Manufacturing a thin wire electrostatic trap for ultracold polar molecules.

PubMed

Kleinert, J; Haimberger, C; Zabawa, P J; Bigelow, N P

2007-11-01

We present a detailed description on how to build a thin wire electrostatic trap (TWIST) for ultracold polar molecules. It is the first design of an electrostatic trap that can be superimposed directly onto a magneto-optical trap (MOT). We can thus continuously produce ultracold polar molecules via photoassociation from a two species MOT and instantaneously trap them in the TWIST without the need for complex transfer schemes. Despite the spatial overlap of the TWIST and the MOT, the two traps can be operated and optimized completely independently due to the complementary nature of the utilized trapping mechanisms.

Spin-orbit-coupled Bose-Einstein condensates of rotating polar molecules

NASA Astrophysics Data System (ADS)

Deng, Y.; You, L.; Yi, S.

2018-05-01

An experimental proposal for realizing spin-orbit (SO) coupling of pseudospin 1 in the ground manifold 1Σ (υ =0 ) of (bosonic) bialkali polar molecules is presented. The three spin components are composed of the ground rotational state and two substates from the first excited rotational level. Using hyperfine resolved Raman processes through two select excited states resonantly coupled by a microwave, an effective coupling between the spin tensor and linear momentum is realized. The properties of Bose-Einstein condensates for such SO-coupled molecules exhibiting dipolar interactions are further explored. In addition to the SO-coupling-induced stripe structures, the singly and doubly quantized vortex phases are found to appear, implicating exciting opportunities for exploring novel quantum physics using SO-coupled rotating polar molecules with dipolar interactions.

Tunable Holstein model with cold polar molecules

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

Herrera, Felipe; Krems, Roman V.

2011-11-15

We show that an ensemble of polar molecules trapped in an optical lattice can be considered as a controllable open quantum system. The coupling between collective rotational excitations and the motion of the molecules in the lattice potential can be controlled by varying the strength and orientation of an external dc electric field as well as the intensity of the trapping laser. The system can be described by a generalized Holstein Hamiltonian with tunable parameters and can be used as a quantum simulator of excitation energy transfer and polaron phenomena. We show that the character of excitation energy transfer canmore » be modified by tuning experimental parameters.« less

Chip-based microtrap arrays for cold polar molecules

NASA Astrophysics Data System (ADS)

Hou, Shunyong; Wei, Bin; Deng, Lianzhong; Yin, Jianping

2017-12-01

Compared to the atomic chip, which has been a powerful platform to perform an astonishing range of applications from rapid Bose-Einstein condensate (BEC) production to the atomic clock, the molecular chip is only in its infant stages. Recently a one-dimensional electric lattice was demonstrated to trap polar molecules on a chip. This excellent work opens up the way to building a molecular chip laboratory. Here we propose a two-dimensional (2D) electric lattice on a chip with concise and robust structure, which is formed by arrays of squared gold wires. Arrays of microtraps that originate in the microsize electrodes offer a steep gradient and thus allow for confining both light and heavy polar molecules. Theoretical analysis and numerical calculations are performed using two types of sample molecules, N D3 and SrF, to justify the possibility of our proposal. The height of the minima of the potential wells is about 10 μm above the surface of the chip and can be easily adjusted in a wide range by changing the voltages applied on the electrodes. These microtraps offer intriguing perspectives for investigating cold molecules in periodic potentials, such as quantum computing science, low-dimensional physics, and some other possible applications amenable to magnetic or optical lattice. The 2D adjustable electric lattice is expected to act as a building block for a future gas-phase molecular chip laboratory.

Consistent force field modeling of matrix isolated molecules. V. Minimum energy path potential to the conformer conversion of 1,2-difluoroethane: Ar 364, ab initio calculation of electric multipole moments and electric polarization contribution to the conversion barrier

NASA Astrophysics Data System (ADS)

Gunde, R.; Ha, T.-K.; Günthard, H. H.

1990-08-01

In this paper results of consistent force field modeling (CFF) of the potential function to conversion of the gauche (g) to the trans (t) conformer of 1,2-difluoroethane (DFE) isolated in an argon matrix will be reported. Starting point are locally stable configurations gDFE:Ar 364 (defect GH1) and tDFE:Ar 364 (TH1) obtained in previous work from CFF modeling of a cube shaped Ar 364 fragment containing one DFE molecule in its center. Using the dihedral angle of DFE as an independent parameter the minimum energy path of the conversion process gDFE:Ar 364→tDFE:Ar 364 will be determined by CFF energy minimization. Determination of the minimum energy path is found to require large numbers of energy minimization steps and to lead to a rather complicated motion of the molecule with respect to the crystal fragment. Surprisingly the molecule-matrix interactions lead to a reduction of the g-t barrier by ≈500 cal/mol and to a stabilization of the trans species by ≈500 cal/mol. This finding is a consequence of a delicate interplay of matrix-molecule and matrix-matrix interactions. Calculation of the electric polarization energy (induced dipole-first-order polarization approximation) is based on extended ab initio calculations of dipole and quadrupole moments and a bond polarizability estimate of the first-order polarizability of DFE as a function of the internal rotation angle, on Fourier expansion of multipole components and use of symmetry for reduction of the order of the linear system defining the (self-consistent) induced dipole moments of all Ar atoms. Electric polarization is found to alter the potential function of the conversion process in a profound way: the g-t barrier and the t-g energy difference are increased to ≈3000 cal/mol and to ≈1500 cal/mol respectively (≈2500 and ≈530 cal/mol respectively for free DFE). Further applications of the technique developed in this work to related problems of matrix isolated molecules, e.g., vibrational matrix

Calibration of polarimetric radar systems with good polarization isolation

NASA Technical Reports Server (NTRS)

Sarabandi, Kamal; Ulaby, Fawwaz T.; Tassoudji, M. Ali

1990-01-01

A practical technique is proposed for calibrating single-antenna polarimetric radar systems using a metal sphere plus any second target with a strong cross-polarized radar cross section. This technique assumes perfect isolation between antenna ports. It is shown that all magnitudes and phases (relative to one of the like-polarized linear polarization configurations) of the radar transfer function can be calibrated without knowledge of the scattering matrix of the second target. Comparison of the values measured (using this calibration technique) for a tilted cylinder at X-band with theoretical values shows agreement within + or - 0.3 dB in magnitude and + or - 5 degrees in phase. The radar overall cross-polarization isolation was 25 dB. The technique is particularly useful for calibrating a radar under field conditions, because it does not require the careful alignment of calibration targets.

Simulating electric field interactions with polar molecules using spectroscopic databases

NASA Astrophysics Data System (ADS)

Owens, Alec; Zak, Emil J.; Chubb, Katy L.; Yurchenko, Sergei N.; Tennyson, Jonathan; Yachmenev, Andrey

2017-03-01

Ro-vibrational Stark-associated phenomena of small polyatomic molecules are modelled using extensive spectroscopic data generated as part of the ExoMol project. The external field Hamiltonian is built from the computed ro-vibrational line list of the molecule in question. The Hamiltonian we propose is general and suitable for any polar molecule in the presence of an electric field. By exploiting precomputed data, the often prohibitively expensive computations associated with high accuracy simulations of molecule-field interactions are avoided. Applications to strong terahertz field-induced ro-vibrational dynamics of PH3 and NH3, and spontaneous emission data for optoelectrical Sisyphus cooling of H2CO and CH3Cl are discussed.

Microwave-mediated magneto-optical trap for polar molecules

NASA Astrophysics Data System (ADS)

Dizhou, Xie; Wenhao, Bu; Bo, Yan

2016-05-01

Realizing a molecular magneto-optical trap has been a dream for cold molecular physicists for a long time. However, due to the complex energy levels and the small effective Lande g-factor of the excited states, the traditional magneto-optical trap (MOT) scheme does not work very well for polar molecules. One way to overcome this problem is the switching MOT, which requires very fast switching of both the magnetic field and the laser polarizations. Switching laser polarizations is relatively easy, but fast switching of the magnetic field is experimentally challenging. Here we propose an alternative approach, the microwave-mediated MOT, which requires a slight change of the current experimental setup to solve the problem. We calculate the MOT force and compare it with the traditional MOT and the switching MOT scheme. The results show that we can operate a good MOT with this simple setup. Project supported by the Fundamental Research Funds for the Central Universities of China.

Prospects for quantum computing with an array of ultracold polar paramagnetic molecules.

PubMed

Karra, Mallikarjun; Sharma, Ketan; Friedrich, Bretislav; Kais, Sabre; Herschbach, Dudley

2016-03-07

Arrays of trapped ultracold molecules represent a promising platform for implementing a universal quantum computer. DeMille [Phys. Rev. Lett. 88, 067901 (2002)] has detailed a prototype design based on Stark states of polar (1)Σ molecules as qubits. Herein, we consider an array of polar (2)Σ molecules which are, in addition, inherently paramagnetic and whose Hund's case (b) free-rotor pair-eigenstates are Bell states. We show that by subjecting the array to combinations of concurrent homogeneous and inhomogeneous electric and magnetic fields, the entanglement of the array's Stark and Zeeman states can be tuned and the qubit sites addressed. Two schemes for implementing an optically controlled CNOT gate are proposed and their feasibility discussed in the face of the broadening of spectral lines due to dipole-dipole coupling and the inhomogeneity of the electric and magnetic fields.

Electric manipulation of ultracold polar ^40K^87Rb molecules in a magnetic field

NASA Astrophysics Data System (ADS)

Quéméner, Goulven; Bohn, John

2009-05-01

Ultracold fermionic polar molecules of ^40K^87Rb in their absolute rovibronic ground state (v=0,n=0,^1σ) have been created recently [1] in a magnetic trap and open new perspectives to create fermionic degenerate gases of polar molecules. To achieve this goal, it is very important to understand the collisional properties of such molecules under magnetic and electric fields. In our presentation, we investigate ground state fermionic ^40K^87Rb + ^40K^87Rb collisions in the presence of a magnetic field and explore the possibility to control these collisions when an electric field is applied. We will explore the main physical processes that can lead to such manipulation. This problem is complicated by the Zeeman and Stark splitting of all levels of the polar molecules and by the possibility of forming ^40K2 + ^87Rb2 chemical products. 1 - K.-K. Ni, S. Ospelkaus, M. H. G. de Miranda, A. Pe'er, B. Neyenhuis, J. J. Zirbel, S. Kotochigova, P. S. Julienne, D. S. Jin, and J. Ye, Science 322, 231 (2008).

3D-Printed Beam Splitter for Polar Neutral Molecules

NASA Astrophysics Data System (ADS)

Gordon, Sean D. S.; Osterwalder, Andreas

2017-04-01

We describe a macroscopic beam splitter for polar neutral molecules. A complex electrode structure is required for the beam splitter which would be very difficult to produce with traditional manufacturing methods. Instead, we make use of a nascent manufacturing technique: 3D printing of a plastic piece, followed by electroplating. This fabrication method opens a plethora of avenues for research, since 3D printing imposes practically no limitations on possible shapes, and the plating produces chemically robust, conductive construction elements with an almost free choice of surface material. It has the added advantage of dramatically reduced production cost and time. Our beam splitter is an electrostatic hexapole guide that smoothly transforms into two bent quadrupoles. We demonstrate the correct functioning of this device by separating a supersonic molecular beam of ND3 into two correlated fractions. It is shown that this device can be used to implement experiments with differential detection wherein one of the fractions serves as a probe and the other as a reference. Reverse operation would allow the merging of two beams of polar neutral molecules.

Toroidal nanotraps for cold polar molecules

DOE PAGES

Salhi, Marouane; Passian, Ali; Siopsis, George

2015-09-14

Electronic excitations in metallic nanoparticles in the optical regime that have been of great importance in surface-enhanced spectroscopy and emerging applications of molecular plasmonics, due to control and confinement of electromagnetic energy, may also be of potential to control the motion of nanoparticles and molecules. Here, we propose a concept for trapping polarizable particles and molecules using toroidal metallic nanoparticles. Specifically, gold nanorings are investigated for their scattering properties and field distribution to computationally show that the response of these optically resonant particles to incident photons permit the formation of a nanoscale trap when proper aspect ratio, photon wavelength, andmore » polarization are considered. However, interestingly the resonant plasmonic response of the nanoring is shown to be detrimental to the trap formation. The results are in good agreement with analytic calculations in the quasistatic limit within the first-order perturbation of the scalar electric potential. The possibility of extending the single nanoring trapping properties to two-dimensional arrays of nanorings is suggested by obtaining the field distribution of nanoring dimers and trimers.« less

Adsorption of polar organic molecules on sediments: Case-study on Callovian-Oxfordian claystone.

PubMed

Rasamimanana, S; Lefèvre, G; Dagnelie, R V H

2017-08-01

The release and transport of anthropogenic organic matter through the geosphere is often an environmental criterion of safety. Sedimentary rocks are widely studied in this context as geological barriers for waste management. It is the case of Callovian-Oxfordian claystone (COx), for which several studies report adsorption of anthropogenic organic molecules. In this study, we evaluated and reviewed adsorption data of polar organic molecules on COx claystone. Experiments were performed on raw claystone, decarbonated and clay fractions. Adsorption isotherms were measured with adsorbates of various polarities: adipate, benzoate, ortho-phthalate, succinate, gluconate, oxalate, EDTA, citrate. A significant adsorption was observed for multidentate polycarboxylic acids as evidenced with phthalate, succinate, oxalate, gluconate, EDTA and citrate (R d  = 1.53, 3.52, 8.4, 8.8, 12.4, 54.7 L kg -1 respectively). Multiple linear regression were performed as a statistical analysis to determine the predictors from these adsorption data. A linear correlation between adsorption data (R d ) and dipole moment (μ) of adsorbates was evidenced (R 2  = 0.91). Molecules with a high dipole moment, μ(D) > 2.5, displayed a significant adsorption, R d ≫1 L kg -1 . A qualitative correlation can be easily estimated using the water/octanol partition coefficient, P ow , of adsorbates (R 2  = 0.77). In this case, two opposite trends were distinguished for polar and apolar molecules. The use of organic carbon content in sediments is relevant for predicting adsorption of apolar compounds, log (P ow )>+1. The oxides/clays contents may be relevant regarding polar molecules, log ( apparent P ow )<-1. The proposed scheme offers a general methodology for investigation of geo-barriers towards heterogeneous organic plumes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Application of ex situ dynamic nuclear polarization in studying small molecules.

PubMed

Ludwig, Christian; Marin-Montesinos, Ildefonso; Saunders, Martin G; Emwas, Abdul-Hamid; Pikramenou, Zoe; Hammond, Stephen P; Günther, Ulrich L

2010-06-14

Dynamic nuclear polarization (DNP) has become an attractive technique to boost the sensitivity of NMR experiments. In the case of ex situ polarizations two-dimensional (2D) spectra are limited by the short lifetime of the polarization after dissolution and sample transfer to a high field NMR magnet. This limitation can be overcome by various approaches. Here we show how the use of (13)C-labelled acetyl tags can help to obtain 2D-HMQC spectra for many small molecules, owing to a nuclear Overhauser enhancement between (13)C spins originating from the long-lived carbonyl carbon, which extends the lifetimes of other (13)C spins with shorter longitudinal relaxation times. We also show an alternative approach of using an optimized polarization matrix.

Artificial dielectric polarizing-beamsplitter and isolator for the terahertz region.

PubMed

Mendis, Rajind; Nagai, Masaya; Zhang, Wei; Mittleman, Daniel M

2017-07-19

We demonstrate a simple and effective strategy for implementing a polarizing beamsplitter for the terahertz spectral region, based on an artificial dielectric medium that is scalable to a range of desired frequencies. The artificial dielectric medium consists of a uniformly spaced stack of metal plates, which is electromagnetically equivalent to a stacked array of parallel-plate waveguides. The operation of the device relies on both the lowest-order, transverse-electric and transverse-magnetic modes of the parallel-plate waveguide. This is in contrast to previous work that relied solely on the transverse-electric mode. The fabricated polarizing beamsplitter exhibits extinction ratios as high as 42 dB along with insertion losses as low as 0.18 dB. Building on the same idea, we also demonstrate an isolator with non-reciprocal transmission, providing high isolation and low insertion loss at a select design frequency. The performance of our isolator far exceeds that of other experimentally demonstrated terahertz isolators, and indeed, even rivals that of commercially available isolators for optical wavelengths. Because these waveguide-based artificial dielectrics are low loss, inexpensive, and easy to fabricate, this approach offers a promising new route for polarization control of free-space terahertz beams.

Generation of isolated asymmetric umbilics in light's polarization

NASA Astrophysics Data System (ADS)

Galvez, Enrique J.; Rojec, Brett L.; Kumar, Vijay; Viswanathan, Nirmal K.

2014-03-01

Polarization-singularity C points, a form of line singularities, are the vectorial counterparts of the optical vortices of spatial modes and fundamental optical features of polarization-spatial modes. Their generation in tailored beams has been limited to so-called "lemon" and "star" C points that contain symmetric dislocations in state-of-polarization patterns. In this Rapid Communication we present the theory and laboratory measurements of two complementary methods to generate isolated asymmetric C points in tailored beams, of which symmetric lemon and star patterns are limiting cases; and we report on the generation of so-called "monstar" patterns, an asymmetric C point with characteristics of both lemons and stars.

Influence of intrinsic decoherence on tripartite entanglement and bipartite fidelity of polar molecules in pendular states.

PubMed

Han, Jia-Xing; Hu, Yuan; Jin, Yu; Zhang, Guo-Feng

2016-04-07

An array of ultracold polar molecules trapped in an external electric field is regarded as a promising carrier of quantum information. Under the action of this field, molecules are compelled to undergo pendular oscillations by the Stark effect. Particular attention has been paid to the influence of intrinsic decoherence on the model of linear polar molecular pendular states, thereby we evaluate the tripartite entanglement with negativity, as well as fidelity of bipartite quantum systems for input and output signals using electric dipole moments of polar molecules as qubits. According to this study, we consider three typical initial states for both systems, respectively, and investigate the temporal evolution with variable values of the external field intensity, the intrinsic decoherence factor, and the dipole-dipole interaction. Thus, we demonstrate the sound selection of these three main parameters to obtain the best entanglement degree and fidelity.

High-Isolation Low Cross-Polarization Phased-Array Antenna for MPAR Application

NASA Astrophysics Data System (ADS)

Saeidi-Manesh, Hadi; Karimkashi, Shaya; Zhang, Guifu; Doviak, Richard J.

2017-12-01

The design and analysis of 12 × 12-element planar array of a dual-polarized aperture-coupled microstrip patch antenna operating in the frequency band of 2.7 GHz to 3.0 GHz for multifunction applications are presented. High-isolation between horizontal and vertical polarization ports and low cross-polarization are achieved through an aperture-coupled feed. The reflection coefficient and the isolation of horizontal and vertical ports at different scan angles are examined. The array antenna is fabricated and its radiation patterns are measured in the far-field and near-field chambers. The embedded element pattern of designed element is measured in the near-field chamber and is used for calculating the array scanning radiation pattern.

Oriented Polar Molecules in a Solid Inert-Gas Matrix: A Proposed Method for Measuring the Electric Dipole Moment of the Electron

NASA Astrophysics Data System (ADS)

Vutha, A.; Horbatsch, M.; Hessels, E.

2018-01-01

We propose a very sensitive method for measuring the electric dipole moment of the electron using polar molecules embedded in a cryogenic solid matrix of inert-gas atoms. The polar molecules can be oriented in the $\\hat{\\rm{z}}$ direction by an applied electric field, as has recently been demonstrated by Park, et al. [Angewandte Chemie {\\bf 129}, 1066 (2017)]. The trapped molecules are prepared into a state which has its electron spin perpendicular to $\\hat{\\rm{z}}$, and a magnetic field along $\\hat{\\rm{z}}$ causes precession of this spin. An electron electric dipole moment $d_e$ would affect this precession due to the up to 100~GV/cm effective electric field produced by the polar molecule. The large number of polar molecules that can be embedded in a matrix, along with the expected long coherence times for the precession, allows for the possibility of measuring $d_e$ to an accuracy that surpasses current measurements by many orders of magnitude. Because the matrix can inhibit molecular rotations and lock the orientation of the polar molecules, it may not be necessary to have an electric field present during the precession. The proposed technique can be applied using a variety of polar molecules and inert gases, which, along with other experimental variables, should allow for careful study of systematic uncertainties in the measurement.

Polar order in nanostructured organic materials

NASA Astrophysics Data System (ADS)

Sayar, M.; Olvera de la Cruz, M.; Stupp, S. I.

2003-02-01

Achiral multi-block liquid crystals are not expected to form polar domains. Recently, however, films of nanoaggregates formed by multi-block rodcoil molecules were identified as the first example of achiral single-component materials with macroscopic polar properties. By solving an Ising-like model with dipolar and asymmetric short-range interactions, we show here that polar domains are stable in films composed of aggregates as opposed to isolated molecules. Unlike classical molecular systems, these nanoaggregates have large intralayer spacings (a approx 8 nm), leading to a reduction in the repulsive dipolar interactions which oppose polar order within layers. In finite-thickness films of nanostructures, this effect enables the formation of polar domains. We compute exactly the energies of the possible structures consistent with the experiments as a function of film thickness at zero temperature (T). We also provide Monte Carlo simulations at non-zero T for a disordered hexagonal lattice that resembles the smectic-like packing in these nanofilms.

Influence of intrinsic decoherence on tripartite entanglement and bipartite fidelity of polar molecules in pendular states

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

Han, Jia-Xing; Hu, Yuan; Jin, Yu

An array of ultracold polar molecules trapped in an external electric field is regarded as a promising carrier of quantum information. Under the action of this field, molecules are compelled to undergo pendular oscillations by the Stark effect. Particular attention has been paid to the influence of intrinsic decoherence on the model of linear polar molecular pendular states, thereby we evaluate the tripartite entanglement with negativity, as well as fidelity of bipartite quantum systems for input and output signals using electric dipole moments of polar molecules as qubits. According to this study, we consider three typical initial states for bothmore » systems, respectively, and investigate the temporal evolution with variable values of the external field intensity, the intrinsic decoherence factor, and the dipole-dipole interaction. Thus, we demonstrate the sound selection of these three main parameters to obtain the best entanglement degree and fidelity.« less

Investigating phonon-mediated interactions with polar molecules

NASA Astrophysics Data System (ADS)

Sous, John; Madison, Kirk; Berciu, Mona; Krems, Roman

2017-04-01

We show that an ensemble of polar molecules in an optical lattice realizes the Peierls polaron model for hard-core particles/ pseudospins. We analyze the quasiparticle spectrum in the one-particle subspace, the two-particle subspace and at finite concentrations. We derive an effective model that describes the low-energy behavior of the system. We show that the Hamiltonian includes phonon-mediated repulsions and phonon-mediated ``pair-hopping'' terms which move the particle pair as a whole. We show that microwave excitations of the system exhibit signatures of these interactions. These results pave the way for the experimental observation of phonon-mediated repulsion. This work was supported by NSERC of Canada and the Stewart Blusson Quantum Matter Institute.

