BL Lacs, whose non-thermal nuclear sources are dim compared to the host galaxy. Browne and Marcha (1993) claim the EMSS missed most of these objects and is incomplete. If their predictions are correct, 20-40% of the BL Lacs we find will fall in this category, enabling us to probe the evolution and internal workings of BL Lacs at lower luminosities than ever before. By removing likely QSOs before optical spectroscopy, WARPS requires only modest amounts of telescope time. It will extend measurement of the cluster XLF both to higher redshifts (z>0.5) and lower luminosities (LX<1x10(44) erg s(-1) ) than previous measurements, confirming or rejecting the 3sigma detection of negative evolution found in the EMSS, and constraining Cold Dark Matter cosmologies. Faint NELGs are a recently discovered major contributor to the X-ray background. They are a mixture of Sy2s, starbursts and galaxies of unknown type. Detailed classification and evolution of their XLF will be determined for the first time.

  12. Light, Molecules, Action: Using Ultrafast Uv-Visible and X-Ray Spectroscopy to Probe Excited State Dynamics in Photoactive Molecules

    Science.gov (United States)

    Sension, R. J.

    2017-06-01

    Light provides a versatile energy source capable of precise manipulation of material systems on size scales ranging from molecular to macroscopic. Photochemistry provides the means for transforming light energy from photon to process via movement of charge, a change in shape, a change in size, or the cleavage of a bond. Photochemistry produces action. In the work to be presented here ultrafast UV-Visible pump-probe, and pump-repump-probe methods have been used to probe the excited state dynamics of stilbene-based molecular motors, cyclohexadiene-based switches, and polyene-based photoacids. Both ultrafast UV-Visible and X-ray absorption spectroscopies have been applied to the study of cobalamin (vitamin B_{12}) based compounds. Optical measurements provide precise characterization of spectroscopic signatures of the intermediate species on the S_{1} surface, while time-resolved XANES spectra at the Co K-edge probe the structural changes that accompany these transformations.

  13. A streptavidin paramagnetic-particle based competition assay for the evaluation of the optical selectivity of quadruplex nucleic acid fluorescent probes.

    Science.gov (United States)

    Largy, Eric; Hamon, Florian; Teulade-Fichou, Marie-Paule

    2012-05-01

    Although quadruplex nucleic acids are thought to be involved in many biological processes, they are massively overwhelmed by duplex DNA in the cell. Small molecules, able to probe quadruplex nucleic acids with high optical selectivity, could possibly achieve the visualization of these processes. The aim of the method described herein is to evaluate quickly the optical selectivity of quadruplex nucleic acid probes, in isothermal conditions, using widely available materials, small quantities of oligonucleotides and virtually any kind and quantity of biological competitor. The assay relies on the use of streptavidin-coated paramagnetic particles and biotinylated quadruplex forming oligonucleotides, allowing a quick and easy separation of the quadruplex target from the competitor. In the present study, two quadruplex nucleic acids (the DNA and RNA human telomeric repeats) have been used as targets while a duplex DNA oligonucleotide, total DNA, total RNA, another quadruplex nucleic acid and a protein have been used as competitors. The optical selectivity of various probes, displaying different photophysical properties and binding selectivities, has been successfully examined, allowing the identification of a best candidate for further cell microscopy experiments. This assay allows a quick and reliable assessment of the labeling properties of a quadruplex binder in cellular environment conditions. It is an interesting alternative to gel electrophoresis experiments since it is performed in solution, has a well-resolved separation system and allows easy quantifications.

  14. Probing the assembly and dynamics of graphene-inspired molecular wires by solid-state NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, Michael Ryan; Graf, Robert; Sebastiani, Daniel; Spiess, Hans-Wolfgang [Max Planck Institute for Polymer Research, Mainz (Germany)

    2010-07-01

    Molecular wires based on polycyclic aromatic hydrocarbons (PAHs) are a promising class of materials for future applications in nano-scale electronic devices. Critical for the performance of such wires are their molecular assembly, which on the NMR length and time scales translates into the local packing arrangement, molecular dynamics, and pitch angle(s) between successive molecules. Here, we show that solid-state NMR in combination with MD and ab-initio calculations can provide unique information with respect to these structural features. To illustrate this we examine two perylene tetracarboxydiimides (PDIs) with different side chains attached and a larger triangular-shaped PAH. Specifically, we measure 1H chemical shifts using fast MAS and their spatial connectivities through 2D 1H-1H DQ-SQ correlation spectra and probe the molecular dynamics via 1H-13C heteronuclear dipolar couplings. To support the experimental findings we have performed CPMD-NMR calculations to reveal the effects of packing on the 1H chemical shifts for the PDIs, including an estimate of the line broadening due to local disorder. This provides a series of finger prints for different pitch angles between neighboring molecules, that are closely related to the electronic conduction properties of the supramolecular stacks.

  15. Facial expression movement enhances the measurement of temporal dynamics of attentional bias in the dot-probe task.

    Science.gov (United States)

    Caudek, Corrado; Ceccarini, Francesco; Sica, Claudio

    2017-08-01

    The facial dot-probe task is one of the most common experimental paradigms used to assess attentional bias toward emotional information. In recent years, however, the psychometric properties of this paradigm have been questioned. In the present study, attentional bias to emotional face stimuli was measured with dynamic and static images of realistic human faces in 97 college students (63 women) who underwent either a positive or a negative mood-induction prior to the experiment. We controlled the bottom-up salience of the stimuli in order to dissociate the top-down orienting of attention from the effects of the bottom-up physical properties of the stimuli. A Bayesian analysis of our results indicates that 1) the traditional global attentional bias index shows a low reliability, 2) reliability increases dramatically when biased attention is analyzed by extracting a series of bias estimations from trial-to-trial (Zvielli, Bernstein, & Koster, 2015), 3) dynamic expression of emotions strengthens biased attention to emotional information, and 4) mood-congruency facilitates the measurement of biased attention to emotional stimuli. These results highlight the importance of using ecologically valid stimuli in attentional bias research, together with the importance of estimating biased attention at the trial level. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Dynamic behaviors of a broad-area diode laser with lateral-mode-selected external feedback

    DEFF Research Database (Denmark)

    Chi, Mingjun; Petersen, Paul Michael

    2014-01-01

    In this paper, we investigate the dynamics of a BAL with lateral-mode selected external feedback experimentally by measuring the far-field profile, intensity noise spectrum and time series of the output beam. The mode-selection is achieved by adjusting a stripe mirror at the pseudo far-field plan...... with a frequency of the single roundtrip external-cavity loop modulated by periodic low-frequency fluctuation. This is the first observation of pulse-package oscillation in a diode laser with long-cavity feedback, to our knowledge........ Different dynamic behaviors are observed when different lateral modes are selected. When the mirror is aligned correctly and high-order modes are selected, in most of the cases periodic dynamics of the output power corresponding to a single roundtrip external-cavity loop is observed, but the dynamic...

  17. Selective host molecules obtained by dynamic adaptive chemistry.

    Science.gov (United States)

    Matache, Mihaela; Bogdan, Elena; Hădade, Niculina D

    2014-02-17

    Up till 20 years ago, in order to endow molecules with function there were two mainstream lines of thought. One was to rationally design the positioning of chemical functionalities within candidate molecules, followed by an iterative synthesis-optimization process. The second was the use of a "brutal force" approach of combinatorial chemistry coupled with advanced screening for function. Although both methods provided important results, "rational design" often resulted in time-consuming efforts of modeling and synthesis only to find that the candidate molecule was not performing the designed job. "Combinatorial chemistry" suffered from a fundamental limitation related to the focusing of the libraries employed, often using lead compounds that limit its scope. Dynamic constitutional chemistry has developed as a combination of the two approaches above. Through the rational use of reversible chemical bonds together with a large plethora of precursor libraries, one is now able to build functional structures, ranging from quite simple molecules up to large polymeric structures. Thus, by introduction of the dynamic component within the molecular recognition processes, a new perspective of deciphering the world of the molecular events has aroused together with a new field of chemistry. Since its birth dynamic constitutional chemistry has continuously gained attention, in particular due to its ability to easily create from scratch outstanding molecular structures as well as the addition of adaptive features. The fundamental concepts defining the dynamic constitutional chemistry have been continuously extended to currently place it at the intersection between the supramolecular chemistry and newly defined adaptive chemistry, a pivotal feature towards evolutive chemistry. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Dynamic Portfolio Selection on Croatian Financial Markets: MGARCH Approach

    Directory of Open Access Journals (Sweden)

    Škrinjarić Tihana

    2016-09-01

    Full Text Available Background: Investors on financial markets are interested in finding trading strategies which could enable them to beat the market. They always look for best possibilities to achieve above-average returns and manage risks successfully. MGARCH methodology (Multivariate Generalized Autoregressive Conditional Heteroskedasticity makes it possible to model changing risks and return dynamics on financial markets on a daily basis. The results could be used in order to enhance portfolio formation and restructuring over time.

  19. Dynamics of Hydrophobic Core Phenylalanine Residues Probed by Solid-State Deuteron NMR

    Energy Technology Data Exchange (ETDEWEB)

    Vugmeyster, Liliya; Ostrovsky, Dmitry; Villafranca, Toni; Sharp, Janelle; Xu, Wei; Lipton, Andrew S.; Hoatson, Gina; Vold, Robert L.

    2015-11-03

    We conducted a detailed investigation of the dynamics of two phenylalanine side chains in the hydrophobic core of the villin headpiece subdomain protein (HP36) in the hydrated powder state over the 298–80 K temperature range. We utilized static deuteron NMR measurements of longitudinal relaxation and line shapes supplemented with computational modeling. The temperature dependence of the relaxation times reveals the presence of two main mechanisms that can be attributed to the ring-flips, dominating at high temperatures, and small-angle fluctuations, dominating at low temperatures. The relaxation is non- exponential at all temperatures with the extent of non-exponentiality increasing from higher to lower temperatures. This behavior suggests a distribution of conformers with unique values of activation energies. The central values of the activation energies for the ring-flipping motions are among the smallest reported for aromatic residues in peptides and proteins and point to a very mobile hydrophobic core. The analysis of the widths of the distributions, in combination with the earlier results on the dynamics of flanking methyl groups (Vugmeyster et al., J. Phys. Chem. 2013, 117, 6129–6137), suggests that the hydrophobic core undergoes concerted fluctuations. There is a pronounced effect of dehydration on the ring-flipping motions, which shifts the distribution toward more rigid conformers. The cross-over temperature between the regions of dominance of the small-angle fluctuations and ring-flips shifts from 195 K in the hydrated protein to 278 K in the dry one. This result points to the role of solvent in the onset of the concerted fluctuations of the core and highlights aromatic residues as markers of the protein dynamical transitions.

  20. MaRIE: Probing Dynamic Processes in Soft Materials Using Advanced Light Sources

    Energy Technology Data Exchange (ETDEWEB)

    Sykora, Milan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Kober, Edward Martin [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-02-16

    Los Alamos National Laboratory has developed a concept for a new research facility, MaRIE: Matter-Radiation Interactions in Extremes. The key motivation for MaRIE is to develop new experimental capabilities needed to fill the existing gaps in our fundamental understanding of materials important for key National Nuclear Security Agency (NNSA) goals. MaRIE will bring two major new capabilities: (a) the ability to characterize the meso- and microstructure of materials in bulk as well as local dynamic response characteristics, and (b) the ability to characterize how this microstructure evolves under NNSA-relevant conditions and impacts the material’s performance in this regime.

  1. Probing carrier dynamics of individual layers in a heterostructure using transient reflectivity

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Salahuddin; Jayabalan, J., E-mail: jjaya@rrcat.gov.in; Singh, Asha; Yogi, Rachana; Chari, Rama [Laser Physics Applications Section, Raja Ramanna Centre for Advanced Technology, Indore 452013 (India)

    2015-09-21

    We report the wavelength dependent transient reflectivity measurements in AlGaAs-GaAs heterostructures having two-dimensional electron (or hole) gas near the interface. Using a multilayer model for transient reflectivity, we show that the magnitude and sign of contributions from the carriers in two-dimensional electron (or hole) gas and GaAs to the total signal depends on the wavelength. Further, it has been shown that it is possible to study the carrier dynamics in a given layer of a heterostructure by performing transient reflectivity at specific wavelengths.

  2. Neural and temporal dynamics underlying visual selection for action

    NARCIS (Netherlands)

    Elk, M. van; Schie, H.T. van; Neggers, S.F.W.; Bekkering, H.

    2010-01-01

    The present study investigated the selection for action hypothesis, according to which a subject's action intention to perform a movement influences the way in which visual information is being processed. Subjects were instructed in separate blocks either to grasp or to point to a three-dimensional

  3. An objective method for High Dynamic Range source content selection

    DEFF Research Database (Denmark)

    Narwaria, Manish; Mantel, Claire; Da Silva, Matthieu Perreira

    2014-01-01

    component of such validation studies is the selection of a challenging and balanced set of source (reference) HDR content. In order to facilitate this, we present an objective method based on the premise that a more challenging HDR scene encapsulates higher contrast, and as a result will show up more...

  4. A Dynamic Supramolecular System Exhibiting Substrate Selectivity in the Catalytic Epoxidation of Olefins

    DEFF Research Database (Denmark)

    Jonsson, Stefan; Odille, Fabrice G. J.; Norrby, Per-Ola;

    2005-01-01

    A dynamic supramolecular system involving hydrogen bonding between a Mn(III) salen catalyst and a Zn(II) porphyrin receptor exhibits selectivity for pyridine appended cis-beta-substituted styrene derivatives over phenyl appended derivatives in a catalytic epoxidation reaction.......A dynamic supramolecular system involving hydrogen bonding between a Mn(III) salen catalyst and a Zn(II) porphyrin receptor exhibits selectivity for pyridine appended cis-beta-substituted styrene derivatives over phenyl appended derivatives in a catalytic epoxidation reaction....

  5. Relaxation dynamics in the excited states of a ketocyanine dye probed by femtosecond transient absorption spectroscopy

    Indian Academy of Sciences (India)

    Jahur A Mondal; Sandeep Verma; Hirendra N Ghosh; Dipak K Palit

    2008-01-01

    Relaxation dynamics of the excited singlet states of 2,5-bis-(N-methyl-N-1,3-propdienylaniline)-cyclopentanone (MPAC), a ketocyanine dye, have been investigated using steady-state absorption and emission as well as femtosecond time-resolved absorption spectroscopic techniques. Following photoexcitation using 400 nm light, the molecule is excited to the S2 state, which is fluorescent in rigid matrices at 77 K. S2 state is nearly non-fluorescent in solution and has a very short lifetime (0.5 ± 0.2 ps). In polar aprotic solvents, the S1 state follows a complex multi-exponential relaxation dynamics consisting of torsional motion of the donor groups, solvent re-organization as well as photoisomerization processes. However, in alcoholic solvents, solvent re-organization via intermolecular hydrogen-bonding interaction is the only relaxation process observed in the S1 state. In trifluoroethanol, a strong hydrogen bonding solvent, conversion of the non-hydrogen-bonded form, which is formed following photoexcitation, to the hydrogen-bonded complex has been clearly evident in the relaxation process of the S1 state.

  6. Probing charge transfer dynamics in self-assembled monolayers by core hole clock approach

    Energy Technology Data Exchange (ETDEWEB)

    Zharnikov, Michael, E-mail: Michael.Zharnikov@urz.uni-heidelberg.de

    2015-04-15

    This article reviews recent progress in the application of core hole clock approach in the framework of resonant Auger electron spectroscopy to the monomolecular assembles of alkyl, oligophenyl, and oligo(phenylene–ethynylene) based molecules on Au(1 1 1) substrates, referring mostly to the work by the author et al. The major goal was to study electron transfer (ET) dynamics in these systems serving as prototypes of molecular electronics (ME) devices. The ET pathway to the conductive substrate was unambiguously defined by resonant excitation of the nitrile tailgroup attached to the molecular backbone. Characteristic ET times within the femtosecond domain were determined, along with the attenuation factors for the ET dynamics, analogous to the case of the static transport. The above parameters were found to exhibit strong dependence on the character of the molecular orbital which mediates the ET process. In addition, certain spectral features, which can be associated with an inverse ET from the molecular backbone to the excitation site, were observed upon exchange of the nitrile group by strongly electronegative nitro moiety. The reported results represent a valuable input for theory and a certain potential for applications such as ME devices where optimization of ET can have significant technological impact.

  7. Photo-induced dynamics in heterocyclic aromatic molecules probed by femtosecond XUV transient absorption spectroscopy

    Science.gov (United States)

    Lackner, Florian; Chatterley, Adam S.; Pemmaraju, Chaitanya D.; Neumark, Daniel M.; Leone, Stephen R.; Gessner, Oliver

    2016-05-01

    We report on the ring-opening and dissociation dynamics of strong-field ionized selenophene (C4 H4 Se), studied by transient XUV absorption spectroscopy at the Se 3d edge. The table-top experiments are facilitated by high-order harmonic generation coupled with a gas phase transient XUV absorption setup that is optimized for the study of organic compounds. Employing element-specific core-to-valence transitions, the ultrafast molecular dynamics are monitored from the perspective of the well-localized Se atoms. Spectral features are assigned based on first principles TDDFT calculations for a large manifold of electronic states. We observe signatures of rapidly (~ 35 fs) decaying highly excited molecular cations, the formation of ring-opened products on a 100 fs time scale and, most notably, the elimination of bare Se+ ions in a very rapid multi-step process. A delayed onset of the Se+ ions provides direct evidence that both selenium-carbon bonds are broken within only ~ 130 fs and that a sequential mechanism, presumably an initial ring-opening followed by a subsequent breaking of the second bond, is required to eliminate the atomic fragments.