Hydration of polar and nonpolar molecules at the surface of amorphous solid water

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

Souda, Ryutaro

2004-10-15

On the basis of time-of-flight secondary ion mass spectrometry, properties of amorphous solid water above the glass transition temperature (136 K) and the hydration of polar (HCOOH,C{sub 3}H{sub 7}OH) and nonpolar (C{sub 6}H{sub 14},C{sub 6}F{sub 14}) molecules on the D{sub 2}O-ice surface have been investigated. No evidence was obtained for the irreversible transition of the amorphous solid water into the crystalline phase: the self-diffusion of water molecules occurs above 140 K irrespective of the preparation temperatures of the water-ice film ranging from 15 K to 165 K, whereas the morphology of the film changes drastically at 165 K due tomore » the evolution of liquidlike water. It is also demonstrated that the change in conformation of the hydrated HCOOH molecule, as well as the occurrence of hydrophilic/hydrophobic hydration of the C{sub 3}H{sub 7}OH molecule, can be analyzed successfully from the temperature evolutions of the secondary-ion intensities. These polar molecules basically stay on the surface and tend to quench the morphological change of the water film due to the reduction of surface tension. The nonpolar C{sub 6}H{sub 14} and C{sub 6}F{sub 14} molecules readily dissolve in the D{sub 2}O layer below 100 K and dehydration of the incorporated molecules occurs at 165 K concomitantly with the evolution of the liquidlike water. It is thus concluded that the hydrophobic hydration of nonpolar molecules is intimately related to the properties of water films.« less

Design of magnetic system to produce intense beam of polarized molecules of H2 and D2

NASA Astrophysics Data System (ADS)

Yurchenko, A. V.; Nikolenko, D. M.; Rachek, I. A.; Shestakov, Yu V.; Toporkov, D. K.; Zorin, A. V.

2017-12-01

A magnetic-separating system is designed to produce polarized molecular high-density beams of H2/D2. The distribution of the magnetic field inside the aperture of the multipole magnet was calculated using the Mermaid software package. The calculation showed that the characteristic value of the magnetic field is 40 kGs, the field gradient is about 60 kGs/cm. A numerical calculation of the trajectories of the motion of molecules with different spin projections in this magnetic system is performed. The article discusses the possibility of using the magnetic system designed for the creation of a high-intensity source of polarized molecules. The expected intensity of this source is calculated. The expected flux of molecules focused in the receiver tube is 3.5·1016 mol/s for the hydrogen molecule and 2.0·1015 mol/s for the deuterium molecule.

The Use of Orthogonal Polarizations in Microwave Imagery of Isolated Canine Kidney

NASA Astrophysics Data System (ADS)

Larsen, L. E.; Jacobi, J. H.

1980-06-01

A method of imaging biological targets using microwave radiation at a frequency of 4 GHz is presented. Linearly polarized radiation is transmitted through an isolated canine kidney and received with co-polarized and cross-polarized antennas. Images are displayed as the spatial variation of the magnitude of the transmission scattering parameter S21 for each mode of polarization. The relationship between the spatial variation of the magnitude of S21 and canine renal anatomy is discussed. It is shown that within the kidney the cross-polarized image tends to emphasize linear or piecewise linear structures, whereas the co-polarized image balances renal cortical lobulations.

Highly efficient spin polarizer based on individual heterometallic cubane single-molecule magnets

NASA Astrophysics Data System (ADS)

Dong, Damin

2015-09-01

The spin-polarized transport across a single-molecule magnet [Mn3Zn(hmp)3O(N3)3(C3H5O2)3].2CHCl3 has been investigated using a density functional theory combined with Keldysh non-equilibrium Green's function formalism. It is shown that this single-molecule magnet has perfect spin filter behaviour. By adsorbing Ni3 cluster onto non-magnetic Au electrode, a large magnetoresistance exceeding 172% is found displaying molecular spin valve feature. Due to the tunneling via discrete quantum-mechanical states, the I-V curve has a stepwise character and negative differential resistance behaviour.

Implementation of quantum logic gates using polar molecules in pendular states.

PubMed

Zhu, Jing; Kais, Sabre; Wei, Qi; Herschbach, Dudley; Friedrich, Bretislav

2013-01-14

We present a systematic approach to implementation of basic quantum logic gates operating on polar molecules in pendular states as qubits for a quantum computer. A static electric field prevents quenching of the dipole moments by rotation, thereby creating the pendular states; also, the field gradient enables distinguishing among qubit sites. Multi-target optimal control theory is used as a means of optimizing the initial-to-target transition probability via a laser field. We give detailed calculations for the SrO molecule, a favorite candidate for proposed quantum computers. Our simulation results indicate that NOT, Hadamard and CNOT gates can be realized with high fidelity, as high as 0.985, for such pendular qubit states.

Low-Temperature Reactivity of C2n+1N(-) Anions with Polar Molecules.

PubMed

Joalland, Baptiste; Jamal-Eddine, Nour; Kłos, Jacek; Lique, François; Trolez, Yann; Guillemin, Jean-Claude; Carles, Sophie; Biennier, Ludovic

2016-08-04

Following the recent discovery of molecular anions in the interstellar medium, we report on the kinetics of proton transfer reactions between cyanopolyynide anions C2n+1N(-) (n = 0, 1, 2) and formic acid HCOOH. The results, obtained from room temperature down to 36 K by means of uniform supersonic flows, show a surprisingly weak temperature dependence of the CN(-) reaction rate, in contrast with longer chain anions. The CN(-) + HCOOH reaction is further studied theoretically via a reduced dimensional quantum model that highlights a tendency of the reaction probability to decrease with temperature, in agreement with experimental data but at the opposite of conventional long-range capture theories. In return, comparing HCOOH to HC3N as target molecules suggests that dipole-dipole interactions must play an active role in overcoming this limiting effect at low temperatures. This work provides new fundamental insights on prototypical reactions between polar anions and polar molecules along with critical data for astrochemical modeling.

Isolated elliptically polarized attosecond soft X-ray with high-brilliance using polarization gating of harmonics from relativistic plasmas at oblique incidence.

PubMed

Chen, Zi-Yu; Li, Xiao-Ya; Li, Bo-Yuan; Chen, Min; Liu, Feng

2018-02-19

The production of intense isolated attosecond pulse is a major goal in ultrafast research. Recent advances in high harmonic generation from relativistic plasma mirrors under oblique incidence interactions gave rise to photon-rich attosecond pulses with circular or elliptical polarization. However, to achieve an isolated elliptical attosecond pulse via polarization gating using currently available long driving pulses remains a challenge, because polarization gating of high harmonics from relativistic plasmas is assumed only possible at normal or near-normal incidence. Here we numerically demonstrate a scheme around this problem. We show that via control of plasma dynamics by managing laser polarization, it is possible to gate an intense single attosecond pulse with high ellipticity extending to the soft X-ray regime at oblique incidence. This approach thus paves the way towards a powerful tool enabling high-time-resolution probe of dynamics of chiral systems and magnetic materials with current laser technology.

Generation of circularly polarized XUV and soft-x-ray high-order harmonics by homonuclear and heteronuclear diatomic molecules subject to bichromatic counter-rotating circularly polarized intense laser fields

NASA Astrophysics Data System (ADS)

Heslar, John; Telnov, Dmitry A.; Chu, Shih-I.

2017-12-01

Recently, studies of bright circularly polarized high-harmonic beams from atoms in the soft-x-ray region as a source for x-ray magnetic circular dichroism measurement in a tabletop-scale setup have received considerable attention. In this paper, we address the problem with molecular targets and perform a detailed quantum study of H2 +, CO, and N2 molecules in bichromatic counter-rotating circularly polarized laser fields where we adopt wavelengths (1300 and 790 nm) and intensities (2 ×1014W /cm2 ) reported in a recent experiment [Proc. Natl. Acad. Sci. USA 112, 14206 (2015), 10.1073/pnas.1519666112]. Our treatment of multiphoton processes in homonuclear and heteronuclear diatomic molecules is nonperturbative and based on the time-dependent density-functional theory for multielectron systems. The calculated radiation spectrum contains doublets of left and right circularly polarized harmonics with high-energy photons in the XUV and soft-x-ray ranges. Our results reveal intriguing and substantially different nonlinear optical responses for homonuclear and heteronuclear diatomic molecules subject to circularly polarized intense laser fields. We study in detail the below- and above-threshold harmonic regions and analyze the ellipticity and phase of the generated harmonic peaks.

Superfluidity of identical fermions in an optical lattice: Atoms and polar molecules

NASA Astrophysics Data System (ADS)

Fedorov, A. K.; Yudson, V. I.; Shlyapnikov, G. V.

2018-02-01

In this work we discuss the emergence of p-wave superfluids of identical fermions in 2D lattices. The optical lattice potential manifests itself in an interplay between an increase in the density of states on the Fermi surface and the modification of the fermion-fermion interaction (scattering) amplitude. The density of states is enhanced due to an increase of the effective mass of atoms. In deep lattices, for short-range interacting atoms the scattering amplitude is strongly reduced compared to free space due to a small overlap of wavefunctions of fermions sitting in the neighboring lattice sites, which suppresses the p-wave superfluidity. However, we show that for a moderate lattice depth there is still a possibility to create atomic p-wave superfluids with sizable transition temperatures. The situation is drastically different for fermionic polar molecules. Being dressed with a microwave field, they acquire a dipole-dipole attractive tail in the interaction potential. Then, due to a long-range character of the dipole-dipole interaction, the effect of the suppression of the scattering amplitude in 2D lattices is absent. This leads to the emergence of a stable topological px + ipy superfluid of identical microwave-dressed polar molecules.

Spherical tensor analysis of polar liquid crystals with biaxial and chiral molecules

NASA Astrophysics Data System (ADS)

Iwamoto, Mitsumasa; Zhong-can, Ou-Yang

2012-11-01

With the help of spherical tensor expression, an irreducible calculus of a Lth-rank macroscopic susceptibility χ for a polar liquid crystal (PLC) of biaxial and chiral molecules written as the average of molecular hyperpolarizability tensor β associated with their spherical orientational order parameters (0⩽l⩽L) is presented. Comprehensive formulas of L=1,2 have been obtained and the latter explains the optical activity and spontaneous splay texture observed in bent-core PLC. The expression of L=3 specifies for the molecules with D2 symmetry which can be applied to analyze the nonlinear optical second harmonic generation (SHG) observed in proteins, peptides, and double-stranded DNA at interfaces.

Major histocompatibility complex class I molecules modulate embryonic neuritogenesis and neuronal polarization

PubMed Central

Bilousova, Tina; Dang, Hoa; Xu, Willem; Gustafson, Sarah; Jin, Yingli; Wickramasinghe, Lalinda; Won, Tony; Bobarnac, Gabriela; Middleton, Blake; Tian, Jide; Kaufman, Daniel L.

2012-01-01

We studied cultured hippocampal neurons from embryonic wildtype, major histocompatibility complex class I (MHCI) heavy chain-deficient (KbDb−/−) and NSE-Db (which have elevated neuronal MHCI expression) C57BL/6 mice. KbDb−/− neurons displayed slower neuritogenesis and establishment of polarity, while NSE-Db neurons had faster neurite outgrowth, more primary neurites, and tended to have accelerated polarization. Additional studies with ϐ2M−/− neurons, exogenous ϐ2M, and a self-MHCI monomer suggest that free heavy chain cis interactions with other surface molecules can promote neuritogenesis while tripartite MHCI interactions with classical MHCI receptors can inhibit axon outgrowth. Together with the results of others, MHCI appears to differentially modulate neuritogenesis and synaptogenesis. PMID:22503373

Entangled photons from single atoms and molecules

NASA Astrophysics Data System (ADS)

Nordén, Bengt

2018-05-01

The first two-photon entanglement experiment performed 50 years ago by Kocher and Commins (KC) provided isolated pairs of entangled photons from an atomic three-state fluorescence cascade. In view of questioning of Bell's theorem, data from these experiments are re-analyzed and shown sufficiently precise to confirm quantum mechanical and dismiss semi-classical theory without need for Bell's inequalities. Polarization photon correlation anisotropy (A) is useful: A is near unity as predicted quantum mechanically and well above the semi-classic range, 0 ⩽ A ⩽ 1 / 2 . Although yet to be found, one may envisage a three-state molecule emitting entangled photon pairs, in analogy with the KC atomic system. Antibunching in fluorescence from single molecules in matrix and entangled photons from quantum dots promise it be possible. Molecules can have advantages to parametric down-conversion as the latter photon distribution is Poissonian and unsuitable for producing isolated pairs of entangled photons. Analytical molecular applications of entangled light are also envisaged.

Why Do Simple Molecules with "Isolated" Phenyl Rings Emit Visible Light?

PubMed

Zhang, Haoke; Zheng, Xiaoyan; Xie, Ni; He, Zikai; Liu, Junkai; Leung, Nelson L C; Niu, Yingli; Huang, Xuhui; Wong, Kam Sing; Kwok, Ryan T K; Sung, Herman H Y; Williams, Ian D; Qin, Anjun; Lam, Jacky W Y; Tang, Ben Zhong

2017-11-15

π-Bonds connected with aromatic rings were generally believed as the standard structures for constructing highly efficient fluorophores. Materials without these typical structures, however, exhibited only low fluorescence quantum yields and emitted in the ultraviolet spectral region. In this work, three molecules, namely bis(2,4,5-trimethylphenyl)methane, 1,1,2,2-tetrakis(2,4,5-trimethylphenyl)ethane, and 1,1,2,2-tetraphenylethane, with nonconjugated structures and isolated phenyl rings were synthesized and their photophysical properties were systematically investigated. Interestingly, the emission spectra of these three molecules could be well extended to 600 nm with high solid-state quantum yields of up to 70%. Experimental and theoretical analyses proved that intramolecular through-space conjugation between the "isolated" phenyl rings played an important role for this abnormal phenomenon.

Ultrafast inter- and intramolecular vibrational energy transfer between molecules at interfaces studied by time- and polarization-resolved SFG spectroscopy.

PubMed

Yamamoto, Susumu; Ghosh, Avishek; Nienhuys, Han-Kwang; Bonn, Mischa

2010-10-28

We present experimental results on femtosecond time-resolved surface vibrational spectroscopy aimed at elucidating the sub-picosecond reorientational dynamics of surface molecules. The approach, which relies on polarization- and time-resolved surface sum frequency generation (SFG), provides a general means to monitor interfacial reorientational dynamics through vibrations inherent in surface molecules in their electronic ground state. The technique requires an anisotropic vibrational excitation of surface molecules using orthogonally polarized infrared excitation light. The decay of the resulting anisotropy is followed in real-time. We employ the technique to reveal the reorientational dynamics of vibrational transition dipoles of long-chain primary alcohols on the water surface, and of water molecules at the water-air interface. The results demonstrate that, in addition to reorientational motion of specific molecules or molecular groups at the interface, inter- and intramolecular energy transfer processes can serve to scramble the initial anisotropy very efficiently. In the two exemplary cases demonstrated here, energy transfer occurs much faster than reorientational motion of interfacial molecules. This has important implications for the interpretation of static SFG spectra. Finally, we suggest experimental schemes and strategies to decouple effects resulting from energy transfer from those associated with surface molecular motion.

Optically stimulated slowing of polar heavy-atom molecules with a constant beat phase

NASA Astrophysics Data System (ADS)

Yin, Yanning; Xu, Supeng; Xia, Meng; Xia, Yong; Yin, Jianping

2018-04-01

Polar heavy-atom molecules have been well recognized as promising candidates for precision measurements and tests of fundamental physics. A much slower molecular beam to increase the interaction time should lead to a more sensitive measurement. Here we theoretically demonstrate the possibility of the stimulated longitudinal slowing of heavy-atom molecules by the coherent optical bichromatic force with a constant beat phase. Taking the YbF meolecule as an example, we show that a rapid and short-distance deceleration of heavy molecules by a phase-compensation method is feasible with moderate conditions. A molecular beam of YbF with a forward velocity of 120 m/s can be decelerated below 10 m/s within a distance of 3.5 cm and with a laser irradiance for each traveling wave of 107.2 W/cm 2 . Our proposed slowing method could be a promising approach to break through the space constraint or the limited capture efficiency of molecules loadable into a magneto-optical trap in traditional deceleration schemes, opening the possibility for a significant improvement of the precision measurement sensitivity.

The swimming polarity of multicellular magnetotactic prokaryotes can change during an isolation process employing magnets: evidence of a relation between swimming polarity and magnetic moment intensity.

PubMed

de Melo, Roger Duarte; Acosta-Avalos, Daniel

2017-09-01

Magnetotactic microorganisms are characterized by swimming in the direction of an applied magnetic field. In nature, two types of swimming polarity have been observed: north-seeking microorganisms that swim in the same direction as the magnetic field, and south-seeking microorganisms that swim in the opposite direction. The present work studies the reversal in the swimming polarity of the multicellular magnetotactic prokaryote Candidatus Magnetoglobus multicellularis following an isolation process using high magnetic fields from magnets. The proportion of north- and south-seeking organisms was counted as a function of the magnetic field intensity used during the isolation of the organisms from sediment. It was observed that the proportion of north-seeking organisms increased when the magnetic field was increased. The magnetic moment for north- and south-seeking populations was estimated using the U-turn method. The average magnetic moment was higher for north- than south-seeking organisms. The results suggest that the reversal of swimming polarity must occur during the isolation process in the presence of high magnetic fields and magnetic field gradients. It is shown for the first time that the swimming polarity reversal depends on the magnetic moment intensity of multicellular magnetotactic prokaryotes, and new studies must be undertaken to understand the role of magnetic moment polarity and oxygen gradients in determination of swimming polarity.

The influence of polarity of additive molecules on micelle structures of polystyrene-block-poly(4-vinylpyridine) in the fabrication of nano-porous templates.

PubMed

Chua, Kee Sze; Koh, Ai Peng; Lam, Yeng Ming

2010-11-01

Block copolymers are useful for in situ synthesis of nanoparticles as well as producing nanoporous templates. As such, the effects of precursors on the block copolymer micelle structure is important. In this study, we investigate the effects of polarity of molecules introduced into block copolymer micelle cores on the micelle structure. The molecular dipole moment of the additive molecules has been evaluated and their effects on the block copolymer micelles investigated using light scattering spectroscopy, small-angle X-ray scattering, transmission electron microscopy and atomic force microscopy. The molecule with the largest dipole moment resulted in spherical structures with a polydispersity of less than 0.06 in a fully translational diffusion system. Surprisingly, the less polar additive molecules produced elongated micelles and the aspect ratio increases with decreasing polarity. The change in structure from spherical to elongated structure was attributed to P4VP chain extension, where compounds with polarity most similar to P4VP induce the most chain extension. The second virial coefficients of the solutions with elongated micelles are lower than that for spherical micelle systems by up to one order in magnitude, indicating a strong tendency for micelles to coalesce. On rinsing the spin-cast films, pores were obtained from spherical micelles and ridges from elongated micelles, suggesting a viable alternative for morphology modification using mild conditions where external annealing treatments to the film are not preferred. The knowledge of polarity effects of additive molecules on micelle structure has wider implications for supramolecular block copolymer systems where, depending on the application requirements, changes to the shape of the micelle structure can be induced or avoided. Copyright 2010 Elsevier Inc. All rights reserved.

Magnetic cooling at a single molecule level: a spectroscopic investigation of isolated molecules on a surface.

PubMed

Corradini, Valdis; Ghirri, Alberto; Candini, Andrea; Biagi, Roberto; del Pennino, Umberto; Dotti, Gianluca; Otero, Edwige; Choueikani, Fadi; Blagg, Robin J; McInnes, Eric J L; Affronte, Marco

2013-05-28

A sub-monolayer distribution of isolated molecular Fe14 (bta)6 nanomagnets is deposited intact on a Au(111) surface and investigated by X-ray magnetic circular dichroism spectroscopy. The entropy variation with respect to the applied magnetic field is extracted from the magnetization curves and evidences high magnetocaloric values at the single molecule level. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigation of N-acyl homoserine lactone (AHL) molecule production in Gram-negative bacteria isolated from cooling tower water and biofilm samples.

PubMed

Haslan, Ezgi; Kimiran-Erdem, Ayten

2013-09-01

In this study, 99 Gram-negative rod bacteria were isolated from cooling tower water, and biofilm samples were examined for cell-to-cell signaling systems, N-acyl homoserine lactone (AHL) signal molecule types, and biofilm formation capacity. Four of 39 (10 %) strains isolated from water samples and 14 of 60 (23 %) strains isolated from biofilm samples were found to be producing a variety of AHL signal molecules. It was determined that the AHL signal molecule production ability and the biofilm formation capacity of sessile bacteria is higher than planktonic bacteria, and there was a statistically significant difference between the AHL signal molecule production of these two groups (p < 0.05). In addition, it was found that bacteria belonging to the same species isolated from cooling tower water and biofilm samples produced different types of AHL signal molecules and that there were different types of AHL signal molecules in an AHL extract of bacteria. In the present study, it was observed that different isolates of the same strains did not produce the same AHLs or did not produce AHL molecules, and bacteria known as AHL producers did not produce AHL. These findings suggest that detection of signal molecules in bacteria isolated from cooling towers may contribute to prevention of biofilm formation, elimination of communication among bacteria in water systems, and blockage of quorum-sensing controlled virulence of these bacteria.

Matrix isolation sublimation: An apparatus for producing cryogenic beams of atoms and molecules

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

Sacramento, R. L.; Alves, B. X.; Silva, B. A.

2015-07-15

We describe the apparatus to generate cryogenic beams of atoms and molecules based on matrix isolation sublimation. Isolation matrices of Ne and H{sub 2} are hosts for atomic and molecular species which are sublimated into vacuum at cryogenic temperatures. The resulting cryogenic beams are used for high-resolution laser spectroscopy. The technique also aims at loading atomic and molecular traps.

Magnetic moment enhancement and spin polarization switch of the manganese phthalocyanine molecule on an IrMn(100) surface

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

Sun, X.; National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047; Wang, B.

2014-07-21

The geometric, electronic, and magnetic structures of a manganese phthalocyanine (MnPc) molecule on an antiferromagnetic IrMn(100) surface are studied by density functional theory calculations. Two kinds of orientation of the adsorbed MnPc molecule are predicted to coexist due to molecular self-assembly on the surface—a top-site geometry with the Mn–N bonds aligned along the 〈100〉 direction, and a hollow-site orientation in which the Mn–N bonds are parallel to the 〈110〉 direction. The MnPc molecule is antiferromagnetically coupled to the substrate at the top site with a slight reduction in the magnetic moment of the Mn atom of the MnPc molecule (Mn{submore » mol}). In contrast, the magnetic moment of the Mn{sub mol} is enhanced to 4.28 μB at the hollow site, a value larger than that in the free MnPc molecule (3.51 μB). Molecular distortion induced by adsorption is revealed to be responsible for the enhancement of the magnetic moment. Furthermore, the spin polarization of the Mn{sub mol} atom at around the Fermi level is found to change from negative to positive through an elongation of the Mn–N bonds of the MnPc. We propose that a reversible switch of the low/high magnetic moment and negative/positive spin polarization might be realized through some mechanical engineering methods.« less

Nuclear magnetic resonance of laser-polarized noble gases in molecules, materials and organisms

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

Goodson, Boyd McLean

1999-12-01

Conventional nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) are fundamentally challenged by the insensitivity that stems from the ordinarily low spin polarization achievable in even the strongest NMR magnets. However, by transferring angular momentum from laser light to electronic and nuclear spins, optical pumping methods can increase the nuclear spin polarization of noble gases by several orders of magnitude, thereby greatly enhancing their NMR sensitivity. This dissertation is primarily concerned with the principles and practice of optically pumped nuclear magnetic resonance (OPNMR). The enormous sensitivity enhancement afforded by optical pumping noble gases can be exploited to permitmore » a variety of novel NMR experiments across many disciplines. Many such experiments are reviewed, including the void-space imaging of organisms and materials, NMR and MRI of living tissues, probing structure and dynamics of molecules in solution and on surfaces, and zero-field NMR and MRI.« less

Effects of Small Polar Molecules (MA+ and H2O) on Degradation Processes of Perovskite Solar Cells.

PubMed

Ma, Chunqing; Shen, Dong; Qing, Jian; Thachoth Chandran, Hrisheekesh; Lo, Ming-Fai; Lee, Chun-Sing

2017-05-03

Degradation mechanisms of methylammonium lead halide perovskite solar cells (PSCs) have drawn much attention recently. Herein, the bulk and surface degradation processes of the perovskite were differentiated for the first time by employing combinational studies using electrochemical impedance spectroscopy (EIS), capacitance frequency (CF), and X-ray diffraction (XRD) studies with particular attention on the roles of small polar molecules (MA + and H 2 O). CF study shows that short-circuit current density of the PSCs is increased by H 2 O at the beginning of the degradation process coupled with an increased surface capacitance. On the basis of EIS and XRD analysis, we show that the bulk degradation of PSCs involves a lattice expansion process, which facilitates MA + ion diffusion by creating more efficient channels. These results provide a better understanding of the roles of small polar molecules on degradation processes in the bulk and on the surface of the perovskite film.

A rapid and sensitive method for the simultaneous analysis of aliphatic and polar molecules containing free carboxyl groups in plant extracts by LC-MS/MS

PubMed Central

2009-01-01

Background Aliphatic molecules containing free carboxyl groups are important intermediates in many metabolic and signalling reactions, however, they accumulate to low levels in tissues and are not efficiently ionized by electrospray ionization (ESI) compared to more polar substances. Quantification of aliphatic molecules becomes therefore difficult when small amounts of tissue are available for analysis. Traditional methods for analysis of these molecules require purification or enrichment steps, which are onerous when multiple samples need to be analyzed. In contrast to aliphatic molecules, more polar substances containing free carboxyl groups such as some phytohormones are efficiently ionized by ESI and suitable for analysis by LC-MS/MS. Thus, the development of a method with which aliphatic and polar molecules -which their unmodified forms differ dramatically in their efficiencies of ionization by ESI- can be simultaneously detected with similar sensitivities would substantially simplify the analysis of complex biological matrices. Results A simple, rapid, specific and sensitive method for the simultaneous detection and quantification of free aliphatic molecules (e.g., free fatty acids (FFA)) and small polar molecules (e.g., jasmonic acid (JA), salicylic acid (SA)) containing free carboxyl groups by direct derivatization of leaf extracts with Picolinyl reagent followed by LC-MS/MS analysis is presented. The presence of the N atom in the esterified pyridine moiety allowed the efficient ionization of 25 compounds tested irrespective of their chemical structure. The method was validated by comparing the results obtained after analysis of Nicotiana attenuata leaf material with previously described analytical methods. Conclusion The method presented was used to detect 16 compounds in leaf extracts of N. attenuata plants. Importantly, the method can be adapted based on the specific analytes of interest with the only consideration that the molecules must contain at

Long-Lived Ultracold Molecules with Electric and Magnetic Dipole Moments.

PubMed

Rvachov, Timur M; Son, Hyungmok; Sommer, Ariel T; Ebadi, Sepehr; Park, Juliana J; Zwierlein, Martin W; Ketterle, Wolfgang; Jamison, Alan O

2017-10-06

We create fermionic dipolar ^{23}Na^{6}Li molecules in their triplet ground state from an ultracold mixture of ^{23}Na and ^{6}Li. Using magnetoassociation across a narrow Feshbach resonance followed by a two-photon stimulated Raman adiabatic passage to the triplet ground state, we produce 3×10^{4} ground state molecules in a spin-polarized state. We observe a lifetime of 4.6 s in an isolated molecular sample, approaching the p-wave universal rate limit. Electron spin resonance spectroscopy of the triplet state was used to determine the hyperfine structure of this previously unobserved molecular state.

Long-Lived Ultracold Molecules with Electric and Magnetic Dipole Moments

NASA Astrophysics Data System (ADS)

Rvachov, Timur M.; Son, Hyungmok; Sommer, Ariel T.; Ebadi, Sepehr; Park, Juliana J.; Zwierlein, Martin W.; Ketterle, Wolfgang; Jamison, Alan O.

2017-10-01

We create fermionic dipolar 23Na 6Li molecules in their triplet ground state from an ultracold mixture of 23Na and 6Li. Using magnetoassociation across a narrow Feshbach resonance followed by a two-photon stimulated Raman adiabatic passage to the triplet ground state, we produce 3 ×1 04 ground state molecules in a spin-polarized state. We observe a lifetime of 4.6 s in an isolated molecular sample, approaching the p -wave universal rate limit. Electron spin resonance spectroscopy of the triplet state was used to determine the hyperfine structure of this previously unobserved molecular state.

Orientation and Rotational Motions of Single Molecules by Polarized Total Internal Reflection Fluorescence Microscopy (polTIRFM)

PubMed Central

Beausang, John F.; Sun, Yujie; Quinlan, Margot E.; Forkey, Joseph N.; Goldman, Yale E.

2013-01-01

In this article, we describe methods to detect the spatial orientation and rotational dynamics of single molecules using polarized total internal reflection fluorescence microscopy (polTIRFM). polTIRFM determines the three-dimensional angular orientation and the extent of wobble of a fluorescent probe bound to the macromolecule of interest. We discuss single-molecule versus ensemble measurements, as well as single-molecule techniques for orientation and rotation, and fluorescent probes for orientation studies. Using calmodulin (CaM) as an example of a target protein, we describe a method for labeling CaM with bifunctional rhodamine (BR). We also describe the physical principles and experimental setup of polTIRFM. We conclude with a brief introduction to assays using polTIRFM to assess the interaction of actin and myosin. PMID:22550303

Preparation of translationally cold neutral molecules.

PubMed

Di Domenicantonio, Giulia; Bertsche, Benjamin; Osterwalder, Andreas

2011-01-01

Efforts at EPFL to obtain translationally cold neutral molecules are described. Active deceleration of polar molecules is performed by confining the molecules in moving three-dimensional electrostatic traps, and by appropriately choosing the velocity of those traps. Alternatively, cold molecules can be obtained by velocity filtering. Here, the velocity of the molecules is not changed, but instead the cold molecules are extracted from a thermal sample by using the competition between the electrostatic force and the centrifugal force inside a bent electrostatic guide for polar molecules.

M-CARS and EFISHG study of the influence of a static electric field on a non-polar molecule

NASA Astrophysics Data System (ADS)

Capitaine, E.; Louot, C.; Ould-Moussa, N.; Lefort, C.; Kaneyasu, J. F.; Kano, H.; Pagnoux, D.; Couderc, V.; Leproux, P.

2016-03-01

The influence of a static electric field on a non-polar molecule has been studied by means of multiplex coherent anti-Stokes Raman scattering (M-CARS). A parallel measurement of electric field induced second harmonic generation (EFISHG) has also been led. Both techniques suggest a reorientation of the molecule due to the presence of an electric field. This phenomenon can be used to increase the chemical selectivity and the signal to non-resonant background ratio, namely, the sensitivity of the M-CARS spectroscopy.

Supercritical fluid extraction of the non-polar organic compounds in meteorites

NASA Astrophysics Data System (ADS)

Sephton, M. A.; Pillinger, C. T.; Gilmour, I.

2001-01-01

The carbonaceous chondrite meteorites contain a variety of extraterrestrial organic molecules. These organic components provide a valuable insight into the formation and evolution of the solar system. Attempts at obtaining and interpreting this information source are hampered by the small sample sizes available for study and the interferences from terrestrial contamination. Supercritical fluid extraction represents an efficient and contamination-free means of isolating extraterrestrial molecules. Gas chromatography-mass spectrometry analyses of extracts from Orgueil and Cold Bokkeveld reveal a complex mixture of free non-polar organic molecules which include normal alkanes, isoprenoid alkanes, tetrahydronaphthalenes and aromatic hydrocarbons. These organic assemblages imply contributions from both terrestrial and extraterrestrial sources.

Effects of molecular asymmetry of optically active molecules on the polarization properties of multiply scattered light

NASA Astrophysics Data System (ADS)

Vitkin, I. Alex; Laszlo, Richard D.; Whyman, Claire L.

2002-02-01

The use of polarized light for investigation of optically turbid systems has generated much recent interest since it has been shown that multiple scattering does not fully scramble the incident polarization states. It is possible under some conditions to measure polarization signals in diffusely scattered light, and use this information to characterize the structure or composition of the turbid medium. Furthermore, the idea of quantitative detection of optically active (chiral) molecules contained in such a system is attractive, particularly in clinical medicine where it may contribute to the development of a non-invasive method of glucose sensing in diabetic patients. This study uses polarization modulation and synchronous detection in the perpendicular and in the exact backscattering orientations to detect scattered light from liquid turbid samples containing varying amounts of L and D (left and right) isomeric forms of a chiral sugar. Polarization preservation increased with chiral concentrations in both orientations. In the perpendicular orientation, the optical rotation of the linearly polarized fraction also increased with the concentration of chiral solute, but in different directions for the two isomeric forms. There was no observed optical rotation in the exact backscattering geometry for either isomer. The presence of the chiral species is thus manifest in both detection directions, but the sense of the chiral asymmetry is not resolvable in retroreflection. The experiments show that useful information may be extracted from turbid chiral samples using polarized light.

An electron spin polarization study of the interaction of photoexcited triplet molecules with mono- and polynitroxyl stable free radicals

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

Turro, N.J.; Khudyakov, I.V.; Bossmann, S.H.

1993-02-11

Time-resolved electron spin resonance (TR ESR) has been used to investigate the chemically induced dynamic electron polarization (CIDEP) generated by the interaction of stable free radicals with the triplet states of benzophenone, benzil, and 2-acetylnaphthalene. The stable radicals were mono-, di-, tri-, and tetranitroxyl free radicals possessing the 2,2,6,6-tetramethylpiperidine-N-oxyl moiety. All of the stable radical systems investigated were found to be emissively polarized by interaction with the triplet states, and the phase of polarization was independent of the sign of zero-field splitting (D) of the interacting triple molecule. Possible and likely mechanisms of polarization transfer (creation) resulting from the interactionmore » of photoexcited triplet molecules with nitroxyls in the strong electron exchange are discussed. The emissive CIDEP of nitroxyls observed in the interactions with triplet benzil, which has D > 0, provides strong support for the operation of the radical-triplet pair mechanism. Within the time scale of TR ESR experiments ([approximately]10[sup [minus]7]--10[sup [minus]6] s) no significant variation in the shape of the CIDEP spectra of the nitroxyls was observed, either in viscous media or in micelles. It is concluded that intramolecular spin exchange (or conformational change) of polynitroyls occurs much faster than the time resolution of the experiment. 24 refs., 6 figs., 1 tab.« less

On the trends of Fukui potential and hardness potential derivatives in isolated atoms vs. atoms in molecules.

PubMed

Bhattacharjee, Rituparna; Roy, Ram Kinkar

2014-10-28

In the present study, trends of electronic contribution to molecular electrostatic potential [Vel(r¯)(r=0)], Fukui potential [v(+)f|(r=0) and v(-)f|(r=0)] and hardness potential derivatives [Δ(+)h(k) and Δ(-)h(k)] for isolated atoms as well as atoms in molecules are investigated. The generated numerical values of these three reactivity descriptors in these two electronically different situations are critically analyzed through the relevant formalism. Values of Vel(r¯) (when r → 0, i.e., on the nucleus) are higher for atoms in molecules than that of isolated atoms. In contrast, higher values of v(+)|(r=0) and v(-)|(r=0) are observed for isolated atoms compared to the values for atoms in a molecule. However, no such regular trend is observed for the Δ(+)h(k) and Δ(-)h(k) values, which is attributed to the uncertainty in the Fukui function values of atoms in molecules. The sum of Fukui potential and the sum of hardness potential derivatives in molecules are also critically analyzed, which shows the efficacy of orbital relaxation effects in quantifying the values of these parameters. The chemical consequence of the observed trends of these descriptors in interpreting electron delocalization, electronic relaxation and non-negativity of atomic Fukui function indices is also touched upon. Several commonly used molecules containing carbon as well as heteroatoms are chosen to make the investigation more insightful.

Lessons from isolable nickel(I) precursor complexes for small molecule activation.

PubMed

Yao, Shenglai; Driess, Matthias

2012-02-21

Small-molecule activation by transition metals is essential to numerous organic transformations, both biological and industrial. Creating useful metal-mediated activation systems often depends on stabilizing the metal with uncommon low oxidation states and low coordination numbers. This provides a redox-active metal center with vacant coordination sites well suited for interacting with small molecules. Monovalent nickel species, with their d(9) electronic configuration, are moderately strong one-electron reducing agents that are synthetically attractive if they can be isolated. They represent suitable reagents for closing the knowledge gap in nickel-mediated activation of small molecules. Recently, the first strikingly stable dinuclear β-diketiminate nickel(I) precursor complexes were synthesized, proving to be suitable promoters for small-molecule binding and activation. They have led to many unprecedented nickel complexes bearing activated small molecules in different reduction stages. In this Account, we describe selected achievements in the activation of nitrous oxide (N(2)O), O(2), the heavier chalcogens (S, Se, and Te), and white phosphorus (P(4)) through this β-diketiminatonickel(I) precursor species. We emphasize the reductive activation of O(2), owing to its promise in oxidation processes. The one-electron-reduced O(2) activation product, that is, the corresponding β-diketiminato-supported Ni-O(2) complex, is a genuine superoxonickel(II) complex, representing an important intermediate in the early stages of O(2) activation. It selectively acts as an oxygen-atom transfer agent, hydrogen-atom scavenger, or both towards exogenous organic substrates to yield oxidation products. The one-electron reduction of the superoxonickel(II) moiety was examined by using elemental potassium, β-diketiminatozinc(II) chloride, and β-diketiminatoiron(I) complexes, affording the first heterobimetallic complexes featuring a [NiO(2)M] subunit (M is K, Zn, or Fe). Through

Polarized components of C=O vibrations Raman spectra for ethylacetate, acetone, and aggregation of molecules

NASA Astrophysics Data System (ADS)

Tukhvatullin, F. H.; Jumabaev, A.; Tashkenbaev, U. N.; Hushvaktov, H. A.; Absanov, A. A.

2002-11-01

For liquid ethylacetate the frequency maximums for parallel (I|| (v)) and perpendicular (I\\highmod(v)) polarized components of C=O vibrations band in Raman spectra are differed on 5.3 cm-1. At dilution ethylacetate in CCl4 and heptane or heating in this difference is decreased by displacement of I|| (v) maximum to the I\\highmod(v) maximum. In polar solvent, nitrometane, the picture is different - the frequency maxima difference is decreased though the displacement of I\\highmod(v) band maximum to the I|| (v)one. The results were explained by the complexity of C=O vibration bands, and existence within the band of two lines with the different depolarization ratio. The complexity of the band is the result existence in liquid ethylacetate the monomer molecules and molecular aggregations.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

DOE PAGES

Huang, Jing; Mei, Ye; König, Gerhard; ...

2017-01-24

Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

PubMed

Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

2017-02-14

In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

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

Huang, Jing; Mei, Ye; König, Gerhard

Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

Functional Fixedness and Functional Reduction as Common Sense Reasonings in Chemical Equilibrium and in Geometry and Polarity of Molecules.

ERIC Educational Resources Information Center

Furio, C.; Calatayud, M. L.; Barcenas, S. L.; Padilla, O. M.

2000-01-01

Focuses on learning difficulties in procedural knowledge, and assesses the procedural difficulties of grade 12 and first- and third-year university students based on common sense reasoning in two areas of chemistry--chemical equilibrium and geometry, and polarity of molecules. (Contains 55 references.) (Author/YDS)

Simple and advanced ferromagnet/molecule spinterfaces

NASA Astrophysics Data System (ADS)

Gruber, M.; Ibrahim, F.; Djedhloul, F.; Barraud, C.; Garreau, G.; Boukari, S.; Isshiki, H.; Joly, L.; Urbain, E.; Peter, M.; Studniarek, M.; Da Costa, V.; Jabbar, H.; Bulou, H.; Davesne, V.; Halisdemir, U.; Chen, J.; Xenioti, D.; Arabski, J.; Bouzehouane, K.; Deranlot, C.; Fusil, S.; Otero, E.; Choueikani, F.; Chen, K.; Ohresser, P.; Bertran, F.; Le Fèvre, P.; Taleb-Ibrahimi, A.; Wulfhekel, W.; Hajjar-Garreau, S.; Wetzel, P.; Seneor, P.; Mattana, R.; Petroff, F.; Scheurer, F.; Weber, W.; Alouani, M.; Beaurepaire, E.; Bowen, M.

2016-10-01

Spin-polarized charge transfer between a ferromagnet and a molecule can promote molecular ferromagnetism 1, 2 and hybridized interfacial states3, 4. Observations of high spin-polarization of Fermi level states at room temperature5 designate such interfaces as a very promising candidate toward achieving a highly spin-polarized, nanoscale current source at room temperature, when compared to other solutions such as half-metallic systems and solid-state tunnelling over the past decades. We will discuss three aspects of this research. 1) Does the ferromagnet/molecule interface, also called an organic spinterface, exhibit this high spin-polarization as a generic feature? Spin-polarized photoemission experiments reveal that a high spin-polarization of electronics states at the Fermi level also exist at the simple interface between ferromagnetic cobalt and amorphous carbon6. Furthermore, this effect is general to an array of ferromagnetic and molecular candidates7. 2) Integrating molecules with intrinsic properties (e.g. spin crossover molecules) into a spinterface toward enhanced functionality requires lowering the charge transfer onto the molecule8 while magnetizing it1,2. We propose to achieve this by utilizing interlayer exchange coupling within a more advanced organic spinterface architecture. We present results at room temperature across the fcc Co(001)/Cu/manganese phthalocyanine (MnPc) system9. 3) Finally, we discuss how the Co/MnPc spinterface's ferromagnetism stabilizes antiferromagnetic ordering at room temperature onto subsequent molecules away from the spinterface, which in turn can exchange bias the Co layer at low temperature10. Consequences include tunnelling anisotropic magnetoresistance across a CoPc tunnel barrier11. This augurs new possibilities to transmit spin information across organic semiconductors using spin flip excitations12.

Luminance and chromatic contributions to a hyperacuity task: isolation by contrast polarity and target separation

PubMed Central

Sun, Hao; Cooper, Bonnie; Lee, Barry B.

2012-01-01

Vernier thresholds are known to be elevated when a target pair has opposite contrast polarity. Polarity reversal is used to assess the role of luminance and chromatic pathways in hyperacuity performance. Psychophysical hyperacuity thresholds were measured for pairs of gratings of various combinations of luminance (Lum) and chromatic (Chr) contrast polarities, at different ratios of luminance to chromatic contrast. With two red-green gratings of matched luminance and chromatic polarity (+Lum+Chr), there was an elevation of threshold at isoluminance. When both luminance and chromatic polarity were mismatched (−Lum−Chr), thresholds were substantially elevated under all conditions. With the same luminance contrast polarity and opposite chromatic polarity (+Lum−Chr) thresholds were only elevated close to isoluminance; in the reverse condition (−Lum+Chr), thresholds were elevated as in the −Lum−Chr condition except close to equiluminance. Similar data were obtained for gratings isolating the short-wavelength cone mechanism. Further psychophysical measurements assessed the role of target separation with matched or mismatched contrast polarity; similar results were found for luminance and chromatic gratings. Comparison physiological data were collected from parafoveal ganglion cells of the macaque retina. Positional precision of ganglion cell signals was assessed under conditions related to the psychophysical measurements. On the basis of these combined observations, it is argued that both magnocellular, parvocellular, and koniocellular pathways have access to cortical positional mechanisms associated with vernier acuity. PMID:22306680

Investigations of electron helicity in optically active molecules using polarized beams of electrons and positrons

NASA Technical Reports Server (NTRS)

Gidley, D. W.; Rich, A.; Van House, J. C.; Zitzewitz, P. W.

1981-01-01

A positronium-formation experiment with a high sensitivity to a possible relation between the helicity of beta particles emitted in nuclear beta decay and the optical asymmetry of biological molecules is presented. The experiment is based on a mechanism in which the electrons in optically active molecules possess a helicity of less than 0.001, too weak to detect in radiolysis experiments, the sign of which depends on the chirality of the isomer. A helicity-dependent asymmetry is sought in the formation of the triplet ground state of positronium when a low-energy beam of polarized positrons of reversible helicity interacts with an optically active substance coating a channel electron multiplier. Asymmetries between positronium decays observed at positive and negative helicities for the same substance can thus be determined with a sensitivity of 0.0001, which represents a factor of 100 improvement over previous positronium experiments.

Synthesis of RNA molecules larger than 45 S by isolated rat-liver nucleoli.