  8. Probing the Evaporation Dynamics of Ethanol/Gasoline Biofuel Blends Using Single Droplet Manipulation Techniques.

    Science.gov (United States)

    Corsetti, Stella; Miles, Rachael E H; McDonald, Craig; Belotti, Yuri; Reid, Jonathan P; Kiefer, Johannes; McGloin, David

    2015-12-24

    Using blends of bioethanol and gasoline as automotive fuel leads to a net decrease in the production of harmful emission compared to the use of pure fossil fuel. However, fuel droplet evaporation dynamics change depending on the mixing ratio. Here we use single particle manipulation techniques to study the evaporation dynamics of ethanol/gasoline blend microdroplets. The use of an electrodynamic balance enables measurements of the evaporation of individual droplets in a controlled environment, while optical tweezers facilitate studies of the behavior of droplets inside a spray. Hence, the combination of both methods is perfectly suited to obtain a complete picture of the evaporation process. The influence of adding varied amounts of ethanol to gasoline is investigated, and we observe that droplets with a greater fraction of ethanol take longer to evaporate. Furthermore, we find that our methods are sensitive enough to observe the presence of trace amounts of water in the droplets. A theoretical model, predicting the evaporation of ethanol and gasoline droplets in dry nitrogen gas, is used to explain the experimental results. Also a theoretical estimation of the saturation of the environment, with other aerosols, in the tweezers is carried out.

  9. Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory.

    Science.gov (United States)

    Buchner, Ginka S; Murphy, Ronan D; Buchete, Nicolae-Viorel; Kubelka, Jan

    2011-08-01

    The problem of spontaneous folding of amino acid chains into highly organized, biologically functional three-dimensional protein structures continues to challenge the modern science. Understanding how proteins fold requires characterization of the underlying energy landscapes as well as the dynamics of the polypeptide chains in all stages of the folding process. In recent years, important advances toward these goals have been achieved owing to the rapidly growing interdisciplinary interest and significant progress in both experimental techniques and theoretical methods. Improvements in the experimental time resolution led to determination of the timescales of the important elementary events in folding, such as formation of secondary structure and tertiary contacts. Sensitive single molecule methods made possible probing the distributions of the unfolded and folded states and following the folding reaction of individual protein molecules. Discovery of proteins that fold in microseconds opened the possibility of atomic-level theoretical simulations of folding and their direct comparisons with experimental data, as well as of direct experimental observation of the barrier-less folding transition. The ultra-fast folding also brought new questions, concerning the intrinsic limits of the folding rates and experimental signatures of barrier-less "downhill" folding. These problems will require novel approaches for even more detailed experimental investigations of the folding dynamics as well as for the analysis of the folding kinetic data. For theoretical simulations of folding, a main challenge is how to extract the relevant information from overwhelmingly detailed atomistic trajectories. New theoretical methods have been devised to allow a systematic approach towards a quantitative analysis of the kinetic network of folding-unfolding transitions between various configuration states of a protein, revealing the transition states and the associated folding pathways at

  10. Highly selective detection of bacterial alarmone ppGpp with an off-on fluorescent probe of copper-mediated silver nanoclusters.

    Science.gov (United States)

    Zhang, Pu; Wang, Yi; Chang, Yong; Xiong, Zu Hong; Huang, Cheng Zhi

    2013-11-15

    In this study, a facile strategy for highly selective and sensitive detection of bacterial alarmone, ppGpp, which is generated when bacteria face stress circumstances such as nutritional deprivation, has been established by developing an off-on fluorescent probe of Cu(2+)-mediated silver nanoclusters (Ag NCs). This work not only achieves highly selective detection of ppGpp in a broad range concentration of 2-200 μM, but also improves our understanding of the specific recognitions among DNA-Ag NCs, Cu(2+), and ppGpp. The present strategy, together with other reports on the Ag NCs-related analytical methods, has also identified that Ag NCs functionalized with different molecules on their surfaces can be engineered fluorescent probes for a wide range of applications such as biosensing and bioimaging.

  11. Vibrational spectroscopy and dynamics of W(CO)6 in solid methane as a probe of lattice properties

    Science.gov (United States)

    Thon, Raphael; Chin, Wutharath; Chamma, Didier; Galaup, Jean-Pierre; Ouvrard, Aimeric; Bourguignon, Bernard; Crépin, Claudine

    2016-12-01

    Methane solids present more than one accessible crystalline phase at low temperature at zero pressure. We trap W(CO)6 in CH4 and CD4 matrices between 8 and 35 K to probe the interaction between an impurity and its surrounding molecular solid under various physical conditions. Linear and nonlinear vibrational spectroscopies of W(CO)6 highlight different kinds of interaction and reveal new and remarkable signatures of the phase transition of methane. The structures in the absorption band of the antisymmetric CO stretching mode exhibit a clear modification at the transition between phase II and phase I in CH4 and motional narrowing is observed upon temperature increase. The vibrational dynamics of this mode is probed in stimulated photon echo experiments performed with a femtosecond IR laser. A short component around 10 ps is detected in the population relaxation lifetime in the high temperature phase of solid CH4 (phase I) and disappears at lower temperatures (phase II) where the vibrational lifetime is in the hundreds of ps. The analysis of the nonlinear time-resolved results suggests that the short component comes from a fast energy transfer between the vibrational excitation of the guest and the lattice in specific families of sites. Such fast transfers are observed in the case of W(CO)6 trapped in CD4 because of an energy overlap of the excitation of W(CO)6 and a lattice vibron. In solid CH4, even when these V-V transfers are not efficient, pure dephasing processes due to the molecular nature of the host occur: they are temperature dependent without a clear modification at the phase transition.

  12. Sexual selection and physical attractiveness : Implications for mating dynamics.

    Science.gov (United States)

    Gangestad, S W

    1993-09-01

    Sexual selection processes have received much attention in recent years, attention reflected in interest in human mate preferences. Among these mate preferences are preferences for physical attractiveness. Preferences in and of themselves, however, do not fully explain the nature of the relationships that individuals attain. A tacit negotiation process underlies relationship formation and maintenance. The notion that preferences for physical attractiveness evolved under parasite-driven "good genes" sexual selection leads to predictions about the nature of trade-offs that individuals make between mates' physical attractiveness and investment potential. These predictions and relevant data are explored, with a primary emphasis on women's preferences for men's qualities. In addition, further implications of trade-offs are examined, most notably (a) the impact of environmental variations on the nature of mating and (b) some effects of trade-offs on infidelity and male attempts to control women.

  13. Probing BFKL dynamics in Mueller-Navelet jet production at the LHC

    CERN Document Server

    Ducloué, B; Wallon, S

    2016-01-01

    We review the results of our studies on the production of two jets with a large interval of rapidity at hadron colliders, which was proposed by Mueller and Navelet as a possible test of the high energy dynamics of QCD, within the next-to-leading logarithm framework. The application of the Brodsky-Lepage-Mackenzie procedure to fix the renormalization scale leads to a very good description of the available CMS data at the LHC for the azimuthal correlations of the jets. We show that the inclusion of next-to-leading order corrections to the jet vertex significantly reduces the importance of energy-momentum non-conservation which is inherent to the BFKL approach, for an asymmetric jet configuration.

  14. Probing Dynamics at Interfaces: Molecular Motions in Lipid Bilayers studied by Neutron Backscattering

    CERN Document Server

    Rheinstädter, M C; Salditt, T; Rheinst\\"adter, Maikel C.; Seydel, Tilo; Salditt, Tim

    2004-01-01

    Lipid membranes in a physiological context cannot be understood without taking into account their mobile environment. Here, we report on a high energy-resolution neutron backscattering study to investigate slow motions on nanosecond time scales in highly oriented solid supported phospholipid bilayers of the model system DMPC -d54 (deuterated 1,2-dimyristoyl-sn-glycero-3-phoshatidylcholine). This technique allows discriminating the Q-dependent onset of mobility and provides a benchmark test regarding the feasibility of dynamical neutron scattering investigations on these sample systems. Apart from freezing of the lipid acyl-chains, we could observe a second freezing temperature that we attribute to the hydration water in between the membrane stacks. The freezing is lowered several degrees as compared to (heavy) bulk water.

  15. Molecular dynamics of dissociative ionization in OCS probed by soft X-ray synchrotron radiation

    CERN Document Server

    Ramadhan, Ali; Gauthier, Isabelle; Karimi, Reza; MacDonald, Michael; Zuin, Lucia; Sanderson, Joe

    2016-01-01

    Soft X-rays (90-173 eV) from the 3rd generation Canadian Light Source have been used in conjunction with a multi coincidence time and position sensitive detection apparatus to observe the dissociative ionization of OCS. By varying the X-ray energy we can compare dynamics from direct and Auger ionization processes, and access ionization channels which result in two or three body breakup, from 2+ to 4+ ionization states. We make several new observations for the 3+ state such as kinetic energy release limited by photon energy, and using Dalitz plots we can see evidence of timescale effects between the direct and Auger ionization process for the first time. Finally, using Dalitz plots for OCS$^{4+}$ we observe for the first time that breakup involving an O$^{2+}$ ion can only proceed from out of equilibrium nuclear arrangement for S(2p) Auger ionization.

  16. Probing the QCD phase diagram with dileptons - a study using coarse-grained transport dynamics

    CERN Document Server

    Endres, Stephan; Bleicher, Marcus

    2016-01-01

    Dilepton production in heavy-ion collisions at various energies is studied using coarse-grained transport simulations. Microscopic output from the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) model is hereby put on a grid of space-time cells which allows to extract the local temperature and chemical potential in each cell via an equation of state. The dilepton emission is then calculated applying in-medium spectral functions from hadronic many-body theory and partonic production rates based on lattice calculations. The comparison of the resulting spectra with experimental data shows that the dilepton excess beyond the decay contributions from a hadronic cocktail reflects the trajectory of the fireball in the $T-\\mu_{\\mathrm{B}}$ plane of the QCD phase diagram.

  17. Dynamics of graphite fiber intercalation: In situ resistivity measurements with a four point probe

    Science.gov (United States)

    Jaworske, D. A.

    1984-01-01

    The dynamics of ferric chloride intercalation of single graphite fibers were studied, in situ, using a four point dc bridge. Measurements before, during and after the intercalation showed that the intercalation occurred within minutes at 200 C. Changes in fiber resistivity after exposure to air suggested hydration of the graphite intercalation compound. Deintercalation of the ferric chloride was initiated at temperatures in excess of 400 C. cycling the intercalant into and out of the graphite fiber gave no improvements in fiber resistivity. The activation energy of the ferric chloride intercalation reaction was found to be 17 + or - 4 kcal/mol 1 consistent with the concept of a preliminary nucleation step in the intercalation reaction.

  18. High-harmonic probing of electronic coherence in dynamically aligned molecules

    CERN Document Server

    Kraus, P M; Gijsbertsen, A; Lucchese, R R; Rohringer, N; Wörner, H J

    2013-01-01

    We introduce and demonstrate a new approach to measuring coherent electron wave packets using high-harmonic spectroscopy. By preparing a molecule in a coherent superposition of electronic states, we show that electronic coherence opens previously unobserved high-harmonic-generation channels that connect distinct but coherently related electronic states. Performing the measurements in dynamically aligned nitric oxide (NO) molecules we observe the complex temporal evolution of the electronic coherence under coupling to nuclear motion. Choosing a weakly allowed transition to prepare the wave packet, we demonstrate an unprecedented sensitivity that arises from optical interference between coherent and incoherent pathways. This mechanism converts a 0.1 $%$ excitation fraction into a $\\sim$20 $%$ signal modulation.

  19. Surface dielectric relaxation: probing technique and its application to thermal activation dynamics of polymer surface.

    Science.gov (United States)

    Ishii, Masashi

    2010-09-01

    For dynamic analyses of a polymer surface, a dielectric relaxation measurement technique with parallel electrodes placed away from the surface was developed. In this technique, a liquid heating medium was filled in the space between the polymer surface and the electrodes. The construction that maintains the surface can clarify the physical interactions between the liquid and the bare surface and controlling the temperature of the liquid reveals the thermal activation property of the surface. The dielectric relaxation spectrum of the surface convoluted into the bulk and liquid spectra can be obtained by a reactance analysis and the surface spectrum is expressed with an equivalent resistance-capacitance parallel circuit. On the basis of the electromechanical analogy, the electric elements can be converted into mechanical elements that indicate the viscoelasticity of the polymer surface. Using these measurement and analysis techniques, the electric and mechanical properties of the surface of a gelatinized chloroprene rubber sample were analyzed.

  20. Architectural mechanisms for dynamic changes of behavior selection strategies in behavior-based systems.

    Science.gov (United States)

    Scheutz, Matthias; Andronache, Virgil

    2004-12-01

    Behavior selection is typically a "built-in" feature of behavior-based architectures and hence, not amenable to change. There are, however, circumstances where changing behavior selection strategies is useful and can lead to better performance. In this paper, we demonstrate that such dynamic changes of behavior selection mechanisms are beneficial in several circumstances. We first categorize existing behavior selection mechanisms along three dimensions and then discuss seven possible circumstances where dynamically switching among them can be beneficial. Using the agent architecture framework activation, priority, observer, and component (APOC), we show how instances of all (nonempty) categories can be captured and how additional architectural mechanisms can be added to allow for dynamic switching among them. In particular, we propose a generic architecture for dynamic behavior selection, which can integrate existing behavior selection mechanisms in a unified way. Based on this generic architecture, we then verify that dynamic behavior selection is beneficial in the seven cases by defining architectures for simulated and robotic agents and performing experiments with them. The quantitative and qualitative analyzes of the results obtained from extensive simulation studies and experimental runs with robots verify the utility of the proposed mechanisms.

  1. Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations.

    Science.gov (United States)

    Lau, Pick-Wei; Grossfield, Alan; Feller, Scott E; Pitman, Michael C; Brown, Michael F

    2007-09-28

    Rhodopsin is currently the only available atomic-resolution template for understanding biological functions of the G protein-coupled receptor (GPCR) family. The structural basis for the phenomenal dark state stability of 11-cis-retinal bound to rhodopsin and its ultrafast photoreaction are active topics of research. In particular, the beta-ionone ring of the retinylidene inverse agonist is crucial for the activation mechanism. We analyzed a total of 23 independent, 100 ns all-atom molecular dynamics simulations of rhodopsin embedded in a lipid bilayer in the microcanonical (N,V,E) ensemble. Analysis of intramolecular fluctuations predicts hydrogen-out-of-plane (HOOP) wagging modes of retinal consistent with those found in Raman vibrational spectroscopy. We show that sampling and ergodicity of the ensemble of simulations are crucial for determining the distribution of conformers of retinal bound to rhodopsin. The polyene chain is rigidly locked into a single, twisted conformation, consistent with the function of retinal as an inverse agonist in the dark state. Most surprisingly, the beta-ionone ring is mobile within its binding pocket; interactions are non-specific and the cavity is sufficiently large to enable structural heterogeneity. We find that retinal occupies two distinct conformations in the dark state, contrary to most previous assumptions. The beta-ionone ring can rotate relative to the polyene chain, thereby populating both positively and negatively twisted 6-s-cis enantiomers. This result, while unexpected, strongly agrees with experimental solid-state (2)H NMR spectra. Correlation analysis identifies the residues most critical to controlling mobility of retinal; we find that Trp265 moves away from the ionone ring prior to any conformational transition. Our findings reinforce how molecular dynamics simulations can challenge conventional assumptions for interpreting experimental data, especially where existing models neglect conformational fluctuations.

  2. Use of the nitrile oxide cycloaddition (NOC) reaction for molecular probe generation: a new class of enzyme selective histone deacetylase inhibitors (HDACIs) showing picomolar activity at HDAC6.

    Science.gov (United States)

    Kozikowski, Alan P; Tapadar, Subhasish; Luchini, Doris N; Kim, Ki Hwan; Billadeau, Daniel D

    2008-08-14

    A series of hydroxamate based HDAC inhibitors containing a phenylisoxazole as the CAP group has been synthesized using nitrile oxide cycloaddition chemistry. An HDAC6 selective inhibitor having a potency of approximately 2 picomolar was identified. Some of the compounds were examined for their ability to block pancreatic cancer cell growth and found to be about 10-fold more potent than SAHA. This research provides valuable, new molecular probes for use in exploring HDAC biology.

  3. A new fluorescent probe for gasotransmitter H₂S: high sensitivity, excellent selectivity, and a significant fluorescence off-on response.

    Science.gov (United States)

    Zhang, Jingyu; Guo, Wei

    2014-04-25

    A fluorescent off-on probe for H2S was exploited by coupling the azide-based strategy with the excited-state intramolecular proton transfer (ESIPT) sensing mechanism, which exhibits a considerably high fluorescence enhancement (1150-fold), an extremely low detection limit (0.78 nM), and a relatively fast response time (3-10 min) as well as excellent selectivity.