PubMed

Grummt, I

1975-09-01

Nucleoli, isolated from rat liver, synthesize in vitro high-molecular-weight RNA, the base composition and sedimentation pattern of which resembles that of ribosomal precursor RNA. In addition, RNA molecules larger than 45 S have been found. In this paper experiments are described which indicate that these large RNA molecules represent geniune transcription products and are not aggregates arising under the experimental conditions employed. This was established by comparing different extraction methods, by sedimentation analysis of the RNA after denaturation with formamide and by pulse-chase experiments. Hybridisation-competition studies showed that 45-S RNA competes with those rapidly molecules to about 80-90%, thus providing evidence for the presence of ribosomal precursor RNA sequences in those long transcription products. Intact nuclei are able to synthesize in the presence of Mg2+ and alpha-amanitin RNA molecules larger than 45 S too, provided that the RNAase activity is suppressed effectively by the addition of cytoplasmic RNAase inhibitor. The significance of these results is discussed with respect to the initial transcript of the rDNA genes in rat liver nucleoli.

JAK2 JH2 Fluorescence Polarization Assay and Crystal Structures for Complexes with Three Small Molecules.

PubMed

Newton, Ana S; Deiana, Luca; Puleo, David E; Cisneros, José A; Cutrona, Kara J; Schlessinger, Joseph; Jorgensen, William L

2017-06-08

A competitive fluorescence polarization (FP) assay is reported for determining binding affinities of probe molecules with the pseudokinase JAK2 JH2 allosteric site. The syntheses of the fluorescent 5 and 6 used in the assay are reported as well as K d results for 10 compounds, including JNJ7706621, NVP-BSK805, and filgotinib (GLPG0634). X-ray crystal structures of JAK2 JH2 in complex with NVP-BSK805, filgotinib, and diaminopyrimidine 8 elucidate the binding poses.

JAK2 JH2 Fluorescence Polarization Assay and Crystal Structures for Complexes with Three Small Molecules

PubMed Central

2017-01-01

A competitive fluorescence polarization (FP) assay is reported for determining binding affinities of probe molecules with the pseudokinase JAK2 JH2 allosteric site. The syntheses of the fluorescent 5 and 6 used in the assay are reported as well as Kd results for 10 compounds, including JNJ7706621, NVP-BSK805, and filgotinib (GLPG0634). X-ray crystal structures of JAK2 JH2 in complex with NVP-BSK805, filgotinib, and diaminopyrimidine 8 elucidate the binding poses. PMID:28626520

Experimental observation and determination of the laser-induced frequency shift of hyperfine levels of ultracold polar molecules

NASA Astrophysics Data System (ADS)

Liu, Wenliang; Wang, Xiaofeng; Wu, Jizhou; Su, Xingliang; Wang, Shen; Sovkov, Vladimir B.; Ma, Jie; Xiao, Liantuan; Jia, Suotang

2017-08-01

We report on the experimental observation and quantitative determination of the laser-induced frequency shift (LIFS) of the ultracold polar molecules formed by photoassociation (PA). The experiments are performed by detecting a series of double PA spectra with a molecular hyperfine structure, which are induced by two PA lasers with a precise and adjustable frequency reference. We find that the LIFS of the molecular hyperfine levels shows a linear dependence on PA laser intensity.

Matrix-Isolation Spectroscopy of Reactive Organic Molecules of Relevance to Interstellar Space

NASA Astrophysics Data System (ADS)

Kopff, Laura A.; Nolan, Alex M.; Kreifels, Terese A.; Draxler, Thomas W.; Esselman, Brian J.; Burrmann, Nicola J.; McMahon, Robert J.

2010-11-01

Matrix isolation, the process of trapping a molecule in an inert gas at low temperature, provides a means for studying highly reactive intermediates, such as carbenes or radicals. Reactive species can be characterized by IR, UV-vis and/or EPR spectroscopy. Comparison of experimental and computed spectral data, as well as chemical reactivity, is used for structural assignment Triplet propynylidene is proposed to exist in the interstellar medium (ISM), due to the detection of a higher-energy isomers via rotational spectroscopy. Currently, we are exploring the structural and photochemical effects of varying substituents on the propynylidne system. A diazo precursor has been synthesized and photolyzed to produce dimethylpropynylidene in an argon matrix. A photochemical hydrogen shift to produce 1-penten-3-yne has been observed through infrared spectroscopy. Cyanocarbons are known to be abundant in the ISM and the atmosphere of Titan, however matrixisolation studies have not yet been carried out for a significant number of these compounds. Photolysis of 3-cyano-3-methyldiazirine should yield methylcyanocarbene, one of the simplest species in this family. Another molecule of interest is l-HC4N, which has been detected in the ISM, but has not yet been matrix-isolated and characterized. The study of arylcarbenes is vital to understanding the chemistry of carbon-rich environments, such as discharges, interstellar clouds, and circumstellar envelopes. The identification of small, sulfur containing molecules, and the identification of aromatics in the ISM make future thiophene and benzothiophene detections a real possibility. Studies on 2- and 3-diazomethyl substituted benzothiophenes are underway to assess their photochemical reactivity and potential for forming benzothiophene carbenes. Macrocylic polyynes are proposed to be involved in carbon condensation via the ring coalescence and annealing model to produce graphitic sheets or fullerenes. To simplify a complex system we

Luminance and chromatic contributions to a hyperacuity task: isolation by contrast polarity and target separation.

PubMed

Sun, Hao; Cooper, Bonnie; Lee, Barry B

2012-03-01

Vernier thresholds are known to be elevated when a target pair has opposite contrast polarity. Polarity reversal is used to assess the role of luminance and chromatic pathways in hyperacuity performance. Psychophysical hyperacuity thresholds were measured for pairs of gratings of various combinations of luminance (Lum) and chromatic (Chr) contrast polarities, at different ratios of luminance to chromatic contrast. With two red-green gratings of matched luminance and chromatic polarity (+Lum+Chr), there was an elevation of threshold at isoluminance. When both luminance and chromatic polarity were mismatched (-Lum-Chr), thresholds were substantially elevated under all conditions. With the same luminance contrast polarity and opposite chromatic polarity (+Lum-Chr) thresholds were only elevated close to isoluminance; in the reverse condition (-Lum+Chr), thresholds were elevated as in the -Lum-Chr condition except close to equiluminance. Similar data were obtained for gratings isolating the short-wavelength cone mechanism. Further psychophysical measurements assessed the role of target separation with matched or mismatched contrast polarity; similar results were found for luminance and chromatic gratings. Comparison physiological data were collected from parafoveal ganglion cells of the macaque retina. Positional precision of ganglion cell signals was assessed under conditions related to the psychophysical measurements. On the basis of these combined observations, it is argued that both magnocellular, parvocellular, and koniocellular pathways have access to cortical positional mechanisms associated with vernier acuity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Quantum Theory of Atoms in Molecules Charge-Charge Transfer-Dipolar Polarization Classification of Infrared Intensities.

PubMed

Duarte, Leonardo J; Richter, Wagner E; Silva, Arnaldo F; Bruns, Roy E

2017-10-26

Fundamental infrared vibrational transition intensities of gas-phase molecules are sensitive probes of changes in electronic structure accompanying small molecular distortions. Models containing charge, charge transfer, and dipolar polarization effects are necessary for a successful classification of the C-H, C-F, and C-Cl stretching and bending intensities. C-H stretching and in-plane bending vibrations involving sp 3 carbon atoms have small equilibrium charge contributions and are accurately modeled by the charge transfer-counterpolarization contribution and its interaction with equilibrium charge movement. Large C-F and C═O stretching intensities have dominant equilibrium charge movement contributions compared to their charge transfer-dipolar polarization ones and are accurately estimated by equilibrium charge and the interaction contribution. The C-F and C-Cl bending modes have charge and charge transfer-dipolar polarization contribution sums that are of similar size but opposite sign to their interaction values resulting in small intensities. Experimental in-plane C-H bends have small average intensities of 12.6 ± 10.4 km mol -1 owing to negligible charge contributions and charge transfer-counterpolarization cancellations, whereas their average out-of-plane experimental intensities are much larger, 65.7 ± 20.0 km mol -1 , as charge transfer is zero and only dipolar polarization takes place. The C-F bending intensities have large charge contributions but very small intensities. Their average experimental out-of-plane intensity of 9.9 ± 12.6 km mol -1 arises from the cancellation of large charge contributions by dipolar polarization contributions. The experimental average in-plane C-F bending intensity, 5.8 ± 7.3 km mol -1 , is also small owing to charge and charge transfer-counterpolarization sums being canceled by their interaction contributions. Models containing only atomic charges and their fluxes are incapable of describing electronic structure

The polarization anisotropy of vibrational quantum beats in resonant pump-probe experiments: Diagrammatic calculations for square symmetric molecules.

PubMed

Farrow, Darcie A; Smith, Eric R; Qian, Wei; Jonas, David M

2008-11-07

By analogy to the Raman depolarization ratio, vibrational quantum beats in pump-probe experiments depend on the relative pump and probe laser beam polarizations in a way that reflects vibrational symmetry. The polarization signatures differ from those in spontaneous Raman scattering because the order of field-matter interactions is different. Since pump-probe experiments are sensitive to vibrations on excited electronic states, the polarization anisotropy of vibrational quantum beats can also reflect electronic relaxation processes. Diagrammatic treatments, which expand use of the symmetry of the two-photon tensor to treat signal pathways with vibrational and vibronic coherences, are applied to find the polarization anisotropy of vibrational and vibronic quantum beats in pump-probe experiments for different stages of electronic relaxation in square symmetric molecules. Asymmetric vibrational quantum beats can be distinguished from asymmetric vibronic quantum beats by a pi phase jump near the center of the electronic spectrum and their disappearance in the impulsive limit. Beyond identification of vibrational symmetry, the vibrational quantum beat anisotropy can be used to determine if components of a doubly degenerate electronic state are unrelaxed, dephased, population exchanged, or completely equilibrated.

Group-velocity-locked vector soliton molecules in fiber lasers.

PubMed

Luo, Yiyang; Cheng, Jianwei; Liu, Bowen; Sun, Qizhen; Li, Lei; Fu, Songnian; Tang, Dingyuan; Zhao, Luming; Liu, Deming

2017-05-24

Physics phenomena of multi-soliton complexes have enriched the life of dissipative solitons in fiber lasers. By developing a birefringence-enhanced fiber laser, we report the first experimental observation of group-velocity-locked vector soliton (GVLVS) molecules. The birefringence-enhanced fiber laser facilitates the generation of GVLVSs, where the two orthogonally polarized components are coupled together to form a multi-soliton complex. Moreover, the interaction of repulsive and attractive forces between multiple pulses binds the particle-like GVLVSs together in time domain to further form compound multi-soliton complexes, namely GVLVS molecules. By adopting the polarization-resolved measurement, we show that the two orthogonally polarized components of the GVLVS molecules are both soliton molecules supported by the strongly modulated spectral fringes and the double-humped intensity profiles. Additionally, GVLVS molecules with various soliton separations are also observed by adjusting the pump power and the polarization controller.

Observation of rotational revivals for iodine molecules in helium droplets using a near-adiabatic laser pulse

NASA Astrophysics Data System (ADS)

Shepperson, Benjamin; Chatterley, Adam S.; Christiansen, Lars; Søndergaard, Anders A.; Stapelfeldt, Henrik

2018-01-01

A 160-ps near-Gaussian, linearly polarized laser pulse is used to align iodine (I2) molecules embedded in helium nanodroplets. The rise time of the laser pulse is sufficiently long and smooth that the alignment, characterized by , behaves adiabatically during the pulse turnon. However, after the laser pulse has turned off stays above 0.50 and a recurrence structure occurs ˜650 ps later. Measurements on isolated (I2) molecules with identical laser pulses are used to identify, through analysis of the observed half- and full-rotational revivals, that the nonadiabatic postpulse alignment dynamics results from a mild truncation of the trailing edge of the laser pulse. This truncation establishes a well-defined starting time for coherent rotation, which leads to the revival structures observed both for isolated molecules and molecules in He droplets. In the latter case the time-dependent trace recorded here is compared to that obtained previously for a 450-fs alignment pulse. It is found that the observed revivals are very similar.

Spin Polarization of Rb and Cs n p P2 3/2 (n =5 , 6) Atoms by Circularly Polarized Photoexcitation of a Transient Diatomic Molecule

NASA Astrophysics Data System (ADS)

Mironov, A. E.; Hewitt, J. D.; Eden, J. G.

2017-03-01

We report the selective population of Rb or Cs n p P2 3/2 (n =5 , 6; F =4 , 5) hyperfine states by the photodissociation of a transient, alkali-rare gas diatomic molecule. Circularly polarized (σ-), amplified spontaneous emission (ASE) on the D2 line of Rb or Cs (780.0 and 852.1 nm, respectively) is generated when Rb-Xe or Cs-Xe ground state collision pairs are photoexcited by a σ+-polarized optical field having a wavelength within the D2 blue satellite continuum, associated with the B Σ2 1/2 +←X Σ2 1/2 + (free←free ) transition of the diatomic molecule. The degree of spin polarization of Cs (6 p P3/2 2 ), specifically, is found to be dependent on the interatomic distance (R ) at which the excited complex is born, a result attributed to the structure of the B Σ2 1/2 + state. For Cs-Xe atomic pairs, tuning the wavelength of the optical field from 843 to 848 nm varies the degree of circular polarization of the ASE from 63% to almost unity because of the perturbation, in the 5 ≤R ≤6 Å interval, of the Σ2 1/2 + potential by a d σ molecular orbital associated with a higher Λ 2 electronic state. Monitoring only the Cs 6 p P3/2 2 spin polarization reveals a previously unobserved interaction of CsXe (B Σ2 1/2 + ) with the lowest vibrational levels of a Λ 2 state derived from Cs (5 d )+Xe . By inserting a molecular intermediate into the alkali atom excitation mechanism, these experiments realize electronic spin polarization through populating no more than two n p P2 3/2 hyperfine states, and demonstrate a sensitive spectroscopic

Chirality-induced spin polarization places symmetry constraints on biomolecular interactions.

PubMed

Kumar, Anup; Capua, Eyal; Kesharwani, Manoj K; Martin, Jan M L; Sitbon, Einat; Waldeck, David H; Naaman, Ron

2017-03-07

Noncovalent interactions between molecules are key for many biological processes. Necessarily, when molecules interact, the electronic charge in each of them is redistributed. Here, we show experimentally that, in chiral molecules, charge redistribution is accompanied by spin polarization. We describe how this spin polarization adds an enantioselective term to the forces, so that homochiral interaction energies differ from heterochiral ones. The spin polarization was measured by using a modified Hall effect device. An electric field that is applied along the molecules causes charge redistribution, and for chiral molecules, a Hall voltage is measured that indicates the spin polarization. Based on this observation, we conjecture that the spin polarization enforces symmetry constraints on the biorecognition process between two chiral molecules, and we describe how these constraints can lead to selectivity in the interaction between enantiomers based on their handedness. Model quantum chemistry calculations that rigorously enforce these constraints show that the interaction energy for methyl groups on homochiral molecules differs significantly from that found for heterochiral molecules at van der Waals contact and shorter (i.e., ∼0.5 kcal/mol at 0.26 nm).

Atomic charge transfer-counter polarization effects determine infrared CH intensities of hydrocarbons: a quantum theory of atoms in molecules model.

PubMed

Silva, Arnaldo F; Richter, Wagner E; Meneses, Helen G C; Bruns, Roy E

2014-11-14

Atomic charge transfer-counter polarization effects determine most of the infrared fundamental CH intensities of simple hydrocarbons, methane, ethylene, ethane, propyne, cyclopropane and allene. The quantum theory of atoms in molecules/charge-charge flux-dipole flux model predicted the values of 30 CH intensities ranging from 0 to 123 km mol(-1) with a root mean square (rms) error of only 4.2 km mol(-1) without including a specific equilibrium atomic charge term. Sums of the contributions from terms involving charge flux and/or dipole flux averaged 20.3 km mol(-1), about ten times larger than the average charge contribution of 2.0 km mol(-1). The only notable exceptions are the CH stretching and bending intensities of acetylene and two of the propyne vibrations for hydrogens bound to sp hybridized carbon atoms. Calculations were carried out at four quantum levels, MP2/6-311++G(3d,3p), MP2/cc-pVTZ, QCISD/6-311++G(3d,3p) and QCISD/cc-pVTZ. The results calculated at the QCISD level are the most accurate among the four with root mean square errors of 4.7 and 5.0 km mol(-1) for the 6-311++G(3d,3p) and cc-pVTZ basis sets. These values are close to the estimated aggregate experimental error of the hydrocarbon intensities, 4.0 km mol(-1). The atomic charge transfer-counter polarization effect is much larger than the charge effect for the results of all four quantum levels. Charge transfer-counter polarization effects are expected to also be important in vibrations of more polar molecules for which equilibrium charge contributions can be large.

Production of Cell-Cell Signaling Molecules by Bacteria Isolated From Human Chronic Wounds

PubMed Central

Rickard, Alexander H.; Colacino, Katelyn R.; Manton, Katelynn M.; Morton, Robert I.; Pulcini, Elinor; Pfeil, Joanne; Rhoads, Daniel; Wolcott, Randall D.; James, Garth

2009-01-01

AIM To (i) identify chronic wound bacteria and to test their ability to produce acyl-homoserine-lactones (AHLs) and autoinducer-2 (AI-2) cell-cell signaling molecules and (ii) determine if chronic wound debridement samples might contain these molecules. METHODS AND RESULTS Partial 16S rRNA gene sequencing revealed the identity of 46 chronic wound strains as belonging to nine genera. Using bio-reporter assays, 69.6% of the chronic wound strains were inferred to produce AI-2 while 19.6% were inferred to produced AHL molecules. At-least one strain from every genus, except those belonging to the genera Acinetobacter and Pseudomonas, were indicated to produce AI-2. Production of AI-2 in batch-cultures was growth-phase-dependent. Cross-feeding assays demonstrated that AHLs were produced by Acinetobacter spp., Pseudomonas aeruginosa and Serratia marcescens. Independent from studies of the bacterial species isolated from wounds, AHL and/or AI-2 signaling molecules were detected in 21 of 30 debridement samples of unknown microbial composition. CONCLUSION Chronic wound bacteria produce cell-cell signaling molecules. Resident species generally produce AI-2 molecules and aggressive transient species associated with chronic wounds typically produce AHLs. Both these classes of cell-cell signals are present in human chronic wounds. SIGNIFICANCE AND IMPACT OF STUDY Inter-bacterial cell-cell signaling may be an important factor influencing wound development and the presence of AHLs and AI-2 could be used as a predictor of wound severity. Manipulation of cell −cell signaling may provide a novel strategy for improving wound healing. PMID:19840177

Dynamic Kerr effect in a strong uniform AC electric field for interacting polar and polarizable molecules in the mean field approximation

NASA Astrophysics Data System (ADS)

Deshmukh, Snehal D.; Déjardin, Pierre-Michel; Kalmykov, Yuri P.

2017-09-01

Analytical formulas for the electric birefringence response of interacting polar and anisotropically polarizable molecules due to a uniform alternating electric field are derived using Berne's forced rotational diffusion model [B. J. Berne, J. Chem. Phys. 62, 1154 (1975)] in the nonlinear version described by Warchol and Vaughan [J. Chem. Phys. 71, 502 (1979)]. It is found for noninteracting molecules that the signal consists of a frequency-dependent DC component superimposed on an oscillatory part with a frequency twice that of the AC driving field. However, unlike noninteracting molecules, the AC part strongly deviates from its dilute counterpart. This suggests a possible way of motivating new experimental studies of intermolecular interactions involving electro-optical methods and complementary nonlinear dielectric relaxation experiments.

Continuous centrifuge decelerator for polar molecules.

PubMed

Chervenkov, S; Wu, X; Bayerl, J; Rohlfes, A; Gantner, T; Zeppenfeld, M; Rempe, G

2014-01-10

Producing large samples of slow molecules from thermal-velocity ensembles is a formidable challenge. Here we employ a centrifugal force to produce a continuous molecular beam with a high flux at near-zero velocities. We demonstrate deceleration of three electrically guided molecular species, CH3F, CF3H, and CF3CCH, with input velocities of up to 200  m s(-1) to obtain beams with velocities below 15  m s(-1) and intensities of several 10(9)  mm(-2) s(-1). The centrifuge decelerator is easy to operate and can, in principle, slow down any guidable particle. It has the potential to become a standard technique for continuous deceleration of molecules.

Functional fixedness and functional reduction as common sense reasonings in chemical equilibrium and in geometry and polarity of molecules

NASA Astrophysics Data System (ADS)

Furió, C.; Calatayud, M. L.; Bárcenas, S. L.; Padilla, O. M.

2000-09-01

Many of the learning difficulties in the specific domain of chemistry are found not only in the ideas already possessed by students but in the strategic and procedural knowledge that is characteristic of everyday thinking. These defects in procedural knowledge have been described as functional fixedness and functional reduction. This article assesses the procedural difficulties of students (grade 12 and first and third year of university) based on common sense reasoning in two areas of chemistry: chemical equilibrium and geometry and polarity of molecules. In the first area, the theme of external factors affecting equilibria (temperature and concentration change) was selected because the explanations given by the students could be analyzed easily. The existence of a functional fixedness where Le Chatelier's principle was almost exclusively applied by rote could be observed, with this being the cause of the incorrect responses given to the proposed items. Functional fixedness of the Lewis structure also led to an incorrect prediction of molecular geometry. When molecular geometry was correctly determined by the students, it seemed that other methodological or procedural difficulties appeared when the task was to determine molecular polarity. The students showed a tendency, in many cases, to reduce the factors affecting molecular polarity in two possible ways: (a) assuming that polarity depends only on shape (geometric functional reduction) or (b) assuming that molecular polarity depends only on the polarity of bonds (bonding functional reduction).

Manipulating the dipole layer of polar organic molecules on metal surfaces via different charge-transfer channels

NASA Astrophysics Data System (ADS)

Lin, Meng-Kai; Nakayama, Yasuo; Zhuang, Ying-Jie; Wang, Chin-Yung; Pi, Tun-Wen; Ishii, Hisao; Tang, S.-J.

The key properties of organic films such as energy level alignment (ELA), work functions, and injection barriers are closely linked to this dipole layer. Using angle resolved photoemission spectroscopy (ARPES), we systemically investigate the coverage-dependent work functions and spectra line shapes of occupied molecular orbital states of a polar molecule, chloroaluminium phthalocyanine (ClAlPc), grown on Ag(111) to show that the orientations of the first ClAlPc layer can be manipulated via the molecule deposition rate and post annealing, causing ELA at organic-metal interface to differ for about 0.3 eV between Cl-up and Cl-down configuration. Moreover, by comparing the experimental results with the calculations based on both gas-phase model and realistic model of ClAlPc on Ag(111) , we evidence that the different orientations of ClAlPc dipole layers lead to different charge-transfer channels between ClAlPc and Ag, a key factor that controls the ELA at organic-metal interface.

AgCl precipitates in isolated cuticular membranes reduce rates of cuticular transpiration.