  4. A Near-infrared Fluorescent Probe for Selective Simultaneous Detection of Fe2+ and CI- in Living Cells%A Near-infrared Fluorescent Probe for Selective Simultaneous Detection of Fe2+ and CI- in Living Cells

    Institute of Scientific and Technical Information of China (English)

    李平; 肖海滨; 唐波

    2012-01-01

    A naked-eyed chromo-near infrared fluorescent probe for simultaneous detection of Fe2+ and C1 has been developed, based on photoinduced electron transfer mechanism (PET). The fluorophore is cyanine (Cy-SO3), and the Fe2+ receptor is 4'-(aminomethylphenyl)-2,2',6',2"-terpyridine (Tpy). The probe responds linearly and rapidly to [Fe2+] and [C1 ] variations under physiological conditions and exhibits high sensitivity, good photostability, and excellent cell membrane permeability. The real-time imaging of cellular Fe2+ was achieved successfully in living HL-7702, HepG2, and RAW264.7 cell lines.

  5. Sex ratio selection and multi-factorial sex determination in the housefly : A dynamic model

    NARCIS (Netherlands)

    Kozielska, M.A.; Pen, I.R.; Beukeboom, L.W.; Weissing, F.J.

    Sex determining (SD) mechanisms are highly variable between different taxonomic groups and appear to change relatively quickly during evolution. Sex ratio selection could be a dominant force causing such changes. We investigate theoretically the effect of sex ratio selection on the dynamics of a

  6. Sex ratio selection and multi-factorial sex determination in the housefly : A dynamic model

    NARCIS (Netherlands)

    Kozielska, M.A.; Pen, I.R.; Beukeboom, L.W.; Weissing, F.J.

    2006-01-01

    Sex determining (SD) mechanisms are highly variable between different taxonomic groups and appear to change relatively quickly during evolution. Sex ratio selection could be a dominant force causing such changes. We investigate theoretically the effect of sex ratio selection on the dynamics of a mul

  7. Probing the Interior Dynamics of Jupiter and Saturn with Gravity and Magnetic Fields

    Science.gov (United States)

    Cao, H.; Stevenson, D. J.

    2015-12-01

    The inner working of solar system gas giant planets remain elusive after decades of exploration. One lasting debate concerns the nature of east-west zonal flows observed on the cloud level of these planets with amplitude on the order of 100 m/s: an observational fact is yet to be established about whether these flows are shallow atmospheric dynamics or surface expression of deep interior dynamics. There is a good chance that such an observational fact can be established within the next few years, given the upcoming gravity and magnetic field measurements to be carried out by the Juno mission and the Cassini Grand Finale. In this presentation, I will first describe a critical assessment of the applicability of the thermal wind equation (TWE) in calculating the gravity field associated with deep zonal flows. The TWE, which is a local diagnostic relation, captures the local density variations associated with the zonal flows while neglects the global shape change and density variations with non-local origins. Our analysis shows that the global corrections to the high degree gravity moments are small (less than a few tens of percent). Our analysis also shows that the applicability of the TWE in calculating the gravity moments does depend crucially on retaining the non-sphericity of the background density and gravity. Only when the background non-sphericity of the planet is taken into account in the calculation, the thermal wind equation (TWE) makes accurate enough prediction for the high-degree gravity moments associated with deep zonal flows (with errors less than a few tens of percent). I will then turn to the magnetic signals associated with deep zonal flows. Using mean field dynamo theory (MFDT), we show that detectable magnetic signals are expected: in the spatial domain, poloidal magnetic fields spatially correlated with deep zonal flows are expected; in the temporal domain, periodic oscillations of the poloidal magnetic field are expected. The period of the

  8. Probing the structure and function of biopolymer-carbon nanotube hybrids with molecular dynamics

    Science.gov (United States)

    Johnson, Robert R.

    2009-12-01

    Nanoscience deals with the characterization and manipulation of matter on the atomic/molecular size scale in order to deepen our understanding of condensed matter and develop revolutionary technology. Meeting the demands of the rapidly advancing nanotechnological frontier requires novel, multifunctional nanoscale materials. Among the most promising nanomaterials to fulfill this need are biopolymer-carbon nanotube hybrids (Bio-CNT). Bio-CNT consists of a single-walled carbon nanotube (CNT) coated with a self-assembled layer of biopolymers such as DNA or protein. Experiments have demonstrated that these nanomaterials possess a wide range of technologically useful properties with applications in nanoelectronics, medicine, homeland security, environmental safety and microbiology. However, a fundamental understanding of the self-assembly mechanics, structure and energetics of Bio-CNT is lacking. The objective of this thesis is to address this deficiency through molecular dynamics (MD) simulation, which provides an atomic-scale window into the behavior of this unique nanomaterial. MD shows that Bio-CNT composed of single-stranded DNA (ssDNA) self-assembles via the formation of high affinity contacts between DNA bases and the CNT sidewall. Calculation of the base-CNT binding free energy by thermodynamic integration reveals that these contacts result from the attractive pi--pi stacking interaction. Binding affinities follow the trend G > A > T > C. MD reveals that long ssDNA sequences are driven into a helical wrapping about CNT with a sub-10 nm pitch by electrostatic and torsional interactions in the backbone. A large-scale replica exchange molecular dynamics simulation reveals that ssDNA-CNT hybrids are disordered. At room temperature, ssDNA can reside in several low-energy conformations that contain a sequence-specific arrangement of bases detached from CNT surface. MD demonstrates that protein-CNT hybrids composed of the Coxsackie-adenovirus receptor are biologically

  9. Isotopic and impurity element probes of mesoscale chemical dynamics at mineral fluid interfaces

    Science.gov (United States)

    DePaolo, D. J.

    2012-12-01

    Mesoscale interactions control important Earth processes including the growth of minerals from aqueous solutions and silicate liquids, the diffusion of ions in solids and silicate liquids, and the solid-state deformation and recrystallization that constitutes metamorphism. Most of these processes are typically understood from the classical side in terms of macroscopic physical and thermodynamic properties and classical kinetics, and from the molecular side in terms of single molecule or nearest-neighbor interactions. However, in many cases the controlling processes occur at intermediate scales of both length and time, and involve complex interactions among multiple chemical species. A major limitation has been in characterizing and modeling the dynamic processes that lead to the macroscopic properties and behavior. Advanced microscopy techniques allow phase changes, for example, to be monitored at high resolution, and this capability continues to improve. However, other important information about the phase changes, such as the molecular exchange fluxes between phases and the detailed mechanisms of reaction, are not revealed by microscopy. High-resolution isotopic characterization now allows the molecular exchange fluxes to be quantified, and models suggest that the incorporation of impurity elements is directly tied to these fluxes. One of the main advances is that precise isotopic measurements have recently been extended to include major stoichiometric cations such as Ca, Mg, Fe, and K, as well as key impurity elements such as U, Cd, Mo, and Sr. Isotopic analysis at the nano- to microscale would further clarify the detailed dynamics of mineral chemistry controls but are not yet possible except in a few instances. Impurity element concentrations are more easily measured at these small scales, and they are a key bridge between isotopic measurements and microscopy.Other limitations to advancing our knowledge of the chemical and isotopic effects associated with

  10. Dynamics and flexibility of human aromatase probed by FTIR and time resolved fluorescence spectroscopy.

    Directory of Open Access Journals (Sweden)

    Giovanna Di Nardo

    Full Text Available Human aromatase (CYP19A1 is a steroidogenic cytochrome P450 converting androgens into estrogens. No ligand-free crystal structure of the enzyme is available to date. The crystal structure in complex with the substrate androstenedione and the steroidal inhibitor exemestane shows a very compact conformation of the enzyme, leaving unanswered questions on the conformational changes that must occur to allow access of the ligand to the active site. As H/D exchange kinetics followed by FTIR spectroscopy can provide information on the conformational changes in proteins where solvent accessibility is affected, here the amide I region was used to measure the exchange rates of the different elements of the secondary structure for aromatase in the ligand-free form and in the presence of the substrate androstenedione and the inhibitor anastrozole. Biphasic exponential functions were found to fit the H/D exchange data collected as a function of time. Two exchange rates were assigned to two populations of protons present in different flexible regions of the protein. The addition of the substrate androstenedione and the inhibitor anastrozole lowers the H/D exchange rates of the α-helices of the enzyme when compared to the ligand-free form. Furthermore, the presence of the inhibitor anastrozole lowers exchange rate constant (k1 for β-sheets from 0.22±0.06 min(-1 for the inhibitor-bound enzyme to 0.12±0.02 min(-1 for the free protein. Dynamics effects localised in helix F were studied by time resolved fluorescence. The data demonstrate that the fluorescence lifetime component associated to Trp224 emission undergoes a shift toward longer lifetimes (from ≈5.0 to ≈5.5 ns when the substrate or the inhibitor are present, suggesting slower dynamics in the presence of ligands. Together the results are consistent with different degrees of flexibility of the access channel and therefore different conformations adopted by the enzyme in the free, substrate- and

  11. Dynamics and flexibility of human aromatase probed by FTIR and time resolved fluorescence spectroscopy.

    Science.gov (United States)

    Di Nardo, Giovanna; Breitner, Maximilian; Sadeghi, Sheila J; Castrignanò, Silvia; Mei, Giampiero; Di Venere, Almerinda; Nicolai, Eleonora; Allegra, Paola; Gilardi, Gianfranco

    2013-01-01

    Human aromatase (CYP19A1) is a steroidogenic cytochrome P450 converting androgens into estrogens. No ligand-free crystal structure of the enzyme is available to date. The crystal structure in complex with the substrate androstenedione and the steroidal inhibitor exemestane shows a very compact conformation of the enzyme, leaving unanswered questions on the conformational changes that must occur to allow access of the ligand to the active site. As H/D exchange kinetics followed by FTIR spectroscopy can provide information on the conformational changes in proteins where solvent accessibility is affected, here the amide I region was used to measure the exchange rates of the different elements of the secondary structure for aromatase in the ligand-free form and in the presence of the substrate androstenedione and the inhibitor anastrozole. Biphasic exponential functions were found to fit the H/D exchange data collected as a function of time. Two exchange rates were assigned to two populations of protons present in different flexible regions of the protein. The addition of the substrate androstenedione and the inhibitor anastrozole lowers the H/D exchange rates of the α-helices of the enzyme when compared to the ligand-free form. Furthermore, the presence of the inhibitor anastrozole lowers exchange rate constant (k1) for β-sheets from 0.22±0.06 min(-1) for the inhibitor-bound enzyme to 0.12±0.02 min(-1) for the free protein. Dynamics effects localised in helix F were studied by time resolved fluorescence. The data demonstrate that the fluorescence lifetime component associated to Trp224 emission undergoes a shift toward longer lifetimes (from ≈5.0 to ≈5.5 ns) when the substrate or the inhibitor are present, suggesting slower dynamics in the presence of ligands. Together the results are consistent with different degrees of flexibility of the access channel and therefore different conformations adopted by the enzyme in the free, substrate- and inhibitor

  12. Specific probe selection from landscape phage display library and its application in enzyme-linked immunosorbent assay of free prostate-specific antigen.

    Science.gov (United States)

    Lang, Qiaolin; Wang, Fei; Yin, Long; Liu, Mingjun; Petrenko, Valery A; Liu, Aihua

    2014-03-01

    Probes against targets can be selected from the landscape phage library f8/8, displaying random octapeptides on the pVIII coat protein of the phage fd-tet and demonstrating many excellent features including multivalency, stability, and high structural homogeneity. Prostate-specific antigen (PSA) is usually determined by immunoassay, by which antibodies are frequently used as the specific probes. Herein we found that more advanced probes against free prostate-specific antigen (f-PSA) can be screened from the landscape phage library. Four phage monoclones were selected and identified by the specificity array. One phage clone displaying the fusion peptide ERNSVSPS showed good specificity and affinity to f-PSA and was used as a PSA capture probe in a sandwich enzyme-linked immunosorbent assay (ELISA) array. An anti-human PSA monoclonal antibody (anti-PSA mAb) was used to recognize the captured antigen, followed by horseradish peroxidase-conjugated antibody (HRP-IgG) and o-phenylenediamine, which were successively added to develop plate color. The ELISA conditions such as effect of blocking agent, coating buffer pH, phage concentration, antigen incubation time, and anti-PSA mAb dilution for phage ELISA were optimized. On the basis of the optimal phage ELISA conditions, the absorbance taken at 492 nm on a microplate reader was linear with f-PSA concentration within 0.825-165 ng/mL with a low limit of detection of 0.16 ng/mL. Thus, the landscape phage is an attractive biomolecular probe in bioanalysis.

  13. Trust-Based Route Selection in Dynamic Source Routin

    DEFF Research Database (Denmark)

    Jensen, Christian D.; Connell, Paul O

    2006-01-01

    Unlike traditional mobile wireless networks, ad hoc networks do not rely on any fixed infrastructure. Nodes rely on each other to route packets to other mobile nodes or toward stationary nodes that may act as a gateway to a fixed network. Mobile nodes are generally assumed to participate as routers......, which selects the route based on a local evaluation of the trustworthiness of all known intermediary nodes (routers) on the route to the destination. We have implemented this mechanism in an existing ad hoc routing protocol, and we show how trust can be built from previous experience and how trust can...

  14. Trust-Based Route Selection in Dynamic Source Routin

    DEFF Research Database (Denmark)

    Jensen, Christian D.; Connell, Paul O

    2006-01-01

    Unlike traditional mobile wireless networks, ad hoc networks do not rely on any fixed infrastructure. Nodes rely on each other to route packets to other mobile nodes or toward stationary nodes that may act as a gateway to a fixed network. Mobile nodes are generally assumed to participate as routers......, which selects the route based on a local evaluation of the trustworthiness of all known intermediary nodes (routers) on the route to the destination. We have implemented this mechanism in an existing ad hoc routing protocol, and we show how trust can be built from previous experience and how trust can...

  15. Dynamic access clustering selecting mechanism based on Markov decision process for MANET

    Institute of Scientific and Technical Information of China (English)

    WANG Dao-yuan; TIAN Hui

    2007-01-01

    Clustering is an important method in the mobile Ad-hoc network (MANET). As a result of their mobility, the cluster selection is inevitable for the mobile nodes during their roaming between the different clusters. In this study, based on the analysis of the cluster-selecting problem in the environment containing multiple clusters, which are overlaying and intercrossing, a novel dynamic selecting mechanism is proposed to resolve the dynamic selection optimization of roaming between the different clusters in MANET. This selecting mechanism is also based on the consideration of the stability of communication system, the communicating bandwidth, and the effect of cluster selecting on the communication and also in accordance with the Markov decision-making model.

  16. A novel approach to neutron scattering instrumentation for probing multiscale dynamics in soft and biological matter

    Science.gov (United States)

    Mamontov, Eugene

    2016-09-01

    We present a concept and ray-tracing simulation of a mechanical device that will enable inelastic neutron scattering measurements where the data at energy transfers from a few μeV to several hundred meV can be collected in a single, gapless spectrum. Besides covering 5 orders of magnitude on the energy (time) scale, the device provides data over 2 orders of magnitude on the scattering momentum (length) scale in a single measurement. Such capabilities are geared primarily toward soft and biological matter, where the broad dynamical features of relaxation origin largely overlap with vibration features, thus necessitating gapless spectral coverage over several orders of magnitude in time and space. Furthermore, neutron scattering experiments with such a device are performed with a fixed neutron final energy, which enables measurements, with neutron energy loss in the sample, at arbitrarily low temperatures over the same broad spectral range. This capability is also invaluable in biological and soft matter research, as the variable temperature dependence of different relaxation components allows their separation in the scattering spectra as a function of temperature.

  17. Ultrafast chemical reactions in shocked nitromethane probed with dynamic ellipsometry and transient absorption spectroscopy.

    Science.gov (United States)

    Brown, Kathryn E; McGrane, Shawn D; Bolme, Cynthia A; Moore, David S

    2014-04-10

    Initiation of the shock driven chemical reactions and detonation of nitromethane (NM) can be sensitized by the addition of a weak base; however, the chemical mechanism by which sensitization occurs remains unclear. We investigated the shock driven chemical reaction in NM and in NM sensitized with diethylenetriamine (DETA), using a sustained 300 ps shock driven by a chirped Ti:sapphire laser. We measured the solutions' visible transient absorption spectra and measured interface particle and shock velocities of the nitromethane solutions using ultrafast dynamic ellipsometry. We found there to be a volume-increasing reaction that takes place around interface particle velocity up = 2.4 km/s and up = 2.2 km/s for neat NM and NM with 5% DETA, respectively. The rate at which transient absorption increases is similar in all mixtures, but with decreasing induction times for solutions with increasing DETA concentrations. This result supports the hypothesis that the chemical reaction mechanisms for shocked NM and NM with DETA are the same. Data from shocked NM are compared to literature experimental and theoretical data.

  18. Satellite Test of the Equivalence Principle as a Probe of Modified Newtonian Dynamics

    CERN Document Server

    Pereira, Jonas P; Poyneer, Alexander J

    2016-01-01

    The proposed Satellite Test of the Equivalence Principle (STEP) will detect possible violations of the Weak Equivalence Principle by measuring relative accelerations between test masses of different composition with a precision of one part in $10^{18}$. A serendipitous byproduct of the experimental design is that the absolute (common-mode) acceleration of the test masses is also measured to high precision as they oscillate along a common axis under the influence of restoring forces produced by the position sensor currents, which in drag-free mode lead to Newtonian accelerations as small as $10^{-14}$ g. This is deep inside the low-acceleration regime where Modified Newtonian Dynamics (MOND) diverges strongly from the Newtonian limit of General Relativity. We show that MOND theories (including those based on the widely-used $n$-family of interpolating functions as well as the covariant Tensor-Vector-Scalar formulation) predict an easily detectable increase in the frequency of oscillations of the STEP test mass...

  19. Probing the dynamics of an optically trapped particle by phase sensitive back focal plane interferometry

    CERN Document Server

    Roy, Basudev; Haldar, Arijit; Gupta, Ratnesh Kumar; Ghosh, Nirmalya; Banerjee, Ayan

    2012-01-01

    The dynamics of an optically trapped particle are often determined by measuring intensity shifts of the back-scattered light from the particle using position sensitive detectors. We present a technique which measures the phase of the back-scattered light using balanced detection in an external Mach-Zender interferometer scheme where we separate out and beat the scattered light from the bead and that from the top surface of our trapping chamber. The technique has improved axial motion resolution over intensity-based detection, and can also be used to measure lateral motion of the trapped particle. In addition, we are able to track the Brownian motion of trapped 1 and 3 $\\mu$m diameter beads from the phase jitter and show that, similar to intensity-based measurements, phase measurements can also be used to simultaneously determine displacements of the trapped bead as well as the spring constant of the trap. For lateral displacements, we have matched our experimental results with a simulation of the overall phas...

  20. Satellite Test of the Equivalence Principle as a Probe of Modified Newtonian Dynamics.

    Science.gov (United States)

    Pereira, Jonas P; Overduin, James M; Poyneer, Alexander J

    2016-08-12

    The proposed satellite test of the equivalence principle (STEP) will detect possible violations of the weak equivalence principle by measuring relative accelerations between test masses of different composition with a precision of one part in 10^{18}. A serendipitous by-product of the experimental design is that the absolute or common-mode acceleration of the test masses is also measured to high precision as they oscillate along a common axis under the influence of restoring forces produced by the position sensor currents, which in drag-free mode lead to Newtonian accelerations as small as 10^{-14}  g. This is deep inside the low-acceleration regime where modified Newtonian dynamics (MOND) diverges strongly from the Newtonian limit of general relativity. We show that MOND theories (including those based on the widely used "n family" of interpolating functions as well as the covariant tensor-vector-scalar formulation) predict an easily detectable increase in the frequency of oscillations of the STEP test masses if the strong equivalence principle holds. If it does not hold, MOND predicts a cumulative increase in oscillation amplitude which is also detectable. STEP thus provides a new and potentially decisive test of Newton's law of inertia, as well as the equivalence principle in both its strong and weak forms.

  1. Dynamic acousto-elastic test using continuous probe wave and transient vibration to investigate material nonlinearity.

    Science.gov (United States)

    Eiras, J N; Vu, Q A; Lott, M; Payá, J; Garnier, V; Payan, C

    2016-07-01

    This study demonstrates the feasibility of the dynamic acousto-elastic effect of a continuous high frequency wave for investigating the material nonlinearity upon transient vibration. The approach is demonstrated on a concrete sample measuring 15×15×60cm(3). Two ultrasonic transducers (emitter and receiver) are placed at its middle span. A continuous high frequency wave of 500kHz propagates through the material and is modulated with a hammer blow. The position of the hammer blow on the sample is configured to promote the first bending mode of vibration. The use of a continuous wave allows discrete time extraction of the nonlinear behavior by a short-time Fourier transform approach, through the simultaneous comparison of a reference non-modulated signal and an impact-modulated signal. The hammer blow results in phase shifts and variations of signal amplitude between reference and perturbed signals, which are driven by the resonant frequency of the sample. Finally, a comprehensive analysis of the relaxation mechanisms (modulus and attenuation recovery) is conducted to untangle the coupled fast and slow hysteretic effects. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Decoherence and fluctuation dynamics of the quantum dot nuclear spin bath probed by nuclear magnetic resonance

    Science.gov (United States)

    Chekhovich, Evgeny A.

    2017-06-01

    Dynamics of nuclear spin decoherence and nuclear spin flip-flops in self-assembled InGaAs/GaAs quantum dots are studied experimentally using optically detected nuclear magnetic resonance (NMR). Nuclear spin-echo decay times are found to be in the range 1-4 ms. This is a factor of ~3 longer than in strain-free GaAs/AlGaAs structures and is shown to result from strain-induced quadrupolar effects that suppress nuclear spin flip-flops. The correlation times of the flip-flops are examined using a novel frequency-comb NMR technique and are found to exceed 1 s, a factor of ~1000 longer than in strain-free structures. These findings complement recent studies of electron spin coherence and reveal the paradoxical dual role of the quadrupolar effects in self-assembled quantum dots: large increase of the nuclear spin bath coherence and at the same time significant reduction of the electron spin-qubit coherence. Approaches to increasing electron spin coherence are discussed. In particular the nanohole filled GaAs/AlGaAs quantum dots are an attractive option: while their optical quality matches the self-assembled dots the quadrupolar effects measured in NMR spectra are a factor of 1000 smaller.

  3. Satellite Test of the Equivalence Principle as a Probe of Modified Newtonian Dynamics

    Science.gov (United States)

    Pereira, Jonas P.; Overduin, James M.; Poyneer, Alexander J.

    2016-08-01

    The proposed satellite test of the equivalence principle (STEP) will detect possible violations of the weak equivalence principle by measuring relative accelerations between test masses of different composition with a precision of one part in 1 018 . A serendipitous by-product of the experimental design is that the absolute or common-mode acceleration of the test masses is also measured to high precision as they oscillate along a common axis under the influence of restoring forces produced by the position sensor currents, which in drag-free mode lead to Newtonian accelerations as small as 10-14 g . This is deep inside the low-acceleration regime where modified Newtonian dynamics (MOND) diverges strongly from the Newtonian limit of general relativity. We show that MOND theories (including those based on the widely used "n family" of interpolating functions as well as the covariant tensor-vector-scalar formulation) predict an easily detectable increase in the frequency of oscillations of the STEP test masses if the strong equivalence principle holds. If it does not hold, MOND predicts a cumulative increase in oscillation amplitude which is also detectable. STEP thus provides a new and potentially decisive test of Newton's law of inertia, as well as the equivalence principle in both its strong and weak forms.

  4. Quantum state-resolved gas/surface reaction dynamics probed by reflection absorption infrared spectroscopy.

    Science.gov (United States)

    Chen, Li; Ueta, Hirokazu; Bisson, Régis; Beck, Rainer D

    2013-05-01

    We report the design and characterization of a new molecular-beam/surface-science apparatus for quantum state-resolved studies of gas/surface reaction dynamics combining optical state-specific reactant preparation in a molecular beam by rapid adiabatic passage with detection of surface-bound reaction products by reflection absorption infrared spectroscopy (RAIRS). RAIRS is a non-invasive infrared spectroscopic detection technique that enables online monitoring of the buildup of reaction products on the target surface during reactant deposition by a molecular beam. The product uptake rate obtained by calibrated RAIRS detection yields the coverage dependent state-resolved reaction probability S(θ). Furthermore, the infrared absorption spectra of the adsorbed products obtained by the RAIRS technique provide structural information, which help to identify nascent reaction products, investigate reaction pathways, and determine branching ratios for different pathways of a chemisorption reaction. Measurements of the dissociative chemisorption of methane on Pt(111) with this new apparatus are presented to illustrate the utility of RAIRS detection for highly detailed studies of chemical reactions at the gas/surface interface.

  5. Probing the dynamic process of encapsulation in Escherichia coli GroEL.

    Directory of Open Access Journals (Sweden)

    Toshifumi Mizuta

    Full Text Available Kinetic analyses of GroE-assisted folding provide a dynamic sequence of molecular events that underlie chaperonin function. We used stopped-flow analysis of various fluorescent GroEL mutants to obtain details regarding the sequence of events that transpire immediately after ATP binding to GroEL and GroEL with prebound unfolded proteins. Characterization of GroEL CP86, a circularly permuted GroEL with the polypeptide ends relocated to the vicinity of the ATP binding site, showed that GroES binding and protection of unfolded protein from solution is achieved surprisingly early in the functional cycle, and in spite of greatly reduced apical domain movement. Analysis of fluorescent GroEL SR-1 and GroEL D398A variants suggested that among other factors, the presence of two GroEL rings and a specific conformational rearrangement of Helix M in GroEL contribute significantly to the rapid release of unfolded protein from the GroEL apical domain.

  6. Probing conformational stability and dynamics of erythroid and nonerythroid spectrin: effects of urea and guanidine hydrochloride.

    Directory of Open Access Journals (Sweden)

    Malay Patra

    Full Text Available We have studied the conformational stability of the two homologous membrane skeletal proteins, the erythroid and non-erythroid spectrins, in their dimeric and tetrameric forms respectively during unfolding in the presence of urea and guanidine hydrochloride (GuHCl. Fluorescence and circular dichroism (CD spectroscopy have been used to study the changes of intrinsic tryptophan fluorescence, anisotropy, far UV-CD and extrinsic fluorescence of bound 1-anilinonapthalene-8-sulfonic acid (ANS. Chemical unfolding of both proteins were reversible and could be described as a two state transition. The folded erythroid spectrin and non-erythroid spectrin were directly converted to unfolded monomer without formation of any intermediate. Fluorescence quenching, anisotropy, ANS binding and dynamic light scattering data suggest that in presence of low concentrations of the denaturants (up-to 1M hydrogen bonding network and van der Waals interaction play a role inducing changes in quaternary as well as tertiary structures without complete dissociation of the subunits. This is the first report of two large worm like, multi-domain proteins obeying twofold rule which is commonly found in small globular proteins. The free energy of stabilization (ΔGuH20 for the dimeric spectrin has been 20 kcal/mol lesser than the tetrameric from.

  7. Probing Conformational Stability and Dynamics of Erythroid and Nonerythroid Spectrin: Effects of Urea and Guanidine Hydrochloride

    Science.gov (United States)

    Patra, Malay; Mukhopadhyay, Chaitali; Chakrabarti, Abhijit

    2015-01-01

    We have studied the conformational stability of the two homologous membrane skeletal proteins, the erythroid and non-erythroid spectrins, in their dimeric and tetrameric forms respectively during unfolding in the presence of urea and guanidine hydrochloride (GuHCl). Fluorescence and circular dichroism (CD) spectroscopy have been used to study the changes of intrinsic tryptophan fluorescence, anisotropy, far UV-CD and extrinsic fluorescence of bound 1-anilinonapthalene-8-sulfonic acid (ANS). Chemical unfolding of both proteins were reversible and could be described as a two state transition. The folded erythroid spectrin and non-erythroid spectrin were directly converted to unfolded monomer without formation of any intermediate. Fluorescence quenching, anisotropy, ANS binding and dynamic light scattering data suggest that in presence of low concentrations of the denaturants (up-to 1M) hydrogen bonding network and van der Waals interaction play a role inducing changes in quaternary as well as tertiary structures without complete dissociation of the subunits. This is the first report of two large worm like, multi-domain proteins obeying twofold rule which is commonly found in small globular proteins. The free energy of stabilization (ΔGuH20) for the dimeric spectrin has been 20 kcal/mol lesser than the tetrameric from. PMID:25617632

  8. Periodic Repolarisation Dynamics: A Natural Probe of the Ventricular Response to Sympathetic Activation

    Science.gov (United States)

    Rizas, Konstantinos D; Hamm, Wolfgang; Kääb, Stefan; Schmidt, Georg; Bauer, Axel

    2016-01-01

    Periodic repolarisation dynamics (PRD) refers to low-frequency (≤0.1Hz) modulations of cardiac repolarisation instability. Spontaneous PRD can be assessed non-invasively from 3D high-resolution resting ECGs. Physiological and experimental studies have indicated that PRD correlates with efferent sympathetic nerve activity, which clusters in low-frequency bursts. PRD is increased by physiological provocations that lead to an enhancement of sympathetic activity, whereas it is suppressed by pharmacological β-blockade. Electrophysiological studies revealed that PRD occurs independently from heart rate variability. Increased PRD under resting conditions is a strong predictor of mortality in post-myocardial infarction (post-MI) patients, yielding independent prognostic value from left-ventricular ejection fraction (LVEF), heart rate variability, the Global Registry of Acute Coronary Events score and other established risk markers. The predictive value of PRD is particularly strong in post-MI patients with preserved LVEF (>35 %) in whom it identifies a new high-risk group of patients. The upcoming Implantable Cardiac Monitors in High-Risk Post-Infarction Patients with Cardiac Autonomic Dysfunction and Moderately Reduced Left Ventricular Ejection Fraction (SMART-MI) trial will test prophylactic strategies in high-risk post-MI patients with LVEF 36–50 % identified by PRD and deceleration capacity of heart rate (NCT02594488). PMID:27403291

  9. Ultrafast probing of ejection dynamics of Rydberg atoms and molecular fragments from electronically excited helium nanodroplets.

    Science.gov (United States)

    Bünermann, Oliver; Kornilov, Oleg; Haxton, Daniel J; Leone, Stephen R; Neumark, Daniel M; Gessner, Oliver

    2012-12-07

    The ejection dynamics of Rydberg atoms and molecular fragments from electronically excited helium nanodroplets are studied with time-resolved extreme ultraviolet ion imaging spectroscopy. At excitation energies of 23.6 ± 0.2 eV, Rydberg atoms in n = 3 and n = 4 states are ejected on different time scales and with significantly different kinetic energy distributions. Specifically, n = 3 Rydberg atoms are ejected with kinetic energies as high as 0.85 eV, but their appearance is delayed by approximately 200 fs. In contrast, n = 4 Rydberg atoms appear within the time resolution of the experiment with considerably lower kinetic energies. Major features in the Rydberg atom kinetic energy distributions for both principal quantum numbers can be described within a simple elastic scattering model of localized perturbed atomic Rydberg atoms that are expelled from the droplet due to their repulsive interaction with the surrounding helium bath. Time-dependent kinetic energy distributions of He(2) (+) and He(3) (+) ions are presented that support the formation of molecular ions in an indirect droplet ionization process and the ejection of neutral Rydberg dimers on a similar time scale as the n = 3 Rydberg atoms.

  10. The 5:1 Neptune Resonance as Probed by CFEPS: Dynamics and Population

    CERN Document Server

    Pike, R E; Petit, J M; Gladman, B J; Alexandersen, M; Volk, K; Shankman, C J

    2015-01-01

    The Canada-France Ecliptic Plane Survey discovered four trans-Neptunian objects with semi-major axes near the 5:1 resonance, revealing a large and previously undetected intrinsic population. Three of these objects are currently resonant with Neptune, and the fourth is consistent with being an object that escaped the resonance at some point in the past. The non-resonant object may be representative of a detached population that is stable at slightly lower semi-major axes than the 5:1 resonance. We generated clones of these objects by resampling the astrometric uncertainty and examined their behavior over a 4.5 Gyr numerical simulation. The majority of the clones of the three resonant objects (>90%) spend a total of 10^7 years in resonance during their 4.5 Gyr integrations; most clones experience multiple periods of resonance capture. Our dynamical integrations reveal an exchange between the 5:1 resonance, the scattering objects, and other large semi-major axis resonances, especially the 4:1, 6:1, and 7:1. The ...

  11. The dynamics of giant unilamellar vesicle oxidation probed by morphological transitions.

    Science.gov (United States)

    Sankhagowit, Shalene; Wu, Shao-Hua; Biswas, Roshni; Riche, Carson T; Povinelli, Michelle L; Malmstadt, Noah

    2014-10-01

    We have studied the dynamics of Lissamine Rhodamine B dye sensitization-induced oxidation of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) giant unilamellar vesicles (GUVs), where the progression of the underlying chemical processes was followed via vesicle membrane area changes. The surface-area-to-volume ratio of our spherical GUVs increased after as little as ten seconds of irradiation. The membrane area expansion was coupled with high amplitude fluctuations not typical of GUVs in isoosmotic conditions. To accurately measure the area of deformed and fluctuating membranes, we utilized a dual-beam optical trap (DBOT) to stretch GUV membranes into a geometrically regular shape. Further oxidation led to vesicle contraction, and the GUVs became tense, with micron-scale pores forming in the bilayer. We analyzed the GUV morphological behaviors as two consecutive rate-limiting steps. We also considered the effects of altering DOPC and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(lissamine rhodamine B sulfonyl) (RhDPPE) concentrations. The resulting kinetic model allows us to measure how lipid molecular area changes during oxidation, as well as to determine the rate constants controlling how quickly oxidation products are formed. Controlled membrane oxidation leading to permeabilization is also a potential tool for drug delivery based on engineered photosensitizer-containing lipid vesicles. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Structural, morphological and optical studies of l-cysteine modified silver nanoparticles and its application as a probe for the selective colorimetric detection of Hg(2+).