PubMed

Schreiber, Lukas; Elshatshat, Salem; Koch, Kerstin; Lin, Jinxing; Santrucek, Jiri

2006-01-01

Counter diffusion of chloride, applied as NaCl at the inner side of isolated cuticles, and silver, applied as AgNO(3) at the outer side, lead to the formation of insoluble AgCl precipitates in isolated cuticles. AgCl precipitates could be visualized by light and scanning electron microscopy. The presence of AgCl precipitates in isolated cuticles was verified by energy dispersive X-ray analysis. It is argued that insoluble AgCl precipitates formed in polar pores of cuticles and as a consequence, cuticular transpiration of 13 out of 15 investigated species was significantly reduced up to three-fold. Water as a small and uncharged but polar molecule penetrates cuticles via two parallel paths: a lipophilic path, formed by lipophilic cutin and wax domains, and a aqueous pathe, formed by polar pores. Thus, permeances P (m s(-1)) of water, which is composed of the two quantities P (Lipid) and P (Pore), decreased, since water transport across polar pores was affected by AgCl precipitates. Cuticles with initially high rates of cuticular transpiration were generally more sensitive towards AgCl precipitates compared to cuticles with initially low rates of transpiration. Results presented here, significantly improves the current model of the structure of the cuticular transpiration barrier, since the pronounced heterogeneity of the cuticular transport barrier, composed of lipophilic as well as polar paths of diffusion, has to be taken into account in future.

Shear-induced desorption of isolated polymer molecules from a planar wall

NASA Astrophysics Data System (ADS)

Dutta, Sarit; Dorfman, Kevin; Kumar, Satish

2014-03-01

Shear-induced desorption of isolated polymer molecules is studied using Brownian dynamics simulations. The polymer molecules are modeled as freely jointed bead-spring chains interacting with a planar wall via a short-range potential. The simulations include both intrachain and chain-wall hydrodynamic interactions. Shear flow is found to cause chain flattening, resulting at low shear rates in an increased fraction of chain segments bound to the wall. However, above a critical shear rate the chains desorb completely. The desorption process is nucleated by random protrusions in the shear gradient direction which evolve under the combined effect of drag, hydrodynamic interaction, and vorticity-induced rotation, and subsequently lead to recapture. Above the critical shear rate, these protrusions grow in length until the entire chain is peeled off the wall. For free-draining chains, the protrusions are not sustained and no desorption is observed even at shear rates much higher than the critical value. These simulations can help in interpreting experiments on shear-induced desorption of polymer films and brushes.

Gravity and light control of the developmental polarity of regenerating protoplasts isolated from prothallial cells of the fern Ceratopteris richardii

NASA Technical Reports Server (NTRS)

Edwards, E. S.; Roux, S. J.

1998-01-01

A procedure has been developed for isolating protoplasts from prothalli of Ceratopteris richardii which can be cultured and are capable of regeneration. Protoplasts were isolated from 2-week-old gametophytes in a medium containing wall-digesting enzymes in 0.5 M sucrose, followed by purification of the released protoplasts by floating them up into a 0.5 M sorbitol layer. Regeneration occurred over a period of 10-24 days, and, under optimal osmotic conditions, followed the developmental pattern seen during spore germination, in that the first division gave rise to a primary rhizoid. Thus, prothallial protoplasts are comparable to germinating spores as suitable models for studies of developmental polarity in single cells. As in germinating spores, the polarity of development in regenerating protoplasts is influenced by the vectors of gravity and unilateral light. However, the relative influence of light in fixing this polarity is greater in regenerating protoplasts, while in germinating spores, the influence of gravity is greater.

Photoionization of water molecules by a train of attosecond pulses assisted by a near-infrared laser: delay and polarization control

NASA Astrophysics Data System (ADS)

Martini, Lara; Boll, Diego I. R.; Fojón, Omar A.

2017-08-01

Basic reactions involving water molecules are essential to understand the interaction between radiation and the biological tissue because living cells are composed mostly by water. Therefore, the knowledge of ionization of the latter is crucial in many domains of Biology and Physics. So, we study theoretically the photoionization of water molecules by extreme ultraviolet attopulse trains assisted by lasers in the near-infrared range. We use a separable Coulomb-Volkov model in which the temporal evolution of the system can be divided into three stages allowing spatial and temporal separation for the Coulomb and Volkov final state wavefunctions. First, we analyze photoelectron angular distributions for different delays between the attopulse train and the assistant laser field. We compare our results for water and Ne atoms as they belong to the same isoelectronic series. Moreover, we contrast our calculations with previous theoretical and experimental work for Ar atoms due to the similarities of the orbitals involved in the reaction. Second, we study the effect of varying the relative orientations of the attopulse and laser field polarizations and we compare our predictions with other theories and experiments. We expect these studies contribute to the improvement of polarization experiments and the development of the attopulse trains and assistant laser fields technologies. Finally, we hope our work promote progress on the control of the chemical reactivity of water molecules since this could be useful in different fields such as radiobiology and medical physics.

The Endoplasmic Reticulum Membrane Is Permeable to Small Molecules

PubMed Central

Le Gall, Sylvie; Neuhof, Andrea; Rapoport, Tom

2004-01-01

The lumen of the endoplasmic reticulum (ER) differs from the cytosol in its content of ions and other small molecules, but it is unclear whether the ER membrane is as impermeable as other membranes in the cell. Here, we have tested the permeability of the ER membrane to small, nonphysiological molecules. We report that isolated ER vesicles allow different chemical modification reagents to pass from the outside into the lumen with little hindrance. In permeabilized cells, the ER membrane allows the passage of a small, charged modification reagent that is unable to cross the plasma membrane or the lysosomal and trans-Golgi membranes. A larger polar reagent of ∼5 kDa is unable to pass through the ER membrane. Permeation of the small molecules is passive because it occurs at low temperature in the absence of energy. These data indicate that the ER membrane is significantly more leaky than other cellular membranes, a property that may be required for protein folding and other functions of the ER. PMID:14617815

Inter-molecule interaction for magnetic property of vanadyl tetrakis(thiadiazole) porphyrazine film on Au(1 1 1)

NASA Astrophysics Data System (ADS)

Hou, Jie; Wang, Yu; Eguchi, Keitaro; Nanjo, Chihiro; Takaoka, Tsuyoshi; Sainoo, Yasuyuki; Awaga, Kunio; Komeda, Tadahiro

2018-05-01

We report scanning tunneling microscope (STM) observation of vanadyl tetrakis(thiadiazole) porphyrazine (VOTTDPz) molecules, which is a family molecule of phthalocyanine (Pc) but without Csbnd H termination in the perimeter, deposited on Au(1 1 1) surface. Well-ordered film corresponding to 4 × 4 superstructure with respect to Au(1 1 1) surface is formed, in which the centers of the molecules are separated by 1.12 nm, which is much smaller than that observed for a VOPc molecule on Au(1 1 1), due to the absence of Csbnd H termination. At the same time, the azimuthal angles of neighboring molecules rotate with each other by 30°. A contrast variation of bright and dark molecules is observed, which are interpreted as O-up and O-down molecules, respectively, based on the density functional theory simulation. Spin-polarized local density of states calculation shows spin-polarized V 3d state, which is delocalized over the ring. Spin detection is executed by measuring Kondo resonance in the tunneling spectroscopy near the Fermi level, which is caused by the interaction of an isolated spin and conduction electron of the substrate. We detected asymmetric and weak Kondo peak for out-of-plane outer magnetic field of 0 T, which becomes strong and symmetric peak at 5 T, which is understood by the shift of the spin center of the Kondo resonance from V 3d to delocalized π state in ring with the magnetic field.

EDITORIAL: Focus on Cold and Ultracold Molecules FOCUS ON COLD AND ULTRACOLD MOLECULES

NASA Astrophysics Data System (ADS)

Carr, Lincoln D.; Ye, Jun

2009-05-01

Cold and ultracold molecules are the next wave of ultracold physics, giving rise to an exciting array of scientific opportunities, including many body physics for novel quantum phase transitions, new states of matter, and quantum information processing. Precision tests of fundamental physical laws benefit from the existence of molecular internal structure with exquisite control. The study of novel collision and reaction dynamics will open a new chapter of quantum chemistry. Cold molecules bring together researchers from a variety of fields, including atomic, molecular, and optical physics, chemistry and chemical physics, quantum information science and quantum simulations, condensed matter physics, nuclear physics, and astrophysics, a truly remarkable synergy of scientific explorations. For the past decade there have been steady advances in direct cooling techniques, from buffer-gas cooling to cold molecular beams to electro- and magneto-molecular decelerators. These techniques have allowed a large variety of molecules to be cooled for pioneering studies. Recent amazing advances in experimental techniques combining the ultracold and the ultraprecise have furthermore brought molecules to the point of quantum degeneracy. These latter indirect cooling techniques magnetically associate atoms from a Bose-Einstein condensate and/or a quantum degenerate Fermi gas, transferring at 90% efficiency highly excited Fano-Feshbach molecules, which are on the order of 10 000 Bohr radii in size, to absolute ground state molecules just a few Bohr across. It was this latter advance, together with significant breakthroughs in internal state manipulations, which inspired us to coordinate this focus issue now, and is the reason why we say the next wave of ultracold physics has now arrived. Whether directly or indirectly cooled, heteronuclear polar molecules offer distinct new features in comparison to cold atoms, while sharing all of their advantages (purity, high coherence

The electron-spin--nuclear-spin interaction studied by polarized neutron scattering.

PubMed

Stuhrmann, Heinrich B

2007-11-01

Dynamic nuclear spin polarization (DNP) is mediated by the dipolar interaction of paramagnetic centres with nuclear spins. This process is most likely to occur near paramagnetic centres at an angle close to 45 degrees with respect to the direction of the external magnetic field. The resulting distribution of polarized nuclear spins leads to an anisotropy of the polarized neutron scattering pattern, even with randomly oriented radical molecules. The corresponding cross section of polarized coherent neutron scattering in terms of a multipole expansion is derived for radical molecules in solution. An application using data of time-resolved polarized neutron scattering from an organic chromium(V) molecule is tested.

Surface enhanced single-molecule magnetism involving 4f spin

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

Zhang, Yachao, E-mail: yachao.zhang@pku.edu.cn

2016-03-28

We study the magnetic anisotropy energy (MAE) of the isolated and deposited Eu(C{sub 8}H{sub 8}){sub 2} by first-principles calculations considering the van der Waals correction and the strong correlation effects. We find that both the molecular spin moment and the easy-axis magnetic anisotropy are enhanced upon deposition on Cu(111). We propose a mechanism in terms of the weakened spin polarization of the π-2p orbitals and the induced anisotropic occupations of the 4f orbitals. Our findings pave the way for raising the MAE of 4f-element single-molecule magnets by tailoring the molecule–surface contacts.

Dynamic Nuclear Polarization of 17O: Direct Polarization

PubMed Central

Michaelis, Vladimir K.; Corzilius, Björn; Smith, Albert A.; Griffin, Robert G.

2014-01-01

Dynamic nuclear polarization of 17O was studied using four different polarizing agents – the biradical TOTAPOL, and the monoradicals trityl and SA-BDPA, as well as a mixture of the latter two. Field profiles, DNP mechanisms and enhancements were measured to better understand and optimize directly polarizing this low-gamma quadrupolar nucleus using both mono- and bi-radical polarizing agents. Enhancements were recorded < 88 K and were > 100 using the trityl (OX063) radical and < 10 with the other polarizing agents. The > 10,000 fold savings in acquisition time enabled a series of biologically relevant small molecules to be studied with small sample sizes and the measurement of various quadrupolar parameters. The results are discussed with comparison to room temperature studies and GIPAW quantum chemical calculations. These experimental results illustrate the strength of high field DNP and the importance of radical selection for studying low-gamma nuclei. PMID:24195759

Dynamic nuclear polarization of 17O: direct polarization.

PubMed

Michaelis, Vladimir K; Corzilius, Björn; Smith, Albert A; Griffin, Robert G

2013-12-05

Dynamic nuclear polarization of (17)O was studied using four different polarizing agents: the biradical TOTAPOL and the monoradicals trityl and SA-BDPA, as well as a mixture of the latter two. Field profiles, DNP mechanisms, and enhancements were measured to better understand and optimize directly polarizing this low-gamma quadrupolar nucleus using both mono- and biradical polarizing agents. Enhancements were recorded at <88 K and were >100 using the trityl (OX063) radical and <10 with the other polarizing agents. The >10,000-fold savings in acquisition time enabled a series of biologically relevant small molecules to be studied with small sample sizes and the measurement of various quadrupolar parameters. The results are discussed with comparison to room temperature studies and GIPAW quantum chemical calculations. These experimental results illustrate the strength of high field DNP and the importance of radical selection for studying low-gamma nuclei.

Polarized Raman Spectroscopy for Determining the Orientation of di-D-phenylalanine Molecules in a Nanotube.

PubMed

Sereda, Valentin; Ralbovsky, Nicole M; Vasudev, Milana C; Naik, Rajesh R; Lednev, Igor K

2016-09-01

Self-assembly of short peptides into nanostructures has become an important strategy for the bottom-up fabrication of nanomaterials. Significant interest to such peptide-based building blocks is due to the opportunity to control the structure and properties of well-structured nanotubes, nanofibrils, and hydrogels. X-ray crystallography and solution NMR, two major tools of structural biology, have significant limitations when applied to peptide nanotubes because of their non-crystalline structure and large weight. Polarized Raman spectroscopy was utilized for structural characterization of well-aligned D-Diphenylalanine nanotubes. The orientation of selected chemical groups relative to the main axis of the nanotube was determined. Specifically, the C-N bond of CNH 3 + groups is oriented parallel to the nanotube axis, the peptides' carbonyl groups are tilted at approximately 54° from the axis and the COO - groups run perpendicular to the axis. The determined orientation of chemical groups allowed the understanding of the orientation of D-diphenylalanine molecule that is consistent with its equilibrium conformation. The obtained data indicate that there is only one orientation of D-diphenylalanine molecules with respect to the nanotube main axis.

Fine-tuning device performances of small molecule solar cells via the more polarized DPP-attached donor units.

PubMed

Huang, Jianhua; Jia, Hui; Li, Liangjie; Lu, Zhenhuan; Zhang, Wenqing; He, Weiwei; Jiang, Bo; Tang, Ailing; Tan, Zhan'ao; Zhan, Chuanlang; Li, Yongfang; Yao, Jiannian

2012-11-07

Three solution-processable small molecules of DPPT, DPPSe and DPPTT were synthesized by Stille coupling through attaching donor units of thiophene (T), selenophene (Se) and thieno[3,2-b]thiophene (TT) to the diketopyrrolopyrrole (DPP) core, respectively. Replacement of the T donors with the more polarized Se units results in a balance between the a and b direction packing and an obvious increase of the power conversion efficiency (PCE) from 1.90% to 2.33% with the increase of the short-circuit current (I(sc)) from 5.59 to 5.81 mA cm(-2) and the open-circuit voltage (V(oc)) from 0.78 V to 0.86 under the small molecule/acceptor ratio of 3 : 1. However, introduction of the conjugation-enlarged TT groups (versus the T units) leads to a decrease of the PCE, down to 1.70%, with a significant decrease of the fill factor (FF) (38% versus 44%), due to its poor film-forming characteristics.

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

NASA Astrophysics Data System (ADS)

Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

2016-03-01

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.

Distilling two-center-interference information during tunneling of aligned molecules with orthogonally polarized two-color laser fields

NASA Astrophysics Data System (ADS)

Gao, F.; Chen, Y. J.; Xin, G. G.; Liu, J.; Fu, L. B.

2017-12-01

When electrons tunnel through a barrier formed by the strong laser field and the two-center potential of a diatomic molecule, a double-slit-like interference can occur. However, this interference effect can not be probed directly right now, as it is strongly coupled with other dynamical processes during tunneling. Here, we show numerically and analytically that orthogonally polarized two-color (OTC) laser fields are capable of resolving the interference effect in tunneling, while leaving clear footprints of this effect in photoelectron momentum distributions. Moreover, this effect can be manipulated by changing the relative field strength of OTC fields.

Production, Manipulation, and Applications of Ultracold Polar Molecules

DTIC Science & Technology

2015-04-30

molecules, cooling, trapping, photoassociation, feshbach resonances, quantum simulation , ultracold collisions, ultracold chemistry, optical lattices...been a multitude of less predictable outcomes: special quantum information processing schemes, uses of entanglement such a spin-squeezing for better...field seeing states to high-field-seeking states (and back) at key points in the magnetic field. The molecules spontaneously emit photons as they are

The local magnetic properties of [MnIII6 CrIII]3+ and [FeIII6 CrIII]3+ single-molecule magnets deposited on surfaces studied by spin-polarized photoemission and XMCD with circularly polarized synchrotron radiation

NASA Astrophysics Data System (ADS)

Heinzmann, U.; Helmstedt, A.; Dohmeier, N.; Müller, N.; Gryzia, A.; Brechling, A.; Hoeke, V.; Krickemeyer, E.; Glaser, T.; Fonin, M.; Bouvron, S.; Leicht, P.; Tietze, T.; Goering, E.; Kuepper, K.

2014-04-01

It is demonstrated that local magnetic moments of single molecule magnets (SMM) normally studied by XMCD at very low temperatures and high magnetic fields can be measured by means of spin-resolved electron emission in the paramagnetic phase at room temperature by use of circularly polarized radiation.

Field-free orientation of diatomic molecule via the linearly polarized resonant pulses

NASA Astrophysics Data System (ADS)

Li, Su-Yu; Guo, Fu-Ming; Wang, Jun; Yang, Yu-Jun; Jin, Ming-Xing

2015-10-01

We propose a scheme to coherently control the field-free orientation of NO molecule whose rotational temperature is above 0 K. It is found that the maximum molecular orientation is affected by two factors: one is the sum of the population of M = 0 rotational states and the other is their distribution, however, their distribution plays a much more significant role in molecular orientation than the sum of their population. By adopting a series of linearly polarized pulses resonant with the rotational states, the distribution of M = 0 rotational states is well rearranged. Though the number of pulses used is small, a relatively high orientation degree can be obtained. This scheme provides a promising approach to the achievement of a good orientation effect. Project supported by the National Basic Research Program of China (Grant No. 2013CB922200), the National Natural Science Foundation of China (Grant Nos. 11034003, 11474129, 11274141, and 11304116), the Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20130061110021), and the Graduate Innovation Fund of Jilin University (Grant No. 2015091).

In vitro isolation of small-molecule-binding aptamers with intrinsic dye-displacement functionality

PubMed Central

Yu, Haixiang; Yang, Weijuan; Alkhamis, Obtin; Canoura, Juan; Yang, Kyung-Ae; Xiao, Yi

2018-01-01

Abstract Aptamer-based sensors offer a powerful tool for molecular detection, but the practical implementation of these biosensors is hindered by costly and laborious sequence engineering and chemical modification procedures. We report a simple strategy for directly isolating signal-reporting aptamers in vitro through systematic evolution of ligands by exponential enrichment (SELEX) that transduce binding events into a detectable change of absorbance via target-induced displacement of a small-molecule dye. We first demonstrate that diethylthiatricarbocyanine (Cy7) can stack into DNA three-way junctions (TWJs) in a sequence-independent fashion, greatly altering the dye's absorbance spectrum. We then design a TWJ-containing structured library and isolate an aptamer against 3,4-methylenedioxypyrovalerone (MDPV), a synthetic cathinone that is an emerging drug of abuse. This aptamer intrinsically binds Cy7 within its TWJ domain, but MDPV efficiently displaces the dye, resulting in a change in absorbance within seconds. This assay is label-free, and detects nanomolar concentrations of MDPV. It also recognizes other synthetic cathinones, offering the potential to detect newly-emerging designer drugs, but does not detect structurally-similar non-cathinone compounds or common cutting agents. Moreover, we demonstrate that the Cy7-displacement colorimetric assay is more sensitive than a conventional strand-displacement fluorescence assay. We believe our strategy offers an effective generalized approach for the development of sensitive dye-displacement colorimetric assays for other small-molecule targets. PMID:29361056

Isolation of a small molecule with anti-MRSA activity from a mangrove symbiont Streptomyces sp. PVRK-1 and its biomedical studies in Zebrafish embryos

PubMed Central

Kannan, Rajaretinam Rajesh; Iniyan, Appadurai Muthamil; Prakash, Vincent Samuel Gnana

2011-01-01

Objective The aim of the present study was to isolate the anti-MRSA (Methicillin Resistant Staphylococcus aureus) molecule from the Mangrove symbiont Streptomyces and its biomedical studies in Zebrafish embryos. Methods MRSA was isolated from the pus samples of Colachal hospitals and confirmed by amplification of mecA gene. Anti-MRSA molecule producing strain was identified by 16s rRNA gene sequencing. Anti-MRSA compound production was optimized by Solid State Fermentation (SSF) and the purification of the active molecule was carried out by TLC and RP-HPLC. The inhibitory concentration and LC50 were calculated using Statistical software SPSS. The Biomedical studies including the cardiac assay and organ toxicity assessment were carried out in Zebrafish. Results The bioactive anti-MRSA small molecule A2 was purified by TLC with Rf value of 0.37 with 1.389 retention time at RP-HPLC. The Inhibitory Concentration of the purified molecule A2 was 30 µg/mL but, the inhibitory concentration of the MRSA in the infected embryo was 32-34 µg/mL for TLC purified molecule A2 with LC50 mean value was 61.504 µg/mL. Zebrafish toxicity was assessed in 48-60 µg/mL by observing the physiological deformities and the heart beat rates (HBR) of embryos for anti MRSA molecule showed the mean of 41.33-41.67 HBR/15 seconds for 40 µg/mL and control was 42.33-42.67 for 15 seconds which significantly showed that the anti-MRSA molecule A2 did not affected the HBR. Conclusions Anti-MRSA molecule from Streptomyces sp PVRK-1 was isolated and biomedical studies in Zebrafish model assessed that the molecule was non toxic at the minimal inhibitory concentration of MRSA. PMID:23569790

Isolation of a small molecule with anti-MRSA activity from a mangrove symbiont Streptomyces sp. PVRK-1 and its biomedical studies in Zebrafish embryos.