    Science.gov (United States)

    Nidya, M; Umadevi, M; Rajkumar, Beulah J M

    2014-12-10

    We report an extensive study on the evolution of a highly facile, selective colorimetric probe for Hg(2+) detection using cysteine modified silver nanoparticles. The nanoparticles are stable in a basic medium and the Surface Enhanced Raman Spectrum (SERS) reveal that the cysteine is bound to the Ag surface through the thiolate moiety with the charged carboxylate group pointing outwards in a morphology that lends itself to sensor applications. In the presence of Hg(2+), the absorption peak is quenched resulting in a drastic colour change. The sensor displays high selectivity to Hg(2+) over other metallic ions.

  13. Dynamic mixtures and combinatorial libraries: imines as probes for molecular evolution at the interface between chemistry and biology.

    Science.gov (United States)

    Herrmann, Andreas

    2009-08-21

    In analogy to evolution in biological processes, "molecular evolution", based on the reversible formation of imines, has successfully been explored for drug discovery, receptor design and as a controlled-release vehicle. Multicomponent systems composed of amines and carbonyl compounds generate structural diversity by reversible reaction of the different components to form equilibrated dynamic mixtures or combinatorial libraries (DCLs). Under thermodynamic control and in the presence of an external factor which influences the equilibrium, these systems evolve by selective adaptation to the changing external conditions. This concept allows the casting of biologically or catalytically active substrates and the molding of receptors from DCLs which are composed of smaller non-active amine and carbonyl moieties. Similarly, if the amine or carbonyl compounds are the biologically active compounds of interest, the corresponding dynamic mixtures are found to be efficient delivery systems, allowing their controlled release over time.

  14. Dual Selectivity Expressed in [2+2+1] Dynamic Clipping of Unsymmetrical [2]Catenanes

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yi

    2010-06-11

    A {pi}-templated dynamic [2+2+1] clipping protocol is established for the synthesis of [2]catenanes from two parts dialdehyde, two parts diamine and one part tetracationic cyclophane. It is further diversified for the selective formation of an unsymmetrical [2]catenane showing great translational selectivity by employing two different dialdehydes in a one-pot reaction. The dual selectivity and the dynamic nature are verified by {sup 1}H NMR spectroscopy, X-ray single crystal structural studies and exchange experiments.

  15. Project Icarus: Preliminary Thoughts on the Selection of Probes and Instruments for an Icarus-style Interstellar Mission

    Science.gov (United States)

    Crawford, Ian A.

    2016-06-01

    In this paper we outline the range of probes and scientific instruments that will be required in order for Icarus to fulfill its scientific mission of exploring a nearby star, its attendant planetary system, and the intervening interstellar medium. Based on this preliminary analysis, we estimate that the minimum total Icarus scientific payload mass (i.e. the mass of probes and instruments which must be decelerated to rest in the target system to enable a meaningful programme of scientific investigation) will be in the region of 100 tonnes. Of this, approximately 10 tonnes would be allocated for cruise-phase science instruments, and about 35 tonnes (i.e. the average of estimated lower and upper limits of 28 and 41 tonnes) would be contributed by the intra-system science payload itself (i.e. the dry mass of the stellar and planetary probes and their instruments). The remaining ~55 tonnes is allocated for the sub-probe intra-system propulsion requirements (crudely estimated from current Solar System missions; detailed modelling of sub-probe propulsion systems will be needed to refine this figure). The overall mass contributed by the science payload to the total that must be decelerated from the interstellar cruise velocity will be considerably more than 100 tonnes, however, as allowance must be made for the payload structural and infrastructural elements required to support, deploy, and communicate with the science probes and instruments. Based on the earlier Daedalus study, we estimate another factor of two to allow for these components. Pending the outcome of more detailed studies, it therefore appears that an overall science-related payload mass of ~200 tonnes will be required. This paper is a submission of the Project Icarus Study Group.

  16. Probing of complete and incomplete fusion dynamics in heavy-ion collision

    Indian Academy of Sciences (India)

    D Singh; Rahbar Ali; M Afzal Ansari; B S Tomar; M H Rashid; R Guin; S K Das; R Kumar; R P Singh; S Muralithar; R K Bhowmik

    2014-04-01

    Three different types of experiments have been performed to explore the complete and incomplete fusion dynamics in heavy-ion collisions. In this respect, first experiment for the measurement of excitation functions of the evaporation residues produced in the 20Ne+165Ho system at projectile energy ranges ≈2–8 MeV/nucleon has been done. Measured cumulative and direct crosssections have been compared with the theoretical model code PACE-2, which takes into account only the complete fusion process. It has been observed that, incomplete fusion fraction is sensitively dependent on projectile energy and mass asymmetry between the projectile and the target systems. Second experiment for measuring the forward recoil range distributions of the evaporation residues produced in the 20Ne+165Ho system at projectile energy ≈8MeV/nucleon has been done. It has been observed that, some evaporation residues have shown additional peaks in the measured forward recoil range distributions at cumulative thicknesses relatively smaller than the expected range of the residues produced via complete fusion. The results indicate the occurrence of incomplete fusion involving the breakup of 20Ne into 4He+16O and/or 8Be+12C followed by one of the fragments with target nucleus 165Ho. Third experiment for the measurement of spin distribution of the evaporation residues produced in the 16O+124Sn system at projectile energy ≈6 MeV/nucleon, showed that the residues produced as incomplete fusion products associated with fast and 2-emission channels observed in the forward cone, are found to be distinctly different from those of the residues produced as complete fusion products. The spin distribution of the evaporation residues also inferred that in incomplete fusion reaction channels input angular momentum ($J_0$) increases with fusion incompleteness when compared to complete fusion reaction channels. Present observation clearly shows that the production of fast forward -particles arises from

  17. A magmatic probe linking mantle temperature and dynamic topography beneath western North America

    Science.gov (United States)

    Klöcking, M.; White, N. J.; Maclennan, J.; Fitton, J. G.

    2016-12-01

    The region in western North America encompassing the Basin and Range Province, Snake River Plain and Colorado Plateau lies at an elevation 2 km higher than cratonic North America. This difference broadly coincides with variations in lithospheric thickness: Mexico, and inverse modeling of river profiles all suggest that regional uplift occurred in at least two distinct phases. USArray seismic tomographic models have imaged low velocity material beneath most of western North America, including a ring-shaped anomaly around the edges of the Colorado Plateau. Magmatism coincides with these low velocity zones and shows an overall increase in volume at 40 Ma as well as a change from lithospheric to asthenospheric signature at 5 Ma. To investigate the relationship between seismic imaging and basaltic magmatism, we have analyzed >260 samples from volcanic centers across western North America for major and trace elements using ICP-MS and XRF. For asthenospheric samples, we observe a strong correlation between slow velocity anomalies and both location and composition of basalts. Using a combination of petrology, forward and inverse modeling of major and rare earth elements, integrated with results from tomographic models, we determine depth of melting and melt fraction. We explore the possibility that volatiles, source composition and/or temperature cause magmatism and uplift of this region. Thus, we use a variety of methods to constrain lithospheric thickness and mantle potential temperature. A dynamic topographic model of progressive lithospheric erosion over an anomalously hot upper mantle could account for regional uplift together with the temporal and spatial distribution of magmatism across western North America.

  18. Probing parton dynamics of QCD matter with Ω and ϕ production

    Science.gov (United States)

    Adamczyk, L.; Adkins, J. K.; Agakishiev, G.; Aggarwal, M. M.; Ahammed, Z.; Alekseev, I.; Aparin, A.; Arkhipkin, D.; Aschenauer, E. C.; Attri, A.; Averichev, G. S.; Bai, X.; Bairathi, V.; Bellwied, R.; Bhasin, A.; Bhati, A. K.; Bhattarai, P.; Bielcik, J.; Bielcikova, J.; Bland, L. C.; Bordyuzhin, I. G.; Bouchet, J.; Brandenburg, J. D.; Brandin, A. V.; Bunzarov, I.; Butterworth, J.; Caines, H.; Calderón de la Barca Sánchez, M.; Campbell, J. M.; Cebra, D.; Chakaberia, I.; Chaloupka, P.; Chang, Z.; Chatterjee, A.; Chattopadhyay, S.; Chen, J. H.; Chen, X.; Cheng, J.; Cherney, M.; Christie, W.; Contin, G.; Crawford, H. J.; Das, S.; De Silva, L. C.; Debbe, R. R.; Dedovich, T. G.; Deng, J.; Derevschikov, A. A.; di Ruzza, B.; Didenko, L.; Dilks, C.; Dong, X.; Drachenberg, J. L.; Draper, J. E.; Du, C. M.; Dunkelberger, L. E.; Dunlop, J. C.; Efimov, L. G.; Engelage, J.; Eppley, G.; Esha, R.; Evdokimov, O.; Eyser, O.; Fatemi, R.; Fazio, S.; Federic, P.; Fedorisin, J.; Feng, Z.; Filip, P.; Fisyak, Y.; Flores, C. E.; Fulek, L.; Gagliardi, C. A.; Garand, D.; Geurts, F.; Gibson, A.; Girard, M.; Greiner, L.; Grosnick, D.; Gunarathne, D. S.; Guo, Y.; Gupta, S.; Gupta, A.; Guryn, W.; Hamad, A. I.; Hamed, A.; Haque, R.; Harris, J. W.; He, L.; Heppelmann, S.; Heppelmann, S.; Hirsch, A.; Hoffmann, G. W.; Horvat, S.; Huang, T.; Huang, X.; Huang, B.; Huang, H. Z.; Huck, P.; Humanic, T. J.; Igo, G.; Jacobs, W. W.; Jang, H.; Jentsch, A.; Jia, J.; Jiang, K.; Judd, E. G.; Kabana, S.; Kalinkin, D.; Kang, K.; Kauder, K.; Ke, H. W.; Keane, D.; Kechechyan, A.; Khan, Z. H.; Kikoła, D. P.; Kisel, I.; Kisiel, A.; Kochenda, L.; Koetke, D. D.; Kosarzewski, L. K.; Kraishan, A. F.; Kravtsov, P.; Krueger, K.; Kumar, L.; Lamont, M. A. C.; Landgraf, J. M.; Landry, K. D.; Lauret, J.; Lebedev, A.; Lednicky, R.; Lee, J. H.; Li, X.; Li, C.; Li, X.; Li, Y.; Li, W.; Lin, T.; Lisa, M. A.; Liu, F.; Ljubicic, T.; Llope, W. J.; Lomnitz, M.; Longacre, R. S.; Luo, X.; Ma, R.; Ma, G. L.; Ma, Y. G.; Ma, L.; Magdy, N.; Majka, R.; Manion, A.; Margetis, S.; Markert, C.; Matis, H. S.; McDonald, D.; McKinzie, S.; Meehan, K.; Mei, J. C.; Minaev, N. G.; Mioduszewski, S.; Mishra, D.; Mohanty, B.; Mondal, M. M.; Morozov, D. A.; Mustafa, M. K.; Nandi, B. K.; Nasim, Md.; Nayak, T. K.; Nigmatkulov, G.; Niida, T.; Nogach, L. V.; Noh, S. Y.; Novak, J.; Nurushev, S. B.; Odyniec, G.; Ogawa, A.; Oh, K.; Okorokov, V. A.; Olvitt, D.; Page, B. S.; Pak, R.; Pan, Y. X.; Pandit, Y.; Panebratsev, Y.; Pawlik, B.; Pei, H.; Perkins, C.; Pile, P.; Pluta, J.; Poniatowska, K.; Porter, J.; Posik, M.; Poskanzer, A. M.; Pruthi, N. K.; Putschke, J.; Qiu, H.; Quintero, A.; Ramachandran, S.; Raniwala, S.; Raniwala, R.; Ray, R. L.; Ritter, H. G.; Roberts, J. B.; Rogachevskiy, O. V.; Romero, J. L.; Ruan, L.; Rusnak, J.; Rusnakova, O.; Sahoo, N. R.; Sahu, P. K.; Sakrejda, I.; Salur, S.; Sandweiss, J.; Sarkar, A.; Schambach, J.; Scharenberg, R. P.; Schmah, A. M.; Schmidke, W. B.; Schmitz, N.; Seger, J.; Seyboth, P.; Shah, N.; Shahaliev, E.; Shanmuganathan, P. V.; Shao, M.; Sharma, A.; Sharma, B.; Sharma, M. K.; Shen, W. Q.; Shi, Z.; Shi, S. S.; Shou, Q. Y.; Sichtermann, E. P.; Sikora, R.; Simko, M.; Singha, S.; Skoby, M. J.; Smirnov, N.; Smirnov, D.; Solyst, W.; Song, L.; Sorensen, P.; Spinka, H. M.; Srivastava, B.; Stanislaus, T. D. S.; Stepanov, M.; Stock, R.; Strikhanov, M.; Stringfellow, B.; Sumbera, M.; Summa, B.; Sun, Z.; Sun, X. M.; Sun, Y.; Surrow, B.; Svirida, D. N.; Tang, Z.; Tang, A. H.; Tarnowsky, T.; Tawfik, A.; Thäder, J.; Thomas, J. H.; Timmins, A. R.; Tlusty, D.; Todoroki, T.; Tokarev, M.; Trentalange, S.; Tribble, R. E.; Tribedy, P.; Tripathy, S. K.; Tsai, O. D.; Ullrich, T.; Underwood, D. G.; Upsal, I.; Van Buren, G.; van Nieuwenhuizen, G.; Vandenbroucke, M.; Varma, R.; Vasiliev, A. N.; Vertesi, R.; Videbæk, F.; Vokal, S.; Voloshin, S. A.; Vossen, A.; Wang, F.; Wang, G.; Wang, J. S.; Wang, H.; Wang, Y.; Wang, Y.; Webb, G.; Webb, J. C.; Wen, L.; Westfall, G. D.; Wieman, H.; Wissink, S. W.; Witt, R.; Wu, Y.; Xiao, Z. G.; Xie, W.; Xie, G.; Xin, K.; Xu, Y. F.; Xu, Q. H.; Xu, N.; Xu, H.; Xu, Z.; Xu, J.; Yang, S.; Yang, Y.; Yang, Y.; Yang, C.; Yang, Y.; Yang, Q.; Ye, Z.; Ye, Z.; Yepes, P.; Yi, L.; Yip, K.; Yoo, I.-K.; Yu, N.; Zbroszczyk, H.; Zha, W.; Zhang, X. P.; Zhang, Y.; Zhang, J.; Zhang, J.; Zhang, S.; Zhang, S.; Zhang, Z.; Zhang, J. B.; Zhao, F.; Zhao, J.; Zhong, C.; Zhou, L.; Zhu, X.; Zoulkarneeva, Y.; Zyzak, M.; STAR Collaboration

    2016-02-01

    We present measurements of Ω and ϕ production at midrapidity from Au+Au collisions at nucleon-nucleon center-of-mass energies √{sN N}=7.7 , 11.5 , 19.6 , 27, and 39 GeV by the STAR experiment at the BNL Relativistic Heavy Ion Collider (RHIC). Motivated by the coalescence formation mechanism for these strange hadrons, we study the ratios of N (Ω-+Ω¯+) /[2 N (ϕ ) ] . These ratios as a function of transverse momentum pT fall on a consistent trend at high collision energies, but start to show deviations in peripheral collisions at √{sN N}=19.6 , 27, and 39 GeV, and in central collisions at 11.5 GeV in the intermediate pT region of 2.4 -3.6 GeV/c . We further evaluate empirically the strange quark pT distributions at hadronization by studying the Ω /ϕ ratios scaled by the number of constituent quarks (NCQ). The NCQ-scaled Ω /ϕ ratios show a suppression of strange quark production in central collisions at 11.5 GeV compared to √{sN N}≥19.6 GeV. The shapes of the presumably thermal strange quark distributions in 0-60% most central collisions at 7.7 GeV show significant deviations from those in 0-10% most central collisions at higher energies. These features suggest that there is likely a change of the underlying strange quark dynamics in the transition from quark matter to hadronic matter at collision energies below 19.6 GeV.

  19. Combining dynamic stretch and tunable stiffness to probe cell mechanobiology in vitro.

    Directory of Open Access Journals (Sweden)

    Angela M Throm Quinlan

    Full Text Available Cells have the ability to actively sense their mechanical environment and respond to both substrate stiffness and stretch by altering their adhesion, proliferation, locomotion, morphology, and synthetic profile. In order to elucidate the interrelated effects of different mechanical stimuli on cell phenotype in vitro, we have developed a method for culturing mammalian cells in a two-dimensional environment at a wide range of combined levels of substrate stiffness and dynamic stretch. Polyacrylamide gels were covalently bonded to flexible silicone culture plates and coated with monomeric collagen for cell adhesion. Substrate stiffness was adjusted from relatively soft (G' = 0.3 kPa to stiff (G' = 50 kPa by altering the ratio of acrylamide to bis-acrylamide, and the silicone membranes were stretched over circular loading posts by applying vacuum pressure to impart near-uniform stretch, as confirmed by strain field analysis. As a demonstration of the system, porcine aortic valve interstitial cells (VIC and human mesenchymal stem cells (hMSC were plated on soft and stiff substrates either statically cultured or exposed to 10% equibiaxial or pure uniaxial stretch at 1 Hz for 6 hours. In all cases, cell attachment and cell viability were high. On soft substrates, VICs cultured statically exhibit a small rounded morphology, significantly smaller than on stiff substrates (p<0.05. Following equibiaxial cyclic stretch, VICs spread to the extent of cells cultured on stiff substrates, but did not reorient in response to uniaxial stretch to the extent of cells stretched on stiff substrates. hMSCs exhibited a less pronounced response than VICs, likely due to a lower stiffness threshold for spreading on static gels. These preliminary data demonstrate that inhibition of spreading due to a lack of matrix stiffness surrounding a cell may be overcome by externally applied stretch suggesting similar mechanotransduction mechanisms for sensing stiffness and

  20. A label-free fluorescence strategy for selective detection of nicotinamide adenine dinucleotide based on a dumbbell-like probe with low background noise.

    Science.gov (United States)

    Chen, Xuexu; Lin, Chunshui; Chen, Yiying; Wang, Yiru; Chen, Xi

    2016-03-15

    In this work we developed a novel label-free fluorescence sensing approach for the detection of nicotinamide adenine dinucleotide (NAD(+)) based on a dumbbell-like DNA probe designed for both ligation reaction and digestion reaction with low background noise. SYBR Green I (SG I), a double-helix dye, was chosen as the readout fluorescence signal. In the absence of NAD(+), the ligation reaction did not occur, but the probe was digested to mononucleotides after the addition of exonuclease I (Exo I) and exonuclease I (Exo III), resulting in a weak fluorescence intensity due to the weak interaction between SG I and mononucleotides. In the presence of NAD(+), the DNA probe was ligated by Escherichia coli DNA ligase, blocking the digestion by Exo I and Exo III. As a result, SG I was intercalated into the stem part of the DNA dumbbell probe and fluorescence enhancement was achieved. This method was simple in design, fast to operate, with good sensitivity and selectivity which could discriminate NAD(+) from its analogs.

  1. Selective chromo-fluorogenic detection of DFP (a Sarin and Soman mimic) and DCNP (a Tabun mimic) with a unique probe based on a boron dipyrromethene (BODIPY) dye.

    Science.gov (United States)

    Barba-Bon, Andrea; Costero, Ana M; Gil, Salvador; Martínez-Máñez, Ramón; Sancenón, Félix

    2014-11-21

    A novel colorimetric probe (P4) for the selective differential detection of DFP (a Sarin and Soman mimic) and DCNP (a Tabun mimic) was prepared. Probe P4 contains three reactive sites; i.e. (i) a nucleophilic phenol group able to undergo phosphorylation with nerve gases, (ii) a carbonyl group as a reactive site for cyanide; and (iii) a triisopropylsilyl (TIPS) protecting group that is known to react with fluoride. The reaction of P4 with DCNP in acetonitrile resulted in both the phosphorylation of the phenoxy group and the release of cyanide, which was able to react with the carbonyl group of P4 to produce a colour modulation from pink to orange. In contrast, phosphorylation of P4 with DFP in acetonitrile released fluoride that hydrolysed the TIPS group in P4 to yield a colour change from pink to blue. Probe P4 was able to discriminate between DFP and DCNP with remarkable sensitivity; limits of detection of 0.36 and 0.40 ppm for DCNP and DFP, respectively, were calculated. Besides, no interference from other organophosphorous derivatives or with presence of acid was observed. The sensing behaviour of P4 was also retained when incorporated into silica gel plates or onto polyethylene oxide membranes, which allowed the development of simple test strips for the colorimetric detection of DCNP and DFP in the vapour phase. P4 is the first probe capable of colorimetrically differentiating between a Tabun mimic (DCNP) and a Sarin and Soman mimic (DFP).

  2. Kinetic adsorption profile and conformation evolution at the DNA-gold nanoparticle interface probed by dynamic light scattering.

    Science.gov (United States)

    Wang, Wenjie; Ding, XiaoFan; He, Miao; Wang, Jing; Lou, Xinhui

    2014-10-21

    The kinetic adsorption profile at the DNA-gold nanoparticle (AuNP) interface is probed by following the binding and organization of thiolated linear DNA and aptamers of varying chain lengths (15, 30, 44, and 51 mer) to the surface of AuNPs (13.0 ± 1.0 nm diameter). A systematic investigation utilizing dynamic light scattering has been performed to directly measure the changes in particle size during the course of a typical aging-salting thiolated DNA/AuNP preparation procedure. We discuss the effect of DNA chain length, composition, salt concentration, and secondary structure on the kinetics and conformation at the DNA-AuNP interface. The adsorption kinetics are chain-length dependent, composition independent, and not diffusion rate limited for the conditions we report here. The kinetic data support a mechanism of stepwise adsorption of thiols to the surface of AuNPs and reorganization of the thiols at the interface. Very interestingly, the kinetic increases of the particle sizes are modeled accurately by the pseudo-second-order rate model, suggesting that DNA could possess the statistically well-defined conformational evolution. Together with other experimental evidence, we propose a dynamic inner-layer and outer-tail (DILOT) model to describe the evolution of the DNA conformation after the initial adsorption of a single oligonucleotide layer. According to this model, the length of the tails that extend from the surface of AuNPs, capable for hybridization or molecular recognition, can be conveniently calculated. Considering the wide applications of DNA/AuNPs, the results should have important implications in sensing and DNA-directed nanoparticle assembly.

  3. Chaotic features of nuclear structure and dynamics: selected topics

    Science.gov (United States)

    Zelevinsky, Vladimir; Volya, Alexander

    2016-03-01

    Quantum chaos has become an important element of our knowledge about physics of complex systems. In typical mesoscopic systems of interacting particles the dynamics invariably become chaotic when the level density, growing by combinatorial reasons, leads to the increasing probability of mixing simple mean-field (particle-hole) configurations. The resulting stationary states have exceedingly complicated structures that are comparable to those in random matrix theory. We discuss the main properties of mesoscopic quantum chaos and show that it can serve as a justification for application of statistical mechanics to mesoscopic systems. We show that quantum chaos becomes a powerful instrument for experimental, theoretical and computational work. The generalization to open systems and effects in the continuum are discussed with the help of the effective non-Hermitian Hamiltonian; it is shown how to formulate this approach for numerous problems of quantum signal transmission. The artificially introduced randomness can also be helpful for a deeper understanding of physics. We indicate the problems that require more investigation so as to be understood further.

  4. Probing the Dynamics of Biomineralization at the Pore Scale Using X-ray Computed Tomography

    Science.gov (United States)

    Armstrong, R. T.; Ajo Franklin, J. B.

    2009-12-01

    Biomineralization is a natural subsurface process that upon stimulation can dramatically affect soil mechanics and hydraulics. This work presents the results of a study where synchrotron based X-Ray Computed Microtomography (CMT) is used to investigate temporal cementation dynamics and the spatial distribution of biogenic CaCO3 at the pore-scale, thus, shedding light on pore clogging and contact cementation. To facilitate these studies we have developed a family of flow-through bioreactors (ID 8 mm) which can be scanned continuously during precipitation experiments. The reactor is also equipped with differential pressure transducers to allow measurement of sample permeability. Porosity permeability correlations, cementation morphology, CaCO3 spatial distribution, and bulk cementation are addressed herein. Sporosarcina pasteurii (formally Bacillus pasteurii), our model organism, is a prevalent aerobic, motile, soil microbe with a very active urease enzyme. Hydrolysis of urea by the urease enzyme generates carbonate ions, ammonium and an increase in pH which favors carbonate precipitation if appropriate metal cations (e.g. Ca2+) are available. Brightfield microscope results show that precipitation occurs within close proximity of the cell membrane reducing microbial motility and forming a CaCO3 precipitate with a "fluffy" appearance. Besides providing an aqueous environment favorable for mineralization S. pasteurii also provides nucleation sites on its cell membrane. Since this microbe is very effective at inducing carbonate precipitation over a relativity short time span (2-3 days), it was used exclusively in our experiments. Prior to CMT imaging the feasibility of temporal imaging was investigated. Viable cell counts taken before and after imaging showed that a considerable amount of bacteria survived the monochromatic (30 KeV) X-ray exposure. Cementation experiments initiated with inoculation of the CMT column with microbes and urea media, cells were allowed to

  5. Probing deformation substructure by synchrotron X-ray diffraction and dislocation dynamics modelling.

    Science.gov (United States)

    Korsunsky, Alexander M; Hofmann, Felix; Song, Xu; Eve, Sophie; Collins, Steve P

    2010-09-01

    Materials characterization at the nano-scale is motivated by the desire to resolve the structural aspects and deformation behavior at length scales relevant to those mechanisms that define the novel and unusual properties of nano-structured materials. A range of novel techniques has recently become accessible with the help of synchrotron X-ray beams that can be focused down to spot sizes of less than a few microns on the sample. The unique combination of tunability (energy selection), parallelism and brightness of synchrotron X-ray beams allows their use for high resolution diffraction (determination of crystal structure and transformations, analysis of dislocation sub-structures, orientation and texture analysis, strain mapping); small angle X-ray scattering (analysis of nano-scale voids and defects; orientation analysis) and imaging (radiography and tomography). After a brief review of the state-of-the-art capabilities for monochromatic and white beam synchrotron diffraction, we consider the usefulness of these techniques for the task of bridging the gap between experiment and modeling. Namely, we discuss how the experiments can be configured to provide information relevant to the validation and improvement of modeling approaches, and also how the results of various simulations can be post-processed to improve the possibility of (more or less) direct comparison with experiments. Using the example of some recent experiments carried out on beamline 116 at Diamond Light Source near Oxford, we discuss how such experimental results can be interpreted in view and in conjunction with numerical deformation models, particularly those incorporating dislocation effects, e.g., finite-element based pseudo-continuum strain gradient formulations, and discrete dislocation simulations. Post-processing of FE and discrete dislocation simulations is described, illustrating the kind of information that can be extracted from comparisons between modeling and experimental data.

  6. A jet emission model to probe the dynamics of accretion and ejection coupling in black hole X-ray binaries

    Science.gov (United States)

    Malzac, Julien

    2016-07-01

    Compact jets are probably the most common form of jets in X-ray binaries and Active Galactic Nuclei. They seem to be present in all sources in the so-called hard X-ray spectral state. They are characterised by a nearly flat Spectral Energy Distribution (SED) extending from the radio to the infrared bands. This emission is usually interpreted as partially self absorbed synchrotron emission from relativistic leptons accelerated in the jet. The observed flat spectral shape requires energy dissipation and acceleration of particules over a wide range of distances along the jet. This distributed energy dissipation is likely to be powered by internal shocks caused by fluctuations of the outflow velocity. I will discuss such an internal shock model in the context of black hole binaries. I will show that internal shocks can produce the observed SEDs and also predict a strong, wavelength dependent, variability that resembles the observed one. The assumed velocity fluctuations of the jet must originate in the accretion flow. The model thus predicts a strong connection between the observable properties of the jet in the radio to IR bands, and the variability of the accretion flow as observed in X-rays. If the model is correct, this offers a unique possibility to probe the dynamics of the coupled accretion and ejection processes leading to the formation of compact jets.

  7. Time-evolution of Peak Energy and Luminosity Relation within Pulses for GRB 061007: Probing Fireball Dynamics

    CERN Document Server

    Ohno, Masanori; Yamaoka, Kazutaka; Tashiro, Makoto; Fukazawa, Yasushi; Nakagawa, Yujin E

    2008-01-01

    We perform a time-resolved spectral analysis of bright, long Gamma-ray burst GRB 061007 using Suzaku/WAM and Swift/BAT. Thanks to the large effective area of the WAM, we can investigate the time evolution of the spectral peak energy, Et_peak and the luminosity Lt_iso with 1-sec time resolution, and we find that luminosity Lt_iso with 1-sec time resolution, and we find that the time-resolved pulses also satisfy the Epeak-Liso relation, which was found for the time-averaged spectra of other bursts, suggesting the same physical conditions in each pulse. Furthermore, the initial rising phase of each pulse could be an outlier of this relation with higher Et_peak value by about factor 2. This difference could suggest that the fireball radius expands by a factor of 2-4 and/or bulk Lorentz factor of the fireball is decelerated by a factor of 4 during the initial phase, providing a new probe of the fireball dynamics in real time.

  8. Application of steered molecular dynamics (SMD) to study DNA-drug complexes and probing helical propensity of amino acids

    Energy Technology Data Exchange (ETDEWEB)

    Orzechowski, Marek [Faculty of Chemistry, Warsaw University, 1 Pasteura Street, Warsaw, 02-093 (Poland); Cieplak, Piotr [Accelrys Incorporated, 9685 Scranton Road, San Diego, CA 92121 (United States)

    2005-05-11

    We present the preliminary results of two computer experiments involving the application of an external force to molecular systems. In the first experiment we simulated the process of pulling out a simple intercalator, the 9-aminoacridine molecule, from its complex with a short DNA oligonucleotide in aqueous solution. Removing a drug from the DNA is assumed to be an opposite process to the complex formation. The force and energy profiles suggest that formation of the DNA-9-aminoacridine complex is preferred when the acridine approaches the DNA from the minor groove rather than the major groove side. For a given mode of pulling the intercalation process is also shown to be nucleotide sequence dependent. In another computer experiment we performed a series of molecular dynamics simulations for stretching short, containing 15 amino acids, helical polypeptides in aqueous solution using an external force. The purpose of these simulations is to check whether this type of approach is sensitive enough to probe the sequence dependent helical propensity of short polypeptides.

  9. Halo Wide Binaries and Moving Clusters as probes of the Dynamical and Merger History of our Galaxy

    CERN Document Server

    Allen, C; Hernandez-Alcantara, A; Allen, Christine; Poveda, Arcadio

    2006-01-01

    Wide or fragile pairs are sensitive probes of the galactic potential, and they have been used to provide information about the galactic tidal field, the density of GMC and the masses of dark matter perturbers present in both the disk and the halo. Halo wide binaries and moving clusters, since they are likely to be the remains of past mergers or of dissolved clusters, can provide information on the dynamical and merger history of our Galaxy. Such remnants should continue to show similar motions over times of the order of their ages. We have looked for phase space groupings among the low-metallicity stars of Schuster et al. (2006) and have identified a number of candidate moving clusters. In several of the moving clusters we found a wide CPM binary already identified in our catalogue of wide binaries among high-velocity and metal-poor stars (Allen et al 2000a). Spectroscopic follow-up studies of these stars would confirm the physical reality of the groups, as well as allow us to distinguish whether their progen...

  10. State selective dynamics of molecules, clusters, and nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Keto, John W. [Univ. of Texas, Austin, TX (United States)

    2005-06-01

    Early objectives of this grant were: (1) Measure two-photon excitation of even parity excitons in liquid an solid xenon, (2) Study state-to-state energy transver between two-photon laser excited states or rare-gas atoms to other rare has atoms, (3) study reactive half-collisions between xenon and chlorine leading to the XeCl* B state, (4) measure the spectra of ro-vibrational states of cluster ions and radicals formed in high-pressure discharges and to study their dynamics, (5) measure the surface and bulk electronic states of nanoparticles produced by a unique method of synthesis--laser ablation of microspheres (LAM). Using near-field and microluminescence techniques, we obtained spectra of single nanocrystals to compare with spectra obtained in a supersonic jet apparatus using resonance excitation followed by photoionization (REMPI) with time-of-flight mass analysis. These materials combine the functional advantages obtained from the size-tunable properties of nanocomposite materials with the fabrication and direct-write advantages of NPs manufactured by LAM. We demostrated that CdSe nanoparticles produced by LAM were efficiient fluorescers, even when deposited dry on sapphire substrates. Si nanoparticles were fluorescent when captured in ethylene glycol. We also obtiained efficient fluorescence from Er doped phosphate glass nanopartiicles which have application to gain wafeguides in integrated optics or to nanoslush lasers. We used a femptosecond laser to study the nonlinear spectra of NC composites. We are currently measuring fluorescence and second and third-order susceptibilities of composites of Ag, Si, and GaN nanoparticles encapsulated within thin films of sapphire or SiO 2.

  11. Coordination ligand exchange of a xanthene probe-Ce(III) complex for selective fluorescence sensing of inorganic pyrophosphate.

    Science.gov (United States)

    Kittiloespaisan, Ekkachai; Takashima, Ippei; Kiatpathomchai, Wansika; Wongkongkatep, Jirarut; Ojida, Akio

    2014-02-28

    A fluorescence sensing system for inorganic pyrophosphate based on ligand exchange of the Ce(III) complex of a xanthene-type probe is developed. This sensing system is successfully applied to the fluorescence detection of polymerase-catalyzed DNA amplification using loop-mediated isothermal amplification.