PubMed

Kannan, Rajaretinam Rajesh; Iniyan, Appadurai Muthamil; Prakash, Vincent Samuel Gnana

2011-10-01

The aim of the present study was to isolate the anti-MRSA (Methicillin Resistant Staphylococcus aureus) molecule from the Mangrove symbiont Streptomyces and its biomedical studies in Zebrafish embryos. MRSA was isolated from the pus samples of Colachal hospitals and confirmed by amplification of mecA gene. Anti-MRSA molecule producing strain was identified by 16s rRNA gene sequencing. Anti-MRSA compound production was optimized by Solid State Fermentation (SSF) and the purification of the active molecule was carried out by TLC and RP-HPLC. The inhibitory concentration and LC50 were calculated using Statistical software SPSS. The Biomedical studies including the cardiac assay and organ toxicity assessment were carried out in Zebrafish. The bioactive anti-MRSA small molecule A2 was purified by TLC with Rf value of 0.37 with 1.389 retention time at RP-HPLC. The Inhibitory Concentration of the purified molecule A2 was 30 µg/mL but, the inhibitory concentration of the MRSA in the infected embryo was 32-34 µg/mL for TLC purified molecule A2 with LC50 mean value was 61.504 µg/mL. Zebrafish toxicity was assessed in 48-60 µg/mL by observing the physiological deformities and the heart beat rates (HBR) of embryos for anti MRSA molecule showed the mean of 41.33-41.67 HBR/15 seconds for 40 µg/mL and control was 42.33-42.67 for 15 seconds which significantly showed that the anti-MRSA molecule A2 did not affected the HBR. Anti-MRSA molecule from Streptomyces sp PVRK-1 was isolated and biomedical studies in Zebrafish model assessed that the molecule was non toxic at the minimal inhibitory concentration of MRSA.

Micro injector sample delivery system for charged molecules

DOEpatents

Davidson, James C.; Balch, Joseph W.

1999-11-09

A micro injector sample delivery system for charged molecules. The injector is used for collecting and delivering controlled amounts of charged molecule samples for subsequent analysis. The injector delivery system can be scaled to large numbers (>96) for sample delivery to massively parallel high throughput analysis systems. The essence of the injector system is an electric field controllable loading tip including a section of porous material. By applying the appropriate polarity bias potential to the injector tip, charged molecules will migrate into porous material, and by reversing the polarity bias potential the molecules are ejected or forced away from the tip. The invention has application for uptake of charged biological molecules (e.g. proteins, nucleic acids, polymers, etc.) for delivery to analytical systems, and can be used in automated sample delivery systems.

Response functions for dimers and square-symmetric molecules in four-wave-mixing experiments with polarized light

NASA Astrophysics Data System (ADS)

Smith, Eric Ryan; Farrow, Darcie A.; Jonas, David M.

2005-07-01

Four-wave-mixing nonlinear-response functions are given for intermolecular and intramolecular vibrations of a perpendicular dimer and intramolecular vibrations of a square-symmetric molecule containing a doubly degenerate state. A two-dimensional particle-in-a-box model is used to approximate the electronic wave functions and obtain harmonic potentials for nuclear motion. Vibronic interactions due to symmetry-lowering distortions along Jahn-Teller active normal modes are discussed. Electronic dephasing due to nuclear motion along both symmetric and asymmetric normal modes is included in these response functions, but population transfer between states is not. As an illustration, these response functions are used to predict the pump-probe polarization anisotropy in the limit of impulsive excitation.

[Permeability of isolated rat hepatocyte plasma membranes for molecules of dimethyl sulfoxide].

PubMed

Kuleshova, L G; Gordienko, E A; Kovalenko, I F

2014-01-01

We have studied permeability of isolated rat hepatocyte membranes for molecules of dimethyl sulfoxide (DMSO) at different hypertonicity of a cryoprotective medium. The permeability coefficient of hepatocyte membranes κ1 for DMSO molecules was shown to be the differential function of osmotic pressure between a cell and an extracellular medium. Ten-fold augmentation of DMSO concentration in the cryoprotective medium causes the decrease of permeability coefficients κ1 probably associated with the increased viscosity in membrane-adjacent liquid layers as well as partial limitations appeared as a result of change in cell membrane shape after hepatocyte dehydration. We have found out that in aqueous solutions of NaCl (2246 mOsm/l) and DMSO (2250 mOsm/l) the filtration coefficient L(p) in the presence of a penetrating cryoprotectant (L(pDMSO) = (4.45 ± 0.04) x 10(-14) m3/Ns) is 3 orders lower compared to the case with electrolyte (L(pNaCl) = (2.25 ± 0.25) x 10(-11) m3/Ns). This phenomenon is stipulated by the cross impact of flows of a cryoprotectant and water at the stage of cell dehydration. Pronounced lipophilicity of DMSO, geometric parameters of its molecule as well as the presence of large aqueous pores in rat hepatocyte membranes allow of suggesting the availability of two ways of penetrating this cryoprotectant into the cells by non-specific diffusion through membrane lipid areas and hydrophilic channels.

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

PubMed Central

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

2016-01-01

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

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

DOE PAGES

Wang, Xu; Le, Anh -Thu; Yu, Chao; ...

2016-03-30

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. Lastly, amore » simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.« less

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

PubMed Central

Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

2016-01-01

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method. PMID:27025410

Diffusion of isolated DNA molecules: dependence on length and topology.

PubMed

Robertson, Rae M; Laib, Stephan; Smith, Douglas E

2006-05-09

The conformation and dynamics of circular polymers is a subject of considerable theoretical and experimental interest. DNA is an important example because it occurs naturally in different topological states, including linear, relaxed circular, and supercoiled circular forms. A fundamental question is how the diffusion coefficients of isolated polymers scale with molecular length and how they vary for different topologies. Here, diffusion coefficients D for relaxed circular, supercoiled, and linear DNA molecules of length L ranging from approximately 6 to 290 kbp were measured by tracking the Brownian motion of single molecules. A topology-independent scaling law D approximately L(-nu) was observed with nu(L) = 0.571 +/- 0.014, nu(C) = 0.589 +/- 0.018, and nu(S) = 0.571 +/- 0.057 for linear, relaxed circular, and supercoiled DNA, respectively, in good agreement with the scaling exponent of nu congruent with 0.588 predicted by renormalization group theory for polymers with significant excluded volume interactions. Our findings thus provide evidence in support of several theories that predict an effective diameter of DNA much greater than the Debye screening length. In addition, the measured ratio D(Circular)/D(Linear) = 1.32 +/- 0.014 was closer to the value of 1.45 predicted by using renormalization group theory than the value of 1.18 predicted by classical Kirkwood hydrodynamic theory and agreed well with a value of 1.31 predicted when incorporating a recently proposed expression for the radius of gyration of circular polymers into the Zimm model.

Molecular electron recollision dynamics in intense circularly polarized laser pulses

NASA Astrophysics Data System (ADS)

Bandrauk, André D.; Yuan, Kai-Jun

2018-04-01

Extreme UV and x-ray table top light sources based on high-order harmonic generation (HHG) are focused now on circular polarization for the generation of circularly polarized attosecond pulses as new tools for controlling electron dynamics, such as charge transfer and migration and the generation of attosecond quantum electron currents for ultrafast magneto-optics. A fundamental electron dynamical process in HHG is laser induced electron recollision with the parent ion, well established theoretically and experimentally for linear polarization. We discuss molecular electron recollision dynamics in circular polarization by theoretical analysis and numerical simulation. The control of the polarization of HHG with circularly polarized ionizing pulses is examined and it is shown that bichromatic circularly polarized pulses enhance recollision dynamics, rendering HHG more efficient, especially in molecules because of their nonspherical symmetry. The polarization of the harmonics is found to be dependent on the compatibility of the rotational symmetry of the net electric field created by combinations of bichromatic circularly polarized pulses with the dynamical symmetry of molecules. We show how the field and molecule symmetry influences the electron recollision trajectories by a time-frequency analysis of harmonics. The results, in principle, offer new unique controllable tools in the study of attosecond molecular electron dynamics.

Optoelectrical Cooling of Polar Molecules to Submillikelvin Temperatures.

PubMed

Prehn, Alexander; Ibrügger, Martin; Glöckner, Rosa; Rempe, Gerhard; Zeppenfeld, Martin

2016-02-12

We demonstrate direct cooling of gaseous formaldehyde (H2CO) to the microkelvin regime. Our approach, optoelectrical Sisyphus cooling, provides a simple dissipative cooling method applicable to electrically trapped dipolar molecules. By reducing the temperature by 3 orders of magnitude and increasing the phase-space density by a factor of ∼10(4), we generate an ensemble of 3×10(5) molecules with a temperature of about 420  μK, populating a single rotational state with more than 80% purity.

Isolated single-molecule magnets on native gold.

PubMed

Zobbi, Laura; Mannini, Matteo; Pacchioni, Mirko; Chastanet, Guillaume; Bonacchi, Daniele; Zanardi, Chiara; Biagi, Roberto; Del Pennino, Umberto; Gatteschi, Dante; Cornia, Andrea; Sessoli, Roberta

2005-03-28

The incorporation of thioether groups in the structure of a Mn12 single-molecule magnet, [Mn12(O12)(L)16(H2O)4] with L = 4-(methylthio)benzoate, is a successful route to the deposition of well-separated clusters on native gold surfaces and to the addressing of individual molecules by scanning tunnelling microscopy.

Functional attributes of a new molecule-2-hydroxymethyl-benzoic acid 2'-hydroxy-tetradecyl ester isolated from Talaromyces purpureogenus CFRM02.

PubMed

Pandit, Saritha Gopal; Puttananjaih, Mohankumari H; Harohally, Nanishankar V; Dhale, Mohan Appasaheb

2018-07-30

An account of antioxidant and antimicrobial characteristics displayed by ethyl acetate extract of Talaromyces purpureogenus CFRM-02 cultivated by submerged fermentation on bengal gram husk (BegH) led to the isolation of a new molecule, which was purified via silica gel column chromatography. The TLC and HPLC data revealed the purity of the isolated compound. By employing an array of spectroscopic techniques, structural elucidation was accomplished, and the molecule was identified as 2-hydroxymethyl-benzoic acid 2'-hydroxy-tetradecyl ester and was also designated with a familiar name pentalsamonin. The pentalsamonin molecule scavenged DPPH (24%), H 2 O 2 (64%), superoxide anion (58%) with a reducing power (0.989 AU) at the given concentration. The MIC and MBC of pentalsamonin against Bacillus subtilis, Staphylococcus aureus, Escherichia coli and Klebsiella pneumoniae are in the range 62.5-125 and 125-250 µg/ml, respectively. The antioxidant and antibacterial functional attributes of pentalsamonin suggest useful applications in food and nutraceuticals. Copyright © 2018 Elsevier Ltd. All rights reserved.

Spin polarization properties of benzene/graphene with transition metals as dopants: First principles calculations

NASA Astrophysics Data System (ADS)

Yuan, X. B.; Tian, Y. L.; Zhao, X. W.; Yue, W. W.; Hu, G. C.; Ren, J. F.

2018-05-01

First principles calculations are used to study the spin polarization properties of benzene molecule adsorbed on the graphene surface which doped with transition metals including Mn, Cr, Fe, Co, and Ni. The densities of states (DOS) of the benzene molecule can be induced to be spin split at the Fermi level only when it is adsorbed on Mn-, and Cr-doped graphene. The p-orbital of the benzene molecule will interact with the d orbital of the doped atoms, which will generate new spin coupling states and lead to obvious spin polarization of the benzene molecule. The spin-polarized density distributions as well as the differential charge density distributions of the systems also suggest that Mn-doped graphene will induce bigger spin polarization than that of Cr-doped graphene. Benzene molecule could be spin-polarized when it is adsorbed on the graphene surface with transition metal dopants, which could be a new method for researching graphene-based organic spintronic devices.

Circular polarization analyzer with polarization tunable focusing of surface plasmon polaritons

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

Wang, Sen; Zhang, Yan, E-mail: yzhang@mail.cnu.edu.cn; Beijing Key Laboratory for Metamaterials and Devices, and Key Laboratory of Terahertz Optoelectronics, Ministry of Education, Department of Physics, Capital Normal University, Beijing 100048

2015-12-14

A practical circular polarization analyzer (CPA) that can selectively focus surface plasmon polaritons (SPPs) at two separate locations, according to the helicity of the circularly polarized light, is designed and experimentally verified in the terahertz frequency range. The CPA consists of fishbone-slit units and is designed using the simulated annealing algorithm. By differentially detecting the intensities of the two SPPs focuses, the helicity of the incident circularly polarized light can be obtained and the CPA is less vulnerable to the noise of incident light. The proposed device may also have wide potential applications in chiral SPPs photonics and the analysismore » of chiral molecules in biology.« less

Control of π-Electron Rotations in Chiral Aromatic Molecules Using Intense Laser Pulses

NASA Astrophysics Data System (ADS)

Kanno, Manabu; Kono, Hirohiko; Fujimura, Yuichi

Our recent theoretical studies on laser-induced π-electron rotations in chiral aromatic molecules are reviewed. π electrons of a chiral aromatic molecule can be rotated along its aromatic ring by a nonhelical, linearly polarized laser pulse. An ansa aromatic molecule with a six-membered ring, 2,5-dichloro[n](3,6) pyrazinophane, which belongs to a planar-chiral molecule group, and its simplified molecule 2,5-dichloropyrazine are taken as model molecules. Electron wavepacket simulations in the frozen-molecular-vibration approximation show that the initial direction of π-electron rotation depends on the polarization direction of a linearly polarized laser pulse applied. Consecutive unidirectional rotation can be achieved by applying a sequence of linearly polarized pump and dump pulses to prevent reverse rotation. Optimal control simulations of π-electron rotation show that another controlling factor for unidirectional rotation is the relative optical phase between the different frequency components of an incident pulse in addition to photon polarization direction. Effects of nonadiabatic coupling between π-electron rotation and molecular vibrations are also presented, where the constraints of the frozen approximation are removed. The angular momentum gradually decays mainly owing to nonadiabatic coupling, while the vibrational amplitudes greatly depend on their rotation direction. This suggests that the direction of π-electron rotation on an attosecond timescale can be identified by detecting femtosecond molecular vibrations.

Magnetoassociation of KRb Feshbach molecules

NASA Astrophysics Data System (ADS)

Cumby, Tyler; Perreault, John; Shewmon, Ruth; Jin, Deborah

2010-03-01

I will discuss experiments in which we study the creation of ^40K^87Rb Feshbach molecules via magnetoassociation. We measure the molecule number as a function of the magnetic-field sweep rate through the interspecies Feshbach resonance and explore the dependence of association on the initial atom gas conditions. This study of the Feshbach molecule creation process may be relevant to the production of ultracold polar molecules, where magnetoassociated Feshbach molecules can be a crucial first step [1].[4pt] [1] K.-K. Ni, S. Ospelkaus, M. H. G. de Miranda, A. Peer, B. Neyenhuis, J. J. Zirbel, S. Kotochigova, P. S. Julienne, D. S. Jin, and J. Ye, Science, 2008, 322, 231- 235.

Magnetoassociation of KRb Feshbach molecules

NASA Astrophysics Data System (ADS)

Cumby, Tyler; Perreault, John; Shewmon, Ruth; Jin, Deborah

2010-03-01

I will discuss experiments in which we study the creation of ^40K^87Rb Feshbach molecules via magnetoassociation. We measure the molecule number as a function of the magnetic-field sweep rate through the interspecies Feshbach resonance and explore the dependence of association on the initial atom gas conditions. This study of the Feshbach molecule creation process may be relevant to the production of ultracold polar molecules, where magnetoassociated Feshbach molecules can be a crucial first step [1].[4pt] [1] K.-K. Ni, S. Ospelkaus, M. H. G. de Miranda, A. Peer, B. Neyenhuis, J. J. Zirbel, S. Kotochigova, P. S. Julienne, D. S. Jin, and J. Ye, Science, 2008, 322, 231-235.

Electrofluorescence polarity in a molecular diode

NASA Astrophysics Data System (ADS)

Petrov, E. G.; Leonov, V. A.; Shevchenko, E. V.

2017-11-01

The kinetic equations describing the transmission of an electron in the molecular compound "electrode 1-molecule-electrode 2" (1M2 system) are derived using the method of a nonequilibrium density matrix. The steady-state transmission regime is considered, for which detailed analysis of the kinetics of electrofluorescence formation in systems with symmetric and asymmetric couplings between the molecule and the electrodes is carried out. It is shown that the optically active state of the molecule is formed as a result of electron hops between the molecule and each of the electrodes, as well as due to inelastic interelectrode tunneling of the electron. The electrofluorescence power for a molecular diode (asymmetric 1M2 system) depends on the polarity of the voltage bias applied to the electrodes. The polarity is explained using a model in which the optically active part of the molecule (chromophore group) is represented by the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). Two mechanisms of the emergence of polarity are revealed. One mechanism is associated with nonidentical Stark shifts of the HOMO and LUMO levels relative to the Fermi levels of the electrodes. The second mechanism is associated with the fact that the rates of an electron hopping between HOMO (LUMO) and one of the electrodes are much higher than the rates of such a hopping with the other electrode. The conditions in which each mechanism can be implemented experimentally are indicated.

Current-induced switching of magnetic molecules on topological insulator surfaces

NASA Astrophysics Data System (ADS)

Locane, Elina; Brouwer, Piet W.

2017-03-01

Electrical currents at the surface or edge of a topological insulator are intrinsically spin polarized. We show that such surface or edge currents can be used to switch the orientation of a molecular magnet weakly coupled to the surface or edge of a topological insulator. For the edge of a two-dimensional topological insulator as well as for the surface of a three-dimensional topological insulator the application of a well-chosen surface or edge current can lead to a complete polarization of the molecule if the molecule's magnetic anisotropy axis is appropriately aligned with the current direction. For a generic orientation of the molecule a nonzero but incomplete polarization is obtained. We calculate the probability distribution of the magnetic states and the switching rates as a function of the applied current.

Polar transport in plants mediated by membrane transporters: focus on mechanisms of polar auxin transport.

PubMed

Naramoto, Satoshi

2017-12-01

Directional cell-to-cell transport of functional molecules, called polar transport, enables plants to sense and respond to developmental and environmental signals. Transporters that localize to plasma membranes (PMs) in a polar manner are key components of these systems. PIN-FORMED (PIN) auxin efflux carriers, which are the most studied polar-localized PM proteins, are implicated in the polar transport of auxin that in turn regulates plant development and tropic growth. In this review, the regulatory mechanisms underlying polar localization of PINs, control of auxin efflux activity, and PIN abundance at PMs are considered. Up to date information on polar-localized nutrient transporters that regulate directional nutrient movement from soil into the root vasculature is also discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantum switching of π-electron rotations in a nonplanar chiral molecule by using linearly polarized UV laser pulses.

PubMed

Mineo, Hirobumi; Yamaki, Masahiro; Teranishi, Yoshiaki; Hayashi, Michitoshi; Lin, Sheng Hsien; Fujimura, Yuichi

2012-09-05

Nonplanar chiral aromatic molecules are candidates for use as building blocks of multidimensional switching devices because the π electrons can generate ring currents with a variety of directions. We employed (P)-2,2'-biphenol because four patterns of π-electron rotations along the two phenol rings are possible and theoretically determine how quantum switching of the π-electron rotations can be realized. We found that each rotational pattern can be driven by a coherent excitation of two electronic states under two conditions: one is the symmetry of the electronic states and the other is their relative phase. On the basis of the results of quantum dynamics simulations, we propose a quantum control method for sequential switching among the four rotational patterns that can be performed by using ultrashort overlapped pump and dump pulses with properly selected relative phases and photon polarization directions. The results serve as a theoretical basis for the design of confined ultrafast switching of ring currents of nonplanar molecules and further current-induced magnetic fluxes of more sophisticated systems.

Symmetry in circularly polarized molecular high-order harmonic generation with intense bicircular laser pulses

NASA Astrophysics Data System (ADS)

Yuan, Kai-Jun; Bandrauk, André D.

2018-02-01

We present symmetry effects of laser fields and molecular geometries in circularly polarized high-order harmonic generation by bichromatic counter-rotating circularly polarized laser pulses. Simulations are performed on oriented molecules by numerically solving time-dependent Schrödinger equations. We discuss how electron recollision trajectories by the orthogonal laser field polarizations influence the harmonic polarization by using a time-frequency analysis of harmonics. It is found that orientation-dependent asymmetric ionization in linear molecules due to Coulomb potentials gives rise to a dependence of the polarization on the harmonic frequency. Effects of Coriolis forces are also presented on harmonic generation. Electron recollision trajectories illustrate the effects of the relative symmetry of the field and the molecule, thus paving a method for circularly polarized attosecond pulse generation and molecular orbital imaging in more complex systems.

Quantum coherent π-electron rotations in a non-planar chiral molecule induced by using a linearly polarized UV laser pulse

NASA Astrophysics Data System (ADS)

Mineo, Hirobumi; Fujimura, Yuichi

2015-06-01

We propose an ultrafast quantum switching method of π-electron rotations, which are switched among four rotational patterns in a nonplanar chiral aromatic molecule (P)-2,2’- biphenol and perform the sequential switching among four rotational patterns which are performed by the overlapped pump-dump laser pulses. Coherent π-electron dynamics are generated by applying the linearly polarized UV pulse laser to create a pair of coherent quasidegenerated excited states. We also plot the time-dependent π-electron ring current, and discussed ring current transfer between two aromatic rings.

Molecular vibrations in metal-single-molecule-metal junctions

NASA Astrophysics Data System (ADS)

Yokota, Kazumichi; Taniguchi, Masateru; Kawai, Tomoji

2010-03-01

Molecular vibrations in a metal-single-molecule-metal junction were studied based on density functional theory using a single benzenedithiolate molecule connected between gold clusters. We found that the difference in vibrational energy between an isolated benzenedithiol and the single-molecule junction is less than 3% in the energy range above 540 cm -1, where sulfur atoms contribute little to molecular vibrations. The finding implies that we can predict the peak energy in the inelastic electron tunneling spectrum of the single-molecule junction in the high energy range by vibrational analyses of isolated molecules.

Electrically tunable terahertz polarization converter based on overcoupled metal-isolator-metal metamaterials infiltrated with liquid crystals

NASA Astrophysics Data System (ADS)

Vasić, Borislav; Zografopoulos, Dimitrios C.; Isić, Goran; Beccherelli, Romeo; Gajić, Radoš

2017-03-01

Large birefringence and its electrical modulation by means of Fréedericksz transition makes nematic liquid crystals (LCs) a promising platform for tunable terahertz (THz) devices. The thickness of standard LC cells is in the order of the wavelength, requiring high driving voltages and allowing only a very slow modulation at THz frequencies. Here, we first present the concept of overcoupled metal-isolator-metal (MIM) cavities that allow for achieving simultaneously both very high phase difference between orthogonal electric field components and large reflectance. We then apply this concept to LC-infiltrated MIM-based metamaterials aiming at the design of electrically tunable THz polarization converters. The optimal operation in the overcoupled regime is provided by properly selecting the thickness of the LC cell. Instead of the LC natural birefringence, the polarization-dependent functionality stems from the optical anisotropy of ultrathin and deeply subwavelength MIM structures. The dynamic electro-optic control of the LC refractive index enables the spectral shift of the resonant mode and, consequently, the tuning of the phase difference between the two orthogonal field components. This tunability is further enhanced by the large confinement of the resonant electromagnetic fields within the MIM cavity. We show that for an appropriately chosen linearly polarized incident field, the polarization state of the reflected field at the target operation frequency can be continuously swept between the north and south pole of the Poincaré sphere. Using a rigorous Q-tensor model to simulate the LC electro-optic switching, we demonstrate that the enhanced light-matter interaction in the MIM resonant cavity allows the polarization converter to operate at driving voltages below 10 Volt and with millisecond switching times.