  12. Organic Liquids-Responsive β-Cyclodextrin-Functionalized Graphene-Based Fluorescence Probe: Label-Free Selective Detection of Tetrahydrofuran

    Directory of Open Access Journals (Sweden)

    Huawen Hu

    2014-06-01

    Full Text Available In this study, a label-free graphene-based fluorescence probe used for detection of volatile organic liquids was fabricated by a simple, efficient and low-cost method. To fabricate the probe, a bio-based β-cyclodextrin (β-CD was firstly grafted on reduced graphene surfaces effectively and uniformly, as evidenced by various characterization techniques such as Ultraviolet/Visible spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, thermogravimetric analysis, scanning electron microscopy and transmission electron microscopy. The subsequent inclusion of Rhodamine B (RhB into the inner cavities of the β-CD grafted on the graphene surfaces was achieved easily by a solution mixing method, which yielded the graphene-based fluorescent switch-on probe. In addition, the gradual and controllable quenching of RhB by Fluorescence Resonance Energy Transfer from RhB to graphene during the process of stepwise accommodation of the RhB molecules into the β-CD-functionalized graphene was investigated in depth. A wide range of organic solvents was examined using the as-fabricated fluorescence probe, which revealed the highest sensitivity to tetrahydrofuran with the detection limit of about 1.7 μg/mL. Some insight into the mechanism of the different responsive behaviors of the fluorescence sensor to the examined targets was also described.

  13. Project Icarus: Preliminary Thoughts on the Selection of Probes and Instruments for an Icarus-style Interstellar Mission

    CERN Document Server

    Crawford, Ian A

    2016-01-01

    In this paper we outline the range of probes and scientific instruments that will be required in order for Icarus to fulfill its scientific mission of exploring a nearby star, its attendant planetary system, and the intervening interstellar medium. Based on this preliminary analysis, we estimate that the minimum total Icarus scientific payload mass (i.e. the mass of probes and instruments which must be decelerated to rest in the target system to enable a meaningful programme of scientific investigation) will be in the region of 100 tonnes. Of this, approximately 10 tonnes would be allocated for cruise-phase science instruments, and about 35 tonnes (i.e. the average of estimated lower and upper limits of 28 and 41 tonnes) would be contributed by the intra-system science payload itself (i.e. the dry mass of the stellar and planetary probes and their instruments). The remaining ~55 tonnes is allocated for the sub-probe intra-system propulsion requirements (crudely estimated from current Solar System missions; de...

  14. Monodisperse REPO4 (RE = Yb, Gd, Y) hollow microspheres covered with nanothorns as affinity probes for selectively capturing and labeling phosphopeptides.

    Science.gov (United States)

    Cheng, Gong; Zhang, Ji-Lin; Liu, Yan-Lin; Sun, De-Hui; Ni, Jia-Zuan

    2012-02-13

    Rare-earth phosphate microspheres with unique structures were developed as affinity probes for the selective capture and tagging of phosphopeptides. Prickly REPO(4) (RE = Yb, Gd, Y) monodisperse microspheres, that have hollow structures, low densities, high specific surface areas, and large adsorptive capacities were prepared by an ion-exchange method. The elemental compositions and crystal structures of these affinity probes were confirmed by energy-dispersive spectroscopy (EDS), powder X-ray diffraction (XRD), and Fourier-transform infrared (FTIR) spectroscopy. The morphologies of these compounds were investigated using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and nitrogen-adsorption isotherms. The potential ability of these microspheres for selectively capturing and labeling target biological molecules was evaluated by using protein-digestion analysis and a real sample as well as by comparison with the widely used TiO(2) affinity microspheres. These results show that these porous rare-earth phosphate microspheres are highly promising probes for the rapid purification and recognition of phosphopeptides.

  15. Highly fluorescent carbon dots as selective and sensitive "on-off-on" probes for iron(III) ion and apoferritin detection and imaging in living cells.

    Science.gov (United States)

    Han, Cuiping; Wang, Ru; Wang, Keying; Xu, Huiting; Sui, Meirong; Li, Jingjing; Xu, Kai

    2016-09-15

    Highly blue luminescent nitrogen-doped carbon dots (N-CDs) with a fluorescence quantum yield of 42.3% were prepared by an efficient one-step pyrolytic route from ethylenediaminetetraacetic acid and urea. The as-synthesized N-CDs were demonstrated as an effective fluorescent probe for label-free, selective and sensitive recognition of Fe(3+) with a linear range of 0.5μM to 2mM and a detection limit of 13.6nM due to Fe(3+)-quenched fluorescence (turn-off). The quenched fluorescence could be turned on after the addition of apoferritin owing to the removal of ferric species from the surface of N-CDs by apoferritin, making complex N-CDs/Fe(3+) a selective apoferritin probe with a linear range of 0.1-25μM and a detection limit as low as 2.6nM. In addition, the application of this novel N-CDs-based probe for imaging Fe(3+) ions and apoferritin in living cells suggest that this sensing system has great potential applications in biosensing, bioimaging, and many other fields.

  16. Modeling and prototyping of a fiber Bragg grating-based dynamic micro-coordinate measuring machine probe

    Science.gov (United States)

    Liu, Fangfang; Chen, Lijuan; Wang, Jingfan; Xia, Haojie; Li, Ruijun; Yu, Liandong; Fei, Yetai

    2016-02-01

    Higher-accuracy measurements of the 3D metrology of nano- and micro-structures are increasingly demanded. This paper details the prototyping of a novel 3D micro-scale coordinate measuring machine probe based on fiber Bragg grating sensors for true 3D measurements at micro- and nanometer scales. A new manufacturing technique for the high-precision cantilever used in the probe is also reported. Simulations are performed during the design and testing to help to test important aspects of the probe and to gain understanding about the influence of the probe geometrical parameters on the sensor sensitivity. The initial performance of the probe has been tested in both the vertical and horizontal directions, and the characterization results are promising. Further experimental results demonstrate that the probe is not affected by surface interaction forces.

  17. Home range dynamics, habitat selection, and survival of Greater Roadrunners

    Science.gov (United States)

    Kelley, S.W.; Ransom, D.; Butcher, J.A.; Schulz, G.G.; Surber, B.W.; Pinchak, W.E.; Santamaria, C.A.; Hurtado, L.A.

    2011-01-01

    Greater Roadrunners (Geococcyx californianus) are common, poorly studied birds of arid and semi-arid ecosystems in the southwestern United States. Conservation of this avian predator requires a detailed understanding of their movements and spatial requirements that is currently lacking. From 2006 to 2009, we quantified home-range and core area sizes and overlap, habitat selection, and survival of roadrunners (N= 14 males and 20 females) in north-central Texas using radio-telemetry and fixed kernel estimators. Median home-range and core-area sizes were 90.4 ha and 19.2 ha for males and 80.1 ha and 16.7 ha for females, respectively. The size of home range and core areas did not differ significantly by either sex or season. Our home range estimates were twice as large (x??= 108.9 ha) as earlier published estimates based on visual observations (x??= 28-50 ha). Mean percent overlap was 38.4% for home ranges and 13.7% for core areas. Male roadrunners preferred mesquite woodland and mesquite savanna cover types, and avoided the grass-forb cover type. Female roadrunners preferred mesquite savanna and riparian woodland cover types, and avoided grass-forb habitat. Kaplan-Meier annual survival probabilities for females (0.452 ?? 0.118[SE]) were twice that estimated for males (0.210 ?? 0.108), but this difference was not significant. Mortality rates of male roadrunners were higher than those of females during the spring when males call from elevated perches, court females, and chase competing males. Current land use practices that target woody-shrub removal to enhance livestock forage production could be detrimental to roadrunner populations by reducing availability of mesquite woodland and mesquite savanna habitat required for nesting and roosting and increasing the amount of grass-forb habitat that roadrunners avoid. ??2011 The Authors. Journal of Field Ornithology ??2011 Association of Field Ornithologists.

  18. Impact of unintentional selective harvesting on the population dynamics of red grouse.

    Science.gov (United States)

    Bunnefeld, Nils; Reuman, Daniel C; Baines, David; Milner-Gulland, E J

    2011-11-01

    1. The effect of selective exploitation of certain age, stage or sex classes (e.g., trophy hunting) on population dynamics is relatively well studied in fisheries and sexually dimorphic mammals. 2. Harvesting of terrestrial species with no morphological differences visible between the different age and sex classes (monomorphic species) is usually assumed to be nonselective because monomorphicity makes intentionally selective harvesting pointless and impractical. But harvesting of the red grouse (Lagopus lagopus scoticus), a monomorphic species, was recently shown to be unintentionally selective. This study uses a sex- and age-specific model to explore the previously unresearched effects of unintentional harvesting selectivity. 3. We examine the effects of selectivity on red grouse dynamics by considering models with and without selectivity. Our models include territoriality and parasitism, two mechanisms known to be important for grouse dynamics. 4. We show that the unintentional selectivity of harvesting that occurs in red grouse decreases population yield compared with unselective harvesting at high harvest rates. Selectivity also dramatically increases extinction risk at high harvest rates. 5. Selective harvesting strengthens the 3- to 13-year red grouse population cycle, suggesting that the selectivity of harvesting is a previously unappreciated factor contributing to the cycle. 6. The additional extinction risk introduced by harvesting selectivity provides a quantitative justification for typically implemented 20-40% harvest rates, which are below the maximum sustainable yield that could be taken, given the observed population growth rates of red grouse. 7. This study shows the possible broad importance of investigating in future research whether unintentionally selective harvesting occurs on other species.

  19. Electrons as probes of dynamics in molecules and clusters: A contribution from Time Dependent Density Functional Theory

    Energy Technology Data Exchange (ETDEWEB)

    Wopperer, P. [CNRS, LPT (IRSAMC), 118 route de Narbonne, F-31062 Toulouse Cédex (France); Université de Toulouse, UPS, Laboratoire de Physique Théorique (IRSAMC), 118 route de Narbonne, F-31062 Toulouse Cédex (France); Dinh, P.M., E-mail: dinh@irsamc.ups-tlse.fr [CNRS, LPT (IRSAMC), 118 route de Narbonne, F-31062 Toulouse Cédex (France); Université de Toulouse, UPS, Laboratoire de Physique Théorique (IRSAMC), 118 route de Narbonne, F-31062 Toulouse Cédex (France); Reinhard, P.-G. [Institut für Theoretische Physik, Universität Erlangen, Staudtstrasse 7, D-91058 Erlangen (Germany); Suraud, E. [CNRS, LPT (IRSAMC), 118 route de Narbonne, F-31062 Toulouse Cédex (France); Université de Toulouse, UPS, Laboratoire de Physique Théorique (IRSAMC), 118 route de Narbonne, F-31062 Toulouse Cédex (France); Physics Department, University at Buffalo, The State University New York, Buffalo, NY 14260 (United States)

    2015-02-28

    simplest total ionization signals to the more elaborate PES and PAD, possibly combining them and/or resolving them in time. This experimental discussion will be complemented in a third part by a presentation of available theoretical tools focusing on TDDFT and detailing the methods used to address ionization observables. We shall also discuss the shortcomings of standard versions of TDDFT, especially what concerns the SIC problem, and show how to improve formally and practically the theory on that aspect. A long fourth part will be devoted to representative results. We shall illustrate the use of total ionization in pump and probe scenarios with fs lasers for tracking ionic dynamics in clusters. More challenging from the experimental point of view is pump and probe setups using attosecond pulses. The effort there is more on the capability to define proper signals to be measured/computed at such a short time scale. TDDFT analysis provides here a valuable tool in the search for the most efficient observables. PES and PAD will allow one to address more directly electronic dynamics itself by means of fs or ns laser pulses. We shall in particular discuss the impact of the dynamical regime in PES and PAD. We shall end this fourth part by addressing the role of temperature in PES and PAD. When possible, the results will be directly compared to experiments. The fifth part of the paper will be devoted to future directions of investigations. From the rich choice of developments, we shall in particular address two aspects. We shall start to discuss the information content of energy/angular spectra of emitted electrons in case of excitation by swift and highly charged ions rather than lasers. The second issue concerns the account of dissipative effects in TDDFT to be able to consider longer laser pulses where the competition between direct electron emission and thermalization is known to play a role as, e.g., in experiments with C{sub 60}. Although such questions have been

  20. Electrons as probes of dynamics in molecules and clusters: A contribution from Time Dependent Density Functional Theory

    Science.gov (United States)

    Wopperer, P.; Dinh, P. M.; Reinhard, P.-G.; Suraud, E.

    2015-02-01

    total ionization signals to the more elaborate PES and PAD, possibly combining them and/or resolving them in time. This experimental discussion will be complemented in a third part by a presentation of available theoretical tools focusing on TDDFT and detailing the methods used to address ionization observables. We shall also discuss the shortcomings of standard versions of TDDFT, especially what concerns the SIC problem, and show how to improve formally and practically the theory on that aspect. A long fourth part will be devoted to representative results. We shall illustrate the use of total ionization in pump and probe scenarios with fs lasers for tracking ionic dynamics in clusters. More challenging from the experimental point of view is pump and probe setups using attosecond pulses. The effort there is more on the capability to define proper signals to be measured/computed at such a short time scale. TDDFT analysis provides here a valuable tool in the search for the most efficient observables. PES and PAD will allow one to address more directly electronic dynamics itself by means of fs or ns laser pulses. We shall in particular discuss the impact of the dynamical regime in PES and PAD. We shall end this fourth part by addressing the role of temperature in PES and PAD. When possible, the results will be directly compared to experiments. The fifth part of the paper will be devoted to future directions of investigations. From the rich choice of developments, we shall in particular address two aspects. We shall start to discuss the information content of energy/angular spectra of emitted electrons in case of excitation by swift and highly charged ions rather than lasers. The second issue concerns the account of dissipative effects in TDDFT to be able to consider longer laser pulses where the competition between direct electron emission and thermalization is known to play a role as, e.g., in experiments with C60. Although such questions have been superficially addressed

  1. Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics.

    Directory of Open Access Journals (Sweden)

    Laura Hindersin

    2015-11-01

    Full Text Available We analyze evolutionary dynamics on graphs, where the nodes represent individuals of a population. The links of a node describe which other individuals can be displaced by the offspring of the individual on that node. Amplifiers of selection are graphs for which the fixation probability is increased for advantageous mutants and decreased for disadvantageous mutants. A few examples of such amplifiers have been developed, but so far it is unclear how many such structures exist and how to construct them. Here, we show that almost any undirected random graph is an amplifier of selection for Birth-death updating, where an individual is selected to reproduce with probability proportional to its fitness and one of its neighbors is replaced by that offspring at random. If we instead focus on death-Birth updating, in which a random individual is removed and its neighbors compete for the empty spot, then the same ensemble of graphs consists of almost only suppressors of selection for which the fixation probability is decreased for advantageous mutants and increased for disadvantageous mutants. Thus, the impact of population structure on evolutionary dynamics is a subtle issue that will depend on seemingly minor details of the underlying evolutionary process.

  2. Ultrafast nuclear dynamics in halomethanes studied with time-resolved Coulomb explosion imaging and channel-selective Fourier spectroscopy

    Science.gov (United States)

    Malakar, Y.; Kaderiya, B.; Pearson, W. L.; Ziaee, F.; Kanaka Raju, P.; Zohrabi, M.; Jensen, K.; Rajput, J.; Ben-Itzhak, I.; Rolles, D.; Rudenko, A.

    2016-05-01

    Halomethanes have recently attracted considerable attention since they often serve as prototype systems for laser-controlled chemistry (e.g., selective bond breaking or concerted elimination reactions), and are important molecules in atmospheric chemistry. Here we combine a femtosecond laser pump-probe setup with coincident 3D ion momentum imaging apparatus to study strong-field induced nuclear dynamics in methane and several of its halogenated derivatives (CH3 I, CH2 I2, CH2 ICl). We apply a time-resolved Coulomb explosion imaging technique to map the nuclear motion on both, bound and continuum potential surfaces, disentangle different fragmentation pathways and, for halogenated molecules, observe clear signatures of vibrational wave packets in neutral or ionized states. Channel-selective and kinetic-energy resolved Fourier analysis of these data allows for unique identification of different electronic states and vibrational modes responsible for a particular structure. Supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U. S. DOE. K. R. P. and W. L. P. supported by NSF Award No. IIA-143049. K.J. supported by the NSF-REU Grant No. PHYS-1461251.

  3. Dynamic nuclear polarization and optimal control spatial-selective 13C MRI and MRS

    DEFF Research Database (Denmark)

    Vinding, Mads Sloth; Laustsen, Christoffer; Maximov, Ivan I.

    2013-01-01

    Aimed at 13C metabolic magnetic resonance imaging (MRI) and spectroscopy (MRS) applications, we demonstrate that dynamic nuclear polarization (DNP) may be combined with optimal control 2D spatial selection to simultaneously obtain high sensitivity and well-defined spatial restriction. This is ach......Aimed at 13C metabolic magnetic resonance imaging (MRI) and spectroscopy (MRS) applications, we demonstrate that dynamic nuclear polarization (DNP) may be combined with optimal control 2D spatial selection to simultaneously obtain high sensitivity and well-defined spatial restriction....... This is achieved through the development of spatial-selective single-shot spiral-readout MRI and MRS experiments combined with dynamic nuclear polarization hyperpolarized [1-13C]pyruvate on a 4.7T pre-clinical MR scanner. The method stands out from related techniques by facilitating anatomic shaped region...