Electrically tunable terahertz polarization converter based on overcoupled metal-isolator-metal metamaterials infiltrated with liquid crystals.

PubMed

Vasić, Borislav; Zografopoulos, Dimitrios C; Isić, Goran; Beccherelli, Romeo; Gajić, Radoš

2017-03-24

Large birefringence and its electrical modulation by means of Fréedericksz transition makes nematic liquid crystals (LCs) a promising platform for tunable terahertz (THz) devices. The thickness of standard LC cells is in the order of the wavelength, requiring high driving voltages and allowing only a very slow modulation at THz frequencies. Here, we first present the concept of overcoupled metal-isolator-metal (MIM) cavities that allow for achieving simultaneously both very high phase difference between orthogonal electric field components and large reflectance. We then apply this concept to LC-infiltrated MIM-based metamaterials aiming at the design of electrically tunable THz polarization converters. The optimal operation in the overcoupled regime is provided by properly selecting the thickness of the LC cell. Instead of the LC natural birefringence, the polarization-dependent functionality stems from the optical anisotropy of ultrathin and deeply subwavelength MIM structures. The dynamic electro-optic control of the LC refractive index enables the spectral shift of the resonant mode and, consequently, the tuning of the phase difference between the two orthogonal field components. This tunability is further enhanced by the large confinement of the resonant electromagnetic fields within the MIM cavity. We show that for an appropriately chosen linearly polarized incident field, the polarization state of the reflected field at the target operation frequency can be continuously swept between the north and south pole of the Poincaré sphere. Using a rigorous Q-tensor model to simulate the LC electro-optic switching, we demonstrate that the enhanced light-matter interaction in the MIM resonant cavity allows the polarization converter to operate at driving voltages below 10 Volt and with millisecond switching times.

Vibrational states of a water molecule in a nano-cavity of beryl crystal lattice

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

Zhukova, Elena S., E-mail: zhukovaelenka@gmail.com; Gorshunov, Boris P.; 1. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart

2014-06-14

Low-energy excitations of a single water molecule are studied when confined within a nano-size cavity formed by the ionic crystal lattice. Optical spectra are measured of manganese doped beryl single crystal Mn:Be{sub 3}Al{sub 2}Si{sub 6}O{sub 18}, that contains water molecules individually isolated in 0.51 nm diameter voids within the crystal lattice. Two types of orientation are distinguished: water-I molecules have their dipole moments aligned perpendicular to the c axis and dipole moments of water-II molecules are parallel to the c-axis. The optical conductivity σ(ν) and permittivity ε{sup ′}(ν) spectra are recorded in terahertz and infrared ranges, at frequencies from severalmore » wavenumbers up to ν = 7000 cm{sup −1}, at temperatures 5–300 K and for two polarizations, when the electric vector E of the radiation is parallel and perpendicular to the c-axis. Comparative experiments on as-grown and on dehydrated samples allow to identify the spectra of σ(ν) and ε{sup ′}(ν) caused exclusively by water molecules. In the infrared range, well-known internal modes ν{sub 1}, ν{sub 2}, and ν{sub 3} of the H{sub 2}O molecule are observed for both polarizations, indicating the presence of water-I and water-II molecules in the crystal. Spectra recorded below 1000 cm{sup −1} reveal a rich set of highly anisotropic features in the low-energy response of H{sub 2}O molecule in a crystalline nano-cavity. While for E∥c only two absorption peaks are detected, at ∼90 cm{sup −1} and ∼160 cm{sup −1}, several absorption bands are discovered for E⊥c, each consisting of narrower resonances. The bands are assigned to librational (400–500 cm{sup −1}) and translational (150–200 cm{sup −1}) vibrations of water-I molecule that is weakly coupled to the nano-cavity “walls.” A model is presented that explains the “fine structure” of the bands by a splitting of the energy levels due to quantum tunneling between the minima in a six

Quantum-rotor-induced polarization.

PubMed

Meier, Benno

2018-07-01

Quantum-rotor-induced polarization is closely related to para-hydrogen-induced polarization. In both cases, the hyperpolarized spin order derives from rotational interaction and the Pauli principle by which the symmetry of the rotational ground state dictates the symmetry of the associated nuclear spin state. In quantum-rotor-induced polarization, there may be several spin states associated with the rotational ground state, and the hyperpolarization is typically generated by hetero-nuclear cross-relaxation. This review discusses preconditions for quantum-rotor-induced polarization for both the 1-dimensional methyl rotor and the asymmetric rotor H 2 17 O@C 60 , that is, a single water molecule encapsulated in fullerene C 60 . Experimental results are presented for both rotors. Copyright © 2018 John Wiley & Sons, Ltd.

Radiation-induced transformations of isolated CH3CN molecules in noble gas matrices

NASA Astrophysics Data System (ADS)

Kameneva, Svetlana V.; Volosatova, Anastasia D.; Feldman, Vladimir I.

2017-12-01

The transformations of isolated CH3CN molecules in various solid noble-gas matrices (Ne, Ar, Kr, and Xe) under the action of X-ray irradiation at 5 K were investigated by FTIR spectroscopy. The main products are CH3NC, CH2CNH and CH2NCH molecular isomers as well as CH2CN and CH2NC radicals. The matrix has a strong effect on the distribution of reaction channels. In particular, the highest relative yield of keteneimine (CH2CNH) was found in Ne matrix, whereas the formation of CH3NC predominates in xenon. It was explained by differences in the matrix ionization energy (IE) resulting in different distributions of hot ionic reactions. The reactions of neutral excited states are mainly involved in Xe matrix with low IE, while the isomerization of the primary acetonitrile positive ions may be quite effective in Ne and Ar. Annealing of the irradiated samples results in mobilization of trapped hydrogen atoms followed by their reactions with radicals to yield parent molecule and its isomers. The scheme of the radiation-induced processes and its implications for the acetonitrile chemistry in cosmic ices are discussed.

Polarization sensitive localization based super-resolution microscopy with a birefringent wedge

NASA Astrophysics Data System (ADS)

Sinkó, József; Gajdos, Tamás; Czvik, Elvira; Szabó, Gábor; Erdélyi, Miklós

2017-03-01

A practical method has been presented for polarization sensitive localization based super-resolution microscopy using a birefringent dual wedge. The measurement of the polarization degree at the single molecule level can reveal the chemical and physical properties of the local environment of the fluorescent dye molecule and can hence provide information about the sub-diffraction sized structure of biological samples. Polarization sensitive STORM imaging of the F-Actins proved correlation between the orientation of fluorescent dipoles and the axis of the fibril.

The effects of metabolite molecules produced by drinking water-isolated bacteria on their single and multispecies biofilms.

PubMed

Simões, Lúcia Chaves; Simões, Manuel; Vieira, Maria João

2011-08-01

The elucidation of the mechanisms by which diverse species survive and interact in drinking water (DW) biofilm communities may allow the identification of new biofilm control strategies. The purpose of the present study was to investigate the effects of metabolite molecules produced by bacteria isolated from DW on biofilm formation. Six opportunistic bacteria, viz. Acinetobacter calcoaceticus, Burkholderia cepacia, Methylobacterium sp., Mycobacterium mucogenicum, Sphingomonas capsulata and Staphylococcus sp. isolated from a drinking water distribution systems (DWDS) were used to form single and multispecies biofilms in the presence and absence of crude cell-free supernatants produced by the partner bacteria. Biofilms were characterized in terms of mass and metabolic activity. Additionally, several physiological aspects regulating interspecies interactions (sessile growth rates, antimicrobial activity of cell-free supernatants, and production of iron chelators) were studied to identify bacterial species with biocontrol potential in DWDS. Biofilms of Methylobacterium sp. had the highest growth rate and M. mucogenicum biofilms the lowest. Only B. cepacia was able to produce extracellular iron-chelating molecules. A. calcoaceticus, B. cepacia, Methylobacterium sp. and M. mucogenicum biofilms were strongly inhibited by crude cell-free supernatants from the other bacteria. The crude cell-free supernatants of M. mucogenicum and S. capsulata demonstrated a high potential for inhibiting the growth of counterpart biofilms. Multispecies biofilm formation was strongly inhibited in the absence of A. calcoaceticus. Only crude cell-free supernatants produced by B. cepacia and A. calcoaceticus had no inhibitory effects on multispecies biofilm formation, while metabolite molecules of M. mucogenicum showed the most significant biocontrol potential.

Photoexcitation circular dichroism in chiral molecules

NASA Astrophysics Data System (ADS)

Beaulieu, S.; Comby, A.; Descamps, D.; Fabre, B.; Garcia, G. A.; Géneaux, R.; Harvey, A. G.; Légaré, F.; Mašín, Z.; Nahon, L.; Ordonez, A. F.; Petit, S.; Pons, B.; Mairesse, Y.; Smirnova, O.; Blanchet, V.

2018-05-01

Chiral effects appear in a wide variety of natural phenomena and are of fundamental importance in science, from particle physics to metamaterials. The standard technique of chiral discrimination—photoabsorption circular dichroism—relies on the magnetic properties of a chiral medium and yields an extremely weak chiral response. Here, we propose and demonstrate an orders of magnitude more sensitive type of circular dichroism in neutral molecules: photoexcitation circular dichroism. This technique does not rely on weak magnetic effects, but takes advantage of the coherent helical motion of bound electrons excited by ultrashort circularly polarized light. It results in an ultrafast chiral response and the efficient excitation of a macroscopic chiral density in an initially isotropic ensemble of randomly oriented chiral molecules. We probe this excitation using linearly polarized laser pulses, without the aid of further chiral interactions. Our time-resolved study of vibronic chiral dynamics opens a way to the efficient initiation, control and monitoring of chiral chemical change in neutral molecules at the level of electrons.

Enhancing and reducing chirality by opposite circularly-polarized light irradiation on crystalline chiral domains consisting of nonchiral photoresponsive W-shaped liquid crystal molecules.

PubMed

Choi, Suk-Won; Takezoe, Hideo

2016-09-28

We found possible chirality enhancement and reduction in chiral domains formed by photoresponsive W-shaped molecules by irradiation with circularly polarized light (CPL). The W-shaped molecules exhibit a unique smectic phase with spontaneously segregated chiral domains, although the molecules are nonchiral. The chirality control was generated in the crystalline phase, which shows chiral segregation as in the upper smectic phase, and the result appeared to be as follows: for a certain chiral domain, right-CPL stimuli enhanced the chirality, while left-CPL stimuli reduced the chirality, and vice versa for another chiral domain. Interestingly, no domain-size change could be observed after CPL irradiation, suggesting some changes in the causes of chirality. In this way, the present system can recognize the handedness of the applied chiral stimuli. In other words, the present material can be used as a sensitive chiral-stimuli-recognizing material and should find invaluable applications, including in chiroptical switches, sensors, and memories as well as in chiral recognition.

Isolated-attosecond-pulse generation from asymmetric molecules with an {omega}+2{omega}/3 multicycle two-color field

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

Li Qianguang; Department of Physics, Xiaogan University, Xiaogan 432000; Hong Weiyi

2010-05-15

The high harmonic generation from asymmetric molecules with an {omega}+2{omega}/3 multicycle bichromatic laser pulse has been investigated. It is shown that the ionization asymmetry in consecutive half optical cycles for asymmetric molecules is further enhanced since the 2{omega}/3 control laser pulse further enhances the amplitude of the ionization peak at the center of the laser pulse. The 2{omega}/3 control laser pulse also significantly enlarges the difference of the photon energies emitted from the ejected electron in the half optical cycle at the central laser pulse and its next half optical cycle. In addition, a broadband supercontinuum is produced in themore » plateau of the spectrum, from which an isolated 90-as pulse can be directly obtained.« less

Physics with Cold Molecules Using Buffer Gas Cooling: Precision Measurement, Collisions, and Laser Cooling

NASA Astrophysics Data System (ADS)

Hutzler, Nicholas R.; Doyle, John M.

2014-06-01

Cryogenic buffer gas cooled beams and cells can be used to study many species, from atoms and polar molecules to biomolecules. We report on recent applications of this technique to improve the limit on the electron electric dipole moment [1], load polar molecules into a magnetic trap through optical pumping [2], perform chirally sensitive microwave spectroscopy on polyatomic molecules [3], progress towards magneto-optical trapping of polar molecules [4], and studies of atom-molecule sticking [5]. [1] The ACME Collaboration: J. Baron et al., Science 343, p. 269 (2014) [2] B. Hemmerling et al., arXiv:1310.2669, to appear in Phys. Rev. Lett. [3] D. Patterson, M. Schnell, & J. M. Doyle, Nature 497, p. 475 (2013) [4] H. Lu et al., arXiv:1310.3239, to appear in New. J. Phys. [5] J. Piskorski et al., under preparation

Magnetic coupling of Fe-porphyrin molecules adsorbed on clean and c(2×2) oxygen-reconstructed Co(100) investigated by spin-polarized photoemission spectroscopy

NASA Astrophysics Data System (ADS)

Weber, A. P.; Caruso, A. N.; Vescovo, E.; Ali, Md. E.; Tarafder, K.; Janjua, S. Z.; Sadowski, J. T.; Oppeneer, P. M.

2013-05-01

The spin-polarized electronic structure of iron octaethylporphyrin (FeOEP) molecules adsorbed on a pristine and on a c(2×2) oxygen-reconstructed Co(100) surface has been analyzed by means of spin-polarized photoemission spectroscopy (SPPES) and first-principles density functional theory with the on-site Coulomb repulsion U term (DFT+U) calculations with and without Van der Waals corrections. The aim is to examine the magnetic exchange mechanism between the FeOEP molecules and the Co(100) substrate in the presence or absence of the oxygen mediator. The results demonstrate that the magnetic coupling from the ferromagnetic substrate to the adsorbed FeOEP molecules is ferromagnetic, whereas, the coupling is antiferromagnetic for the FeOEP on the c(2×2)O/Co(100) system. Spin-resolved partial densities of states extracted from ab initio DFT+U modeling are in fairly good comparison with the electronic spectral densities seen in angle-integrated SPPES energy dispersion curves for submonolayer coverages of FeOEP. Through combined analysis of these spectra and theoretical results, we determine that hybridization of 2p orbitals of N and O with Co 3d orbitals facilitates indirect magnetic exchange interactions between Fe and Co, whereas, a direct Fe-Co interaction involving the Fe dz2 orbital is also found for FeOEP on Co. It is observed through SPPES that the spin polarization of the photoemission-visible molecular overlayers decreases to zero as coverage is increased beyond the submonolayer regime, indicating that only interfacial magnetic coupling is at work. Microspot low-energy electron diffraction and low-energy electron microscopy were performed to characterize the physical order of the molecular coverage, revealing that FeOEP structural domains are orders of magnitude greater in size on c(2×2)O/Co(100) than on clean Co(100), which coincides with reduced scattering from the disorder and sharper features seen in SPPES.

Theoretical study on the ground state of the polar alkali-metal-barium molecules: Potential energy curve and permanent dipole moment

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

Gou, Dezhi; Kuang, Xiaoyu, E-mail: scu-kuang@163.com; Gao, Yufeng

2015-01-21

In this paper, we systematically investigate the electronic structure for the {sup 2}Σ{sup +} ground state of the polar alkali-metal-alkaline-earth-metal molecules BaAlk (Alk = Li, Na, K, Rb, and Cs). Potential energy curves and permanent dipole moments (PDMs) are determined using power quantum chemistry complete active space self-consistent field and multi-reference configuration interaction methods. Basic spectroscopic constants are derived from ro-vibrational bound state calculation. From the calculations, it is shown that BaK, BaRb, and BaCs molecules have moderate values of PDM at the equilibrium bond distance (BaK:1.62 D, BaRb:3.32 D, and BaCs:4.02 D). Besides, the equilibrium bond length (4.93 Åmore » and 5.19 Å) and dissociation energy (0.1825 eV and 0.1817 eV) for the BaRb and BaCs are also obtained.« less

[Predominant polarity in type-I bipolar patients: Study in an isolated population with a high prevalence of mood disorders].

PubMed

Obando, Antonio Carlos Toro; García, Ángela María Agudelo; Rodríguez, María Aurora Gallo; Palacio, Tomás Felipe Restrepo; Ontoso, Miguel Soto; Tamayo, Alejandra; Jaramillo, Carlos Alberto López

2012-12-01

Recent studies have shown that the predominant description of polarity has effects upon early detection and the timely beginning of treatment in patients with bipolar affective disorder (BAD). Cross sectional cut and descriptive study in 101 BAD patients coming from a genetically isolated population from the Colombian Region of Antioquia. The study covered a population of 101 patients with type-I BAD diagnosis, out of which 57,4% met the criteria for maniac polarity (MP), 10,1% exhibited depressive polarity (DP) and 25,7% were classified with Indefinite Polarity (IP). In comparison, MP patients have a lower education level and less starting age, including a greater number of single people. The MP group showed the greatest prevalence of suicide and greater use of cannabinoids and cocaine. Within the DP group there was a strong tendency to cigarette and alcohol consumption. With respect to pharmaceutical drugs consumed by the study patients during their lives, antipsychotics were the most widely used group, followed by lithium and anti-convulsivants. There is high percentage of MP patients who have used antidepressants during their lives. The polarity of the first episode of the disease seems to be a valid predictive parameter concerning the polarity of subsequent episodes; therefore, it works indirectly as a valid predictor of the disease's course. Copyright © 2012 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Resonance-inclined optical nuclear spin polarization of liquids in diamond structures

NASA Astrophysics Data System (ADS)

Chen, Q.; Schwarz, I.; Jelezko, F.; Retzker, A.; Plenio, M. B.

2016-02-01

Dynamic nuclear polarization (DNP) of molecules in a solution at room temperature has the potential to revolutionize nuclear magnetic resonance spectroscopy and imaging. The prevalent methods for achieving DNP in solutions are typically most effective in the regime of small interaction correlation times between the electron and nuclear spins, limiting the size of accessible molecules. To solve this limitation, we design a mechanism for DNP in the liquid phase that is applicable for large interaction correlation times. Importantly, while this mechanism makes use of a resonance condition similar to solid-state DNP, the polarization transfer is robust to a relatively large detuning from the resonance due to molecular motion. We combine this scheme with optically polarized nitrogen-vacancy (NV) center spins in nanodiamonds to design a setup that employs optical pumping and is therefore not limited by room temperature electron thermal polarization. We illustrate numerically the effectiveness of the model in a flow cell containing nanodiamonds immobilized in a hydrogel, polarizing flowing water molecules 4700-fold above thermal polarization in a magnetic field of 0.35 T, in volumes detectable by current NMR scanners.

Helically assembled π-conjugated polymers with circularly polarized luminescence.

PubMed

Watanabe, Kazuyoshi; Akagi, Kazuo

2014-08-01

We review the recent progress in the field of helically assembled π -conjugated polymers, focusing on aromatic conjugated polymers with interchain helical π -stacking that exhibit circularly polarized luminescence (CPL). In Part 1, we discuss optically active polymers with white-colored CPL and the amplification of the circular polarization through liquid crystallinity. In Part 2, we focus on the stimuli-responsive CPL that results from changes in the conformation and aggregation state of π -conjugated molecules and polymers. In Part 3, we discuss the self-assembly of achiral cationic π -conjugated polymers into circularly polarized luminescent supramolecular nanostructures with the aid of other chiral molecules.

Isolation and purification of an early pregnancy factor-like molecule from culture supernatants obtained from lymphocytes of pregnant women.

PubMed

Aranha, C; Natraj, U; Iyer, K S; Shahani, S

1998-03-01

Our purpose was to determine whether lymphocytes synthesize proteins during pregnancy, to observe whether one of the proteins synthesized has early pregnancy factor (EPF)-like activity and to isolate and purify this molecule from culture supernatants obtained from stimulated lymphocytes of pregnant women. Lymphocyte proliferation assay and 35S-methionine labeling were done to study de novo synthesis of proteins followed by autoradiography to confirm synthesis of proteins. The rosette inhibition assay was used for detection of the EPF-like molecule. Gel filtration on Sephadex G-100 and RPHPLC were used for purification of the EPF-like molecule. The rate of incorporation of 35S-methionine was significantly higher in the lymphocytes of pregnant women compared to those of the control, and autoradiography confirmed the synthesis of proteins during pregnancy. There is a total protein enhancement trend observed during the first trimester that declines toward term. The EPF-like molecule is observed to be synthesized during all the trimesters of pregnancy. This molecule, when purified, showed a single homogeneous biologically active peak. The results indicated that there is an enhancement of existing protein or synthesis of new proteins during pregnancy. The EPF-like molecule is one of the many proteins synthesized and secreted by lymphocytes during pregnancy that, when purified, is biologically active.

Molecular orientation in aligned electrospun polyimide nanofibers by polarized FT-IR spectroscopy.

PubMed

Yang, Haoqi; Jiang, Shaohua; Fang, Hong; Hu, Xiaowu; Duan, Gaigai; Hou, Haoqing

2018-07-05

Quantitative explanation on the improved mechanical properties of aligned electrospun polyimide (PI) nanofibers as the increased imidization temperatures is highly required. In this work, polarized FT-IR spectroscopy is applied to solve this problem. Based on the polarized FT-IR spectroscopy and the molecular model in the fibers, the length of the repeat unit of PI molecule, the angle between the fiber axis and the symmetric stretching direction of carbonyl group on the imide ring, and the angle between the PI molecular axis and fiber axis are all investigated. The Mark-Howink equation is used to calculate the number-average molar mass of PI molecules. The orientation states of PI molecules in the electrospun nanofibers are studied from the number-average molar mass of PI molecules and the average fiber diameter. Quantitative analysis of the orientation factor of PI molecules in the electrospun nanofibers is performed by polarized FT-IR spectroscopy. Copyright © 2018 Elsevier B.V. All rights reserved.

Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation

PubMed Central

Ramirez, Samuel A.; Elston, Timothy C.