  4. Mobile Probing and Probes

    DEFF Research Database (Denmark)

    2013-01-01

    Mobile probing is a method, developed for learning about digital work situations, as an approach to discover new grounds. The method can be used when there is a need to know more about users and their work with certain tasks, but where users at the same time are distributed (in time and space......). Mobile probing was inspired by the cultural probe method, and was influenced by qualitative interview and inquiry approaches. The method has been used in two subsequent projects, involving school children (young adults at 15-17 years old) and employees (adults) in a consultancy company. Findings point...... to mobile probing being a flexible method for uncovering the unknowns, as a way of getting rich data to the analysis and design phases. On the other hand it is difficult to engage users to give in depth explanations, which seem easier in synchronous dialogs (whether online or face2face). The development...

  5. Mobile Probing and Probes

    DEFF Research Database (Denmark)

    2012-01-01

    Mobile probing is a method, which has been developed for learning about digital work situations, as an approach to discover new grounds. The method can be used when there is a need to know more about users and their work with certain tasks, but where users at the same time are distributed (in time...... and space). Mobile probing was inspired by the cultural probe method, and was influenced by qualitative interview and inquiry approaches. The method has been used in two subsequent projects, involving school children (young adults at 15-17 years old) and employees (adults) in a consultancy company. Findings...... point to mobile probing being a flexible method for uncovering the unknowns, as a way of getting rich data to the analysis and design phases. On the other hand it is difficult to engage users to give in depth explanations, which seem easier in synchronous dialogs (whether online or face2face...

  6. Mobile Probing and Probes

    DEFF Research Database (Denmark)

    2012-01-01

    Mobile probing is a method, which has been developed for learning about digital work situations, as an approach to discover new grounds. The method can be used when there is a need to know more about users and their work with certain tasks, but where users at the same time are distributed (in time...... and space). Mobile probing was inspired by the cultural probe method, and was influenced by qualitative interview and inquiry approaches. The method has been used in two subsequent projects, involving school children (young adults at 15-17 years old) and employees (adults) in a consultancy company. Findings...... point to mobile probing being a flexible method for uncovering the unknowns, as a way of getting rich data to the analysis and design phases. On the other hand it is difficult to engage users to give in depth explanations, which seem easier in synchronous dialogs (whether online or face2face...

  7. 6-N,N-dimethylamino-2,3-naphthalimide: a new environment-sensitive fluorescent probe in delta- and mu-selective opioid peptides.

    Science.gov (United States)

    Vázquez, M Eugenio; Blanco, Juan B; Salvadori, Severo; Trapella, Claudio; Argazzi, Roberto; Bryant, Sharon D; Jinsmaa, Yunden; Lazarus, Lawrence H; Negri, Lucia; Giannini, Elisa; Lattanzi, Roberta; Colucci, Mariantonella; Balboni, Gianfranco

    2006-06-15

    A new environment-sensitive fluorophore, 6-N,N-(dimethylamino)-2,3-naphthalimide (6DMN) was introduced in the delta-selective opioid peptide agonist H-Dmt-Tic-Glu-NH(2) and in the mu-selective opioid peptide agonist endomorphin-2 (H-Tyr-Pro-Phe-Phe-NH(2)). Environment-sensitive fluorophores are a special class of chromophores that generally exhibit a low quantum yield in aqueous solution but become highly fluorescent in nonpolar solvents or when bound to hydrophobic sites in proteins or membranes. New fluorescent delta-selective irreversible antagonists (H-Dmt-Tic-Glu-NH-(CH(2))(5)-CO-Dap(6DMN)-NH(2) (1) and H-Dmt-Tic-Glu-Dap(6DMN)-NH(2) (2)) were identified as potential fluorescent probes showing good properties for use in studies of distribution and internalization of delta receptors by confocal laser scanning microscopy.

  8. Electromagnetic radiation as a probe of the initial state and of viscous dynamics in relativistic nuclear collisions

    CERN Document Server

    Vujanovic, Gojko; Denicol, Gabriel S; Luzum, Matthew; Jeon, Sangyong; Gale, Charles

    2016-01-01

    The penetrating nature of electromagnetic signals makes them suitable probes to explore the properties of the strongly-interacting medium created in relativistic nuclear collisions. We examine the effects of the initial conditions and shear relaxation time on the spectra and flow coefficients of electromagnetic probes, using an event-by-event 3+1D viscous hydrodynamic simulation (MUSIC).

  9. Unraveling the sub-processes of selective attention: insights from dynamic modeling and continuous behavior.

    Science.gov (United States)

    Frisch, Simon; Dshemuchadse, Maja; Görner, Max; Goschke, Thomas; Scherbaum, Stefan

    2015-11-01

    Selective attention biases information processing toward stimuli that are relevant for achieving our goals. However, the nature of this bias is under debate: Does it solely rely on the amplification of goal-relevant information or is there a need for additional inhibitory processes that selectively suppress currently distracting information? Here, we explored the processes underlying selective attention with a dynamic, modeling-based approach that focuses on the continuous evolution of behavior over time. We present two dynamic neural field models incorporating the diverging theoretical assumptions. Simulations with both models showed that they make similar predictions with regard to response times but differ markedly with regard to their continuous behavior. Human data observed via mouse tracking as a continuous measure of performance revealed evidence for the model solely based on amplification but no indication of persisting selective distracter inhibition.

  10. Gravity Probe-B Spacecraft attitude control based on the dynamics of slosh wave-induced fluid stress distribution on rotating dewar container of cryogenic propellant

    Science.gov (United States)

    Hung, R. J.; Lee, C. C.; Leslie, F. W.

    1991-01-01

    The dynamical behavior of fluids, in particular the effect of surface tension on partially-filled rotating fluids, in a full-scale Gravity Probe-B Spacecraft propellant dewar tank imposed by various frequencies of gravity jitters have been investigated. Results show that fluid stress distribution exerted on the outer and inner walls of rotating dewar are closely related to the characteristics of slosh waves excited on the liquid-vapor interface in the rotating dewar tank. This can provide a set of tool for the spacecraft dynamic control leading toward the control of spacecraft unbalance caused by the uneven fluid stress distribution due to slosh wave excitations.

  11. Spatio-temporal dynamics of word selection in speech production: Insights from electrocorticography

    Directory of Open Access Journals (Sweden)

    Stephanie K Ries

    2015-04-01

    Our results suggest that the posterior inferior LTC is involved in word selection as semantic concepts become available. Posterior medial and left PFC regions may be involved in trial-by-trial top-down control over LTC to help overcome interference caused by semantically-related alternatives in word selection. The single-case result supports this hypothesis and suggests that the posterior medial PFC plays a causal role in resolving this interference in word selection. Lastly, the sensitivity to semantic interference of the post-vocal onset posterior LTC activity suggests the semantic interference effect does not only reflect word selection difficulty but is also present at post-selection stages such as verbal response monitoring. In sum, this study reveals a dynamic network of interacting brain regions that support word selection in language production.

  12. 示波器阻抗匹配及探头选择问题研究%Research of Impedance Matching of Oscilloscope and Probe Selection

    Institute of Scientific and Technical Information of China (English)

    张秀华

    2013-01-01

    简要介绍了阻抗匹配的原理,分析了示波器测试通道输入阻抗匹配问题以及测试探头的选择问题,为测试人员在进行系统信号测试时提供了参考依据。%It introduces principle of impedance matching , analyses impedance matching of oscilloscope channel and probe selection.References are given to testing personnel during signal of system tested .

  13. Probing the role of Skyrme interactions on the fission dynamics of the 6Li + 238U reaction

    Science.gov (United States)

    Sharma, Ishita; Kumar, Raj; Sharma, Manoj K.

    2017-06-01

    The performance of selected five Skyrme forces (out of a set of 240), tested by Dutra et al., is analyzed in view of fusion-fission dynamics. These forces are assumed to perform better for neutron-rich systems, so the choice of the reaction is accordingly made by opting for a neutron-rich target in 6Li + 238U reaction. This reaction is diagnosed further in reference to fusion hindrance within the dynamical approach of the cluster-decay model (DCM). In order to reduce the computational time, three Skyrme forces are figured out with the criteria that these forces cover the barrier characteristics of the remaining two forces as well. The fission cross-sections are successfully addressed at low energies for the 6Li + 238U reaction. However, at relatively higher energies, the excitation functions show theoretical suppression with respect to experimental data, which may be associated with the possible existence of incomplete fusion (ICF). For ICF, we have considered that the 6Li broke into 4He + 2H, as mentioned in the experimental work. The calculations of ICF are carried out for the 4He + 238U reaction with the selected Skyrme forces at E_{c.m.} = 26.20 and 27.51 MeV. These forces address the data nicely for the compound nucleus (CN) as well as ICF processes. Here, the NRAPR force seems to require lesser barrier modification as compared to the other forces, therefore it can be used as an alternate choice for calculating the interaction potential. Additionally, the prediction of cross-sections at lower energies has been done with DCM using the NRAPR force. The ℓ-dependent % barrier modification of the Skyrme forces undertaken is also worked out in reference to fusion hindrance at below barrier energies.

  14. 11C-MCG: Synthesis, Uptake Selectivity, and Primate PET of a Probe for Glutamate Carboxypeptidase II (NAALADase)

    OpenAIRE

    Pomper, Martin G.; MUSACHIO, JOHN L.; Jiazhong Zhang; Ursula Scheffel; Yun Zhou; John Hilton; Atul Maini; Dannals, Robert F.; Wong, Dean F.; Kozikowski, Alan P.

    2002-01-01

    Imaging of glutamate carboxypeptidase II (GCP II), also known as N-acetylated α-linked l-amino dipeptidase (NAALADase), may enable study of glutamatergic transmission, prostate cancer, and tumor neovasculature in vivo. Our goal was to develop a probe for GCP II for use with positron emission tomography (PET). Radiosynthesis of 11C–MeCys–C(O)–Glu or 11C-(S)-2-[3-((R)-1-carboxy-2-methylsulfanyl-ethyl)-ureido]-pentanedioic acid (11C-MCG), an asymmetric urea and potent (Ki = 1.9 nM) inhibitor of ...

  15. Selective attention to phonology dynamically modulates initial encoding of auditory words within the left hemisphere.

    Science.gov (United States)

    Yoncheva, Yuliya; Maurer, Urs; Zevin, Jason D; McCandliss, Bruce D

    2014-08-15

    Selective attention to phonology, i.e., the ability to attend to sub-syllabic units within spoken words, is a critical precursor to literacy acquisition. Recent functional magnetic resonance imaging evidence has demonstrated that a left-lateralized network of frontal, temporal, and posterior language regions, including the visual word form area, supports this skill. The current event-related potential (ERP) study investigated the temporal dynamics of selective attention to phonology during spoken word perception. We tested the hypothesis that selective attention to phonology dynamically modulates stimulus encoding by recruiting left-lateralized processes specifically while the information critical for performance is unfolding. Selective attention to phonology was captured by manipulating listening goals: skilled adult readers attended to either rhyme or melody within auditory stimulus pairs. Each pair superimposed rhyming and melodic information ensuring identical sensory stimulation. Selective attention to phonology produced distinct early and late topographic ERP effects during stimulus encoding. Data-driven source localization analyses revealed that selective attention to phonology led to significantly greater recruitment of left-lateralized posterior and extensive temporal regions, which was notably concurrent with the rhyme-relevant information within the word. Furthermore, selective attention effects were specific to auditory stimulus encoding and not observed in response to cues, arguing against the notion that they reflect sustained task setting. Collectively, these results demonstrate that selective attention to phonology dynamically engages a left-lateralized network during the critical time-period of perception for achieving phonological analysis goals. These findings suggest a key role for selective attention in on-line phonological computations. Furthermore, these findings motivate future research on the role that neural mechanisms of attention may

  16. A Method for Selecting Software for Dynamic Event Analysis II: the Taylor Anvil and Dynamic Brazilian Tests

    Energy Technology Data Exchange (ETDEWEB)

    W. D. Richins; J. M. Lacy; T. K. Larson; S. R. Novascone

    2008-05-01

    New nuclear power reactor designs will require resistance to a variety of possible malevolent attacks as well as traditional dynamic accident scenarios. The design/analysis team may be faced with a broad range of phenomena including air and ground blasts, high-velocity penetrators or shaped charges, and vehicle or aircraft impacts. With a host of software tools available to address these high-energy events, the analysis team must evaluate and select the software most appropriate for their particular set of problems. The accuracy of the selected software should then be validated with respect to the phenomena governing the interaction of the threat and structure. Several software codes are available for the study of blast, impact, and other shock phenomena. At the Idaho National Laboratory (INL), a study is underway to investigate the comparative characteristics of a group of shock and high-strain rate physics codes including ABAQUS, LS-DYNA, CTH, ALEGRA, and ALE-3D. In part I of this report, a series of five benchmark problems to exercise some important capabilities of the subject software was identified. The benchmark problems selected are a Taylor cylinder test, a split Hopkinson pressure bar test, a free air blast, the dynamic splitting tension (Brazilian) test, and projectile penetration of a concrete slab. Part II-- this paper-- reports the results of two of the benchmark problems: the Taylor cylinder and the dynamic Brazilian test. The Taylor cylinder test is a method to determine the dynamic yield properties of materials. The test specimen is a right circular cylinder which is impacted against a theoretically rigid target. The cylinder deforms upon impact, with the final shape depending upon the dynamic yield stress, in turn a function of strain and strain rate. The splitting tension test, or Brazilian test, is a method to measure the tensile strength of concrete using a cylindrical specimen. The specimen is loaded diametrically in compression, producing a

  17. Probe dependent anomalies in the solvation dynamics of coumarin dyes in dimethyl sulfoxide-glycerol binary solvent: confirming the local environments are different for coumarin dyes.

    Science.gov (United States)

    Koley, Somnath; Kaur, Harveen; Ghosh, Subhadip

    2014-10-28

    The solvation dynamics of coumarin dyes in dimethyl sulfoxide (DMSO)-glycerol (GLY) binary mixtures were studied across the GLY concentrations. Three coumarin dyes with widely different hydrophobicities were used for probing the entire polarity regions of this solvent mixture. Multiple anomalous concentration regions with significantly slow solvation times were detected from all three coumarin dyes. However, their precise positions were found to be probe molecule dependent. The solvation dynamics of the moderately hydrophobic dye coumarin 480 (C480) maintain a plateau region with a similar solvation time (∼550 ps) with the increase in GLY concentration until X(GLY) (the mole fraction of glycerol) reaches 0.5. This plateau region is followed by a sudden slowdown (to ∼975 ps) on the addition of more GLY to the DMSO-GLY mixture, and then this slow region persists from X(GLY)∼ 0.55 to 0.65 (peak at 0.6). On further addition of GLY (X(GLY) > 0.7), the solvation dynamics again become slower to ∼828 ps (at X(GLY)∼ 0.8) from ∼612 ps (at X(GLY)∼ 0.7). For very high GLY-content samples (X(GLY) > 0.85), the solvation times remain similar on further changes of the GLY concentrations. In contrast to C480, the most hydrophobic dye coumarin 153 (C153) shows a linear increase of solvation time in the DMSO-GLY mixture, from 102 ps (at X(GLY)∼ 0.1) to 946 ps (at X(GLY)∼ 0.9) with increase in GLY concentration, except for the concentration region, X(GLY)∼ 0.45-0.55 (peak at 0.5), where a substantial slowdown of the solvation time is observed. The highly hydrophilic probe coumarin 343 (C343) demonstrates multiple concentration regions (X(GLY)∼ 0.05-0.10, 0.25-0.35 and 0.55-0.65) where the solvation dynamics are significantly retarded. The presence of probe dependent anomalies in the DMSO-GLY mixture is a clear indication of there being different locations of probe molecules within this solvent mixture. We assume that the slowing-down of the solvation time could

  18. Selective Adsorption of CO2 from Light Gas Mixtures Using a Structurally Dynamic Porous Coordination Polymer**

    Energy Technology Data Exchange (ETDEWEB)

    Kristi L. Kauffman, Jeffrey T. Culp, Andrew J. Allen, Laura Espinal, Winnie Wong-Ng, Thomas D.

    2010-01-01

    The selective adsorption of CO{sub 2} from mixtures with N{sub 2}, CH{sub 4}, and N{sub 2}O in a dynamic porous coordination polymer (see monomer structure) was evaluated by ATR-FTIR spectroscopy, GC, and SANS. All three techniques indicate highly selective adsorption of CO{sub 2} from CO{sub 2}/CH{sub 4} and CO{sub 2}/N{sub 2} mixtures at 30 C, with no selectivity observed for the CO{sub 2}/N{sub 2}O system.

  19. On dynamic selection of households for direct marketing based on Markov chain models with memory

    NARCIS (Netherlands)

    Otter, Pieter W.

    2007-01-01

    A simple, dynamic selection procedure is proposed, based on conditional, expected profits using Markov chain models with memory. The method is easy to apply, only frequencies and mean values have to be calculated or estimated. The method is empirically illustrated using a data set from a charitable

  20. Selection Dynamics in Joint Matching to Rate and Magnitude of Reinforcement

    Science.gov (United States)

    McDowell, J. J.; Popa, Andrei; Calvin, Nicholas T.

    2012-01-01

    Virtual organisms animated by a selectionist theory of behavior dynamics worked on concurrent random interval schedules where both the rate and magnitude of reinforcement were varied. The selectionist theory consists of a set of simple rules of selection, recombination, and mutation that act on a population of potential behaviors by means of a…