2018-01-01

Polarity establishment, the spontaneous generation of asymmetric molecular distributions, is a crucial component of many cellular functions. Saccharomyces cerevisiae (yeast) undergoes directed growth during budding and mating, and is an ideal model organism for studying polarization. In yeast and many other cell types, the Rho GTPase Cdc42 is the key molecular player in polarity establishment. During yeast polarization, multiple patches of Cdc42 initially form, then resolve into a single front. Because polarization relies on strong positive feedback, it is likely that the amplification of molecular-level fluctuations underlies the generation of multiple nascent patches. In the absence of spatial cues, these fluctuations may be key to driving polarization. Here we used particle-based simulations to investigate the role of stochastic effects in a Turing-type model of yeast polarity establishment. In the model, reactions take place either between two molecules on the membrane, or between a cytosolic and a membrane-bound molecule. Thus, we developed a computational platform that explicitly simulates molecules at and near the cell membrane, and implicitly handles molecules away from the membrane. To evaluate stochastic effects, we compared particle simulations to deterministic reaction-diffusion equation simulations. Defining macroscopic rate constants that are consistent with the microscopic parameters for this system is challenging, because diffusion occurs in two dimensions and particles exchange between the membrane and cytoplasm. We address this problem by empirically estimating macroscopic rate constants from appropriately designed particle-based simulations. Ultimately, we find that stochastic fluctuations speed polarity establishment and permit polarization in parameter regions predicted to be Turing stable. These effects can operate at Cdc42 abundances expected of yeast cells, and promote polarization on timescales consistent with experimental results. To our

Improved Dual-Polarized Microstrip Antenna

NASA Technical Reports Server (NTRS)

Huang, John

1993-01-01

Dual-polarized microstrip antenna features microstrip transmission-line feeds arranged in such configuration that cross-polarized components of radiation relatively low and degree of isolation between feed ports relatively high. V and H feed ports offset from midpoints of feed lines to obtain required opposite phases at feed-point connections to microstrip patches. Two independent beams of same frequency with electric fields polarized orthogonally to each other transmitted or received via antenna. Improved design saves space.

Robust Quantum Computing using Molecules with Switchable Dipole

DTIC Science & Technology

2010-06-15

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

Host-guest interaction between Acridine orange molecules and AFI or CHA zeolite crystals

NASA Astrophysics Data System (ADS)

Chen, Yanping; Fu, Ling; Xu, Xintong; Li, Irene Ling; Ruan, Shuangchen; Jian, Dunliang; Zhai, Jianpang

2017-02-01

Acridine orange (AO) molecules were incorporated in AlPO4-5, SAPO-5 and SAPO-47 single crystals by vapor-phase diffusion method. Polarized absorption spectra show that AO molecules are well aligned by the one-dimensional channel systems of AlPO4-5 and SAPO-5 matrices. While the orientation of AO molecules in SAPO-47 crystals is diverse owing to the three-dimensional cage structure of chabazite (structure code CHA). The absorption peak and emission peak of AO/SAPO-5 blue shift compared with that of AO/AlPO4-5 because the channel environment changes from non-polar medium to polar medium when Si substituted in the framework of AlPO4-5. The greater blue shift in absorption band and emission band of AO/SAPO-47 are expected to originate from the polar channel medium and smaller channel size of SAPO-47.

A cryofuge for cold-collision experiments with slow polar molecules

NASA Astrophysics Data System (ADS)

Wu, Xing; Gantner, Thomas; Koller, Manuel; Zeppenfeld, Martin; Chervenkov, Sotir; Rempe, Gerhard

2017-11-01

Ultracold molecules represent a fascinating research frontier in physics and chemistry, but it has proven challenging to prepare dense samples at low velocities. Here, we present a solution to this goal by means of a nonconventional approach dubbed cryofuge. It uses centrifugal force to bring cryogenically cooled molecules to kinetic energies below 1 K × kB in the laboratory frame, where kB is the Boltzmann constant, with corresponding fluxes exceeding 1010 per second at velocities below 20 meters per second. By attaining densities higher than 109 per cubic centimeter and interaction times longer than 25 milliseconds in samples of fluoromethane as well as deuterated ammonia, we observed cold dipolar collisions between molecules and determined their collision cross sections.

Calamitic Smectic A-Polar Smectic APA Transition Observed in Bent Molecules with Large Bent-Angle Central Core of 4,6-Dichlorobenzene and Alkylthio Terminal Tail

NASA Astrophysics Data System (ADS)

Nguyen, Ha; Kang, Sungmin; Tokita, Masatoshi; Watanabe, Junji

2011-07-01

New homologs of bent molecules with a large bent-angle central core of 4,6-dichloro benzene and an alkylthio terminal tail have been synthesized. Although the corresponding alkoxy-tail homologs show only the calamitic phases because of its large bent angles around 160°, the new homologs with an alkylthio tail exhibit the antiferroelectric smectic APA (SmAPA) banana phase that is transformed on cooling from the calamitic smectic A (SmA) phase. The biaxial polar packing of bent molecules in the SmAPA phase is considered to arise from the hindered rotation around the molecular long axis due to the expansion of the mesophase temperatures to a lower temperature region. This study indicates that the bent molecules, even with a large bent angle, have the potential to form a switchable banana phase with a remarkable decrease in its phase temperature range to around 60 °C.

Directional charge separation in isolated organic semiconductor crystalline nanowires

DOE PAGES

Labastide, J. A.; Thompson, H. B.; Marques, S. R.; ...

2016-02-25

One of the fundamental design paradigms in organic photovoltaic device engineering is based on the idea that charge separation is an extrinsically driven process requiring an interface for exciton fission. This idea has driven an enormous materials science engineering effort focused on construction of domain sizes commensurate with a nominal exciton diffusion length of order 10 nm. Here, we show that polarized optical excitation of isolated pristine crystalline nanowires of a small molecule n-type organic semiconductor, 7,8,15,16-tetraazaterrylene, generates a significant population of charge-separated polaron pairs along the π-stacking direction. Charge separation was signalled by pronounced power-law photoluminescence decay polarized alongmore » the same axis. In the transverse direction, we observed exponential decay associated with excitons localized on individual monomers. We propose that this effect derives from an intrinsic directional charge-transfer interaction that can ultimately be programmed by molecular packing geometry.« less

Strong-field ionization of linear molecules by a bicircular laser field: Symmetry considerations

NASA Astrophysics Data System (ADS)

Gazibegović-Busuladžić, A.; Busuladžić, M.; Hasović, E.; Becker, W.; Milošević, D. B.

2018-04-01

Using the improved molecular strong-field approximation, we investigate (high-order) above-threshold ionization [(H)ATI] of various linear polyatomic molecules by a two-color laser field of frequencies r ω and s ω (with integer numbers r and s ) having coplanar counter-rotating circularly polarized components (a so-called bicircular field). Reflection and rotational symmetries for molecules aligned in the laser-field polarization plane, analyzed for diatomic homonuclear molecules in Phys. Rev. A 95, 033411 (2017), 10.1103/PhysRevA.95.033411, are now considered for diatomic heteronuclear molecules and symmetric and asymmetric linear triatomic molecules. There are additional rotational symmetries for (H)ATI spectra of symmetric linear molecules compared to (H)ATI spectra of the asymmetric ones. It is shown that these symmetries manifest themselves differently for r +s odd and r +s even. For example, HATI spectra for symmetric molecules with r +s even obey inversion symmetry. For ATI spectra of linear molecules, reflection symmetry appears only for certain molecular orientation angles ±90∘-j r 180∘/(r +s ) (j integer). For symmetric linear molecules, reflection symmetry appears also for the angles -j r 180∘/(r +s ) . For perpendicular orientation of molecules with respect to the laser-field polarization plane, the HATI spectra are very similar to those of the atomic targets, i.e., both spectra are characterized by the same type of the (r +s )-fold symmetry.

High-harmonic spectroscopy of aligned molecules

NASA Astrophysics Data System (ADS)

Yun, Hyeok; Yun, Sang Jae; Lee, Gae Hwang; Nam, Chang Hee

2017-01-01

High harmonics emitted from aligned molecules driven by intense femtosecond laser pulses provide the opportunity to explore the structural information of molecules. The field-free molecular alignment technique is an expedient tool for investigating the structural characteristics of linear molecules. The underlying physics of field-free alignment, showing the characteristic revival structure specific to molecular species, is clearly explained from the quantum-phase analysis of molecular rotational states. The anisotropic nature of molecules is shown from the harmonic polarization measurement performed with spatial interferometry. The multi-orbital characteristics of molecules are investigated using high-harmonic spectroscopy, applied to molecules of N2 and CO2. In the latter case the two-dimensional high-harmonic spectroscopy, implemented using a two-color laser field, is applied to distinguish harmonics from different orbitals. Molecular high-harmonic spectroscopy will open a new route to investigate ultrafast dynamics of molecules.

Membrane Transport across Polarized Epithelia.

PubMed

Garcia-Castillo, Maria Daniela; Chinnapen, Daniel J-F; Lencer, Wayne I

2017-09-01

Polarized epithelial cells line diverse surfaces throughout the body forming selective barriers between the external environment and the internal milieu. To cross these epithelial barriers, large solutes and other cargoes must undergo transcytosis, an endocytic pathway unique to polarized cell types, and significant for the development of cell polarity, uptake of viral and bacterial pathogens, transepithelial signaling, and immunoglobulin transport. Here, we review recent advances in our knowledge of the transcytotic pathway for proteins and lipids. We also discuss briefly the promise of harnessing the molecules that undergo transcytosis as vehicles for clinical applications in drug delivery. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL Kinase Function

PubMed Central

Grover, Prerna; Shi, Haibin; Baumgartner, Matthew; Camacho, Carlos J.; Smithgall, Thomas E.

2015-01-01

The ABL protein-tyrosine kinase regulates intracellular signaling pathways controlling diverse cellular processes and contributes to several forms of cancer. The kinase activity of ABL is repressed by intramolecular interactions involving its regulatory Ncap, SH3 and SH2 domains. Small molecules that allosterically regulate ABL kinase activity through its non-catalytic domains may represent selective probes of ABL function. Here we report a screening assay for chemical modulators of ABL kinase activity that target the regulatory interaction of the SH3 domain with the SH2-kinase linker. This fluorescence polarization (FP) assay is based on a purified recombinant ABL protein consisting of the N-cap, SH3 and SH2 domains plus the SH2-kinase linker (N32L protein) and a short fluorescein-labeled probe peptide that binds to the SH3 domain. In assay development experiments, we found that the probe peptide binds to the recombinant ABL N32L protein in vitro, producing a robust FP signal that can be competed with an excess of unlabeled peptide. The FP signal is not observed with control N32L proteins bearing either an inactivating mutation in the SH3 domain or enhanced SH3:linker interaction. A pilot screen of 1200 FDA-approved drugs identified four compounds that specifically reduced the FP signal by at least three standard deviations from the untreated controls. Secondary assays showed that one of these hit compounds, the antithrombotic drug dipyridamole, enhances ABL kinase activity in vitro to a greater extent than the previously described ABL agonist, DPH. Docking studies predicted that this compound binds to a pocket formed at the interface of the SH3 domain and the linker, suggesting that it activates ABL by disrupting this regulatory interaction. These results show that screening assays based on the non-catalytic domains of ABL can identify allosteric small molecule regulators of kinase function, providing a new approach to selective drug discovery for this important

Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL Kinase Function.

PubMed

Grover, Prerna; Shi, Haibin; Baumgartner, Matthew; Camacho, Carlos J; Smithgall, Thomas E

2015-01-01

The ABL protein-tyrosine kinase regulates intracellular signaling pathways controlling diverse cellular processes and contributes to several forms of cancer. The kinase activity of ABL is repressed by intramolecular interactions involving its regulatory Ncap, SH3 and SH2 domains. Small molecules that allosterically regulate ABL kinase activity through its non-catalytic domains may represent selective probes of ABL function. Here we report a screening assay for chemical modulators of ABL kinase activity that target the regulatory interaction of the SH3 domain with the SH2-kinase linker. This fluorescence polarization (FP) assay is based on a purified recombinant ABL protein consisting of the N-cap, SH3 and SH2 domains plus the SH2-kinase linker (N32L protein) and a short fluorescein-labeled probe peptide that binds to the SH3 domain. In assay development experiments, we found that the probe peptide binds to the recombinant ABL N32L protein in vitro, producing a robust FP signal that can be competed with an excess of unlabeled peptide. The FP signal is not observed with control N32L proteins bearing either an inactivating mutation in the SH3 domain or enhanced SH3:linker interaction. A pilot screen of 1200 FDA-approved drugs identified four compounds that specifically reduced the FP signal by at least three standard deviations from the untreated controls. Secondary assays showed that one of these hit compounds, the antithrombotic drug dipyridamole, enhances ABL kinase activity in vitro to a greater extent than the previously described ABL agonist, DPH. Docking studies predicted that this compound binds to a pocket formed at the interface of the SH3 domain and the linker, suggesting that it activates ABL by disrupting this regulatory interaction. These results show that screening assays based on the non-catalytic domains of ABL can identify allosteric small molecule regulators of kinase function, providing a new approach to selective drug discovery for this important

Versatility of Biofilm Matrix Molecules in Staphylococcus epidermidis Clinical Isolates and Importance of Polysaccharide Intercellular Adhesin Expression during High Shear Stress

PubMed Central

Schaeffer, Carolyn R.; Hoang, Tra-My N.; Sudbeck, Craig M.; Alawi, Malik; Tolo, Isaiah E.; Robinson, D. Ashley; Horswill, Alexander R.; Rohde, Holger

2016-01-01

ABSTRACT Staphylococcus epidermidis is a leading cause of hospital-associated infections, including those of intravascular catheters, cerebrospinal fluid shunts, and orthopedic implants. Multiple biofilm matrix molecules with heterogeneous characteristics have been identified, including proteinaceous, polysaccharide, and nucleic acid factors. Two of the best-studied components in S. epidermidis include accumulation-associated protein (Aap) and polysaccharide intercellular adhesin (PIA), produced by the enzymatic products of the icaADBC operon. Biofilm composition varies by strain as well as environmental conditions, and strains producing PIA-mediated biofilms are more robust. Clinically, biofilm-mediated infections occur in a variety of anatomical sites with diverse physiological properties. To test the hypothesis that matrix composition exhibits niche specificity, biofilm-related genetic and physical properties were compared between S. epidermidis strains isolated from high-shear and low-shear environments. Among a collection of 105 clinical strains, significantly more isolates from high-shear environments carried the icaADBC operon than did those from low-shear settings (43.9% versus 22.9%, P < 0.05), while there was no significant difference in the presence of aap (77.2% versus 75.0%, P > 0.05). Additionally, a significantly greater number of high-shear isolates were capable of forming biofilm in vitro in a microtiter assay (82.5% versus 45.8%, P < 0.0001). However, even among high-shear clinical isolates, less than half contained the icaADBC locus; therefore, we selected for ica-negative variants with increased attachment to abiotic surfaces to examine PIA-independent biofilm mechanisms. Sequencing of selected variants identified substitutions capable of enhancing biofilm formation in multiple genes, further highlighting the heterogeneity of S. epidermidis biofilm molecules and mechanisms. IMPORTANCE Staphylococcus epidermidis is a leading cause of

Prediction and interpretation of infrared intensities of polymethylene chain molecules

NASA Astrophysics Data System (ADS)

Jona, P.; Gussoni, M.; Zerbi, G.

1986-03-01

We have calculated the IR intensities of some polymethylene chain molecules containing conformational defects or polar heads. Calculations provide spectroscopic markers of end-TG, GTG', GTG, GG and GGTGG defects. Further, a spectroscopical study of interactions between polar heads and alkyl chain is allowed.

Polar Lipids of Burkholderia pseudomallei Induce Different Host Immune Responses

PubMed Central

Gonzalez-Juarrero, Mercedes; Mima, Naoko; Trunck, Lily A.; Schweizer, Herbert P.; Bowen, Richard A.; Dascher, Kyle; Mwangi, Waithaka; Eckstein, Torsten M.

2013-01-01

Melioidosis is a disease in tropical and subtropical regions of the world that is caused by Burkholderia pseudomallei. In endemic regions the disease occurs primarily in humans and goats. In the present study, we used the goat as a model to dissect the polar lipids of B. pseudomallei to identify lipid molecules that could be used for adjuvants/vaccines or as diagnostic tools. We showed that the lipidome of B. pseudomallei and its fractions contain several polar lipids with the capacity to elicit different immune responses in goats, namely rhamnolipids and ornithine lipids which induced IFN-γ, whereas phospholipids and an undefined polar lipid induced strong IL-10 secretion in CD4+ T cells. Autologous T cells co-cultured with caprine dendritic cells (cDCs) and polar lipids of B. pseudomallei proliferated and up-regulated the expression of CD25 (IL-2 receptor) molecules. Furthermore, we demonstrated that polar lipids were able to up-regulate CD1w2 antigen expression in cDCs derived from peripheral blood monocytes. Interestingly, the same polar lipids had only little effect on the expression of MHC class II DR antigens in the same caprine dendritic cells. Finally, antibody blocking of the CD1w2 molecules on cDCs resulted in decreased expression for IFN-γ by CD4+ T cells. Altogether, these results showed that polar lipids of B. pseudomallei are recognized by the caprine immune system and that their recognition is primarily mediated by the CD1 antigen cluster. PMID:24260378

Effect of open metal sites on adsorption of polar and nonpolar molecules in metal-organic framework Cu-BTC.

PubMed

Karra, Jagadeswara R; Walton, Krista S

2008-08-19

Atomistic grand canonical Monte Carlo simulations were performed in this work to investigate the role of open copper sites of Cu-BTC in affecting the separation of carbon monoxide from binary mixtures containing methane, nitrogen, or hydrogen. Mixtures containing 5%, 50%, or 95% CO were examined. The simulations show that electrostatic interactions between the CO dipole and the partial charges on the metal-organic framework (MOF) atoms dominate the adsorption mechanism. The binary simulations show that Cu-BTC is quite selective for CO over hydrogen and nitrogen for all three mixture compositions at 298 K. The removal of CO from a 5% mixture with methane is slightly enhanced by the electrostatic interactions of CO with the copper sites. However, the pore space of Cu-BTC is large enough to accommodate both molecules at their pure-component loadings, and in general, Cu-BTC exhibits no significant selectivity for CO over methane for the equimolar and 95% mixtures. On the basis of the pure-component and low-concentration behavior of CO, the results indicate that MOFs with open metal sites have the potential for enhancing adsorption separations of molecules of differing polarities, but the pore size relative to the sorbate size will also play a significant role.

Range contraction and increasing isolation of a polar bear subpopulation in an era of sea-ice loss.

PubMed

Laidre, Kristin L; Born, Erik W; Atkinson, Stephen N; Wiig, Øystein; Andersen, Liselotte W; Lunn, Nicholas J; Dyck, Markus; Regehr, Eric V; McGovern, Richard; Heagerty, Patrick

2018-02-01

Climate change is expected to result in range shifts and habitat fragmentation for many species. In the Arctic, loss of sea ice will reduce barriers to dispersal or eliminate movement corridors, resulting in increased connectivity or geographic isolation with sweeping implications for conservation. We used satellite telemetry, data from individually marked animals (research and harvest), and microsatellite genetic data to examine changes in geographic range, emigration, and interpopulation connectivity of the Baffin Bay (BB) polar bear ( Ursus maritimus ) subpopulation over a 25-year period of sea-ice loss. Satellite telemetry collected from n  = 43 (1991-1995) and 38 (2009-2015) adult females revealed a significant contraction in subpopulation range size (95% bivariate normal kernel range) in most months and seasons, with the most marked reduction being a 70% decline in summer from 716,000 km 2 (SE 58,000) to 211,000 km 2 (SE 23,000) ( p  < .001). Between the 1990s and 2000s, there was a significant shift northward during the on-ice seasons (2.6 ° shift in winter median latitude, 1.1 ° shift in spring median latitude) and a significant range contraction in the ice-free summers. Bears in the 2000s were less likely to leave BB, with significant reductions in the numbers of bears moving into Davis Strait (DS) in winter and Lancaster Sound (LS) in summer. Harvest recoveries suggested both short and long-term fidelity to BB remained high over both periods (83-99% of marked bears remained in BB). Genetic analyses using eight polymorphic microsatellites confirmed a previously documented differentiation between BB, DS, and LS; yet weakly differentiated BB from Kane Basin (KB) for the first time. Our results provide the first multiple lines of evidence for an increasingly geographically and functionally isolated subpopulation of polar bears in the context of long-term sea-ice loss. This may be indicative of future patterns for other polar bear subpopulations under

Secondary Metabolites from Polar Organisms

PubMed Central

Tian, Yuan; Li, Yan-Ling; Zhao, Feng-Chun

2017-01-01

Polar organisms have been found to develop unique defences against the extreme environment environment, leading to the biosynthesis of novel molecules with diverse bioactivities. This review covers the 219 novel natural products described since 2001, from the Arctic and the Antarctic microoganisms, lichen, moss and marine faunas. The structures of the new compounds and details of the source organism, along with any relevant biological activities are presented. Where reported, synthetic and biosynthetic studies on the polar metabolites have also been included. PMID:28241505

Ab Initio Study of Ultracold Polar Molecules in Optical Lattices

DTIC Science & Technology

2010-01-01

collisions of Li and alkaline-earth or rare- earth atoms, such LiSr and LiYb. Finally, we calculated the isotropic and anisotropic interaction potentials... LiSr and LiYb molecules. To the best of our knowledge, only LiMg was experimentally investigated [3], which allowed us to compare our predictions...alkaline-earth or rare-earth atoms. Interest in the LiSr and LiYb molecules stems from prospects to achieve optical Feshbach tuning of scattering properties

Selective photocatalytic transformations on microporous titanosilicate ETS-10 driven by size and polarity of molecules.

PubMed

Shiraishi, Yasuhiro; Tsukamoto, Daijiro; Hirai, Takayuki

2008-11-04

Photocatalytic activity of microporous titanosilicate ETS-10 has been studied in water. The photoactivated ETS-10 shows catalytic activity driven by size and polarity of substrates. ETS-10 efficiently catalyzes a conversion of substrates with a size larger than the pore diameter of ETS-10. In contrast, the reactivity of small substrates depends strongly on substrate polarity; less polar substrates show higher reactivity on ETS-10. Electron spin resonance analysis reveals that large substrates or less polar substrates scarcely diffuse inside the highly polarized micropores of ETS-10 and, hence, react efficiently with hydroxyl radicals (*OH) formed on titanol (Ti-OH) groups exposed on the external surface of ETS-10. In contrast, small polar substrates diffuse easily inside the micropores of ETS-10 and scarcely react with *OH, resulting in low reactivity. The photocatalytic activity of ETS-10 is successfully applicable to selective transformations of large reactants or less polar reactants to small polar products, enabling highly selective dehalogenation and hydroxylation of aromatics.

Modelling Polar Self Assembly

NASA Astrophysics Data System (ADS)

Olvera de La Cruz, Monica; Sayar, Mehmet; Solis, Francisco J.; Stupp, Samuel I.

2001-03-01

Recent experimental studies in our group have shown that self assembled thin films of noncentrosymmetric supramolecular objects composed of triblock rodcoil molecules exhibit finite polar order. These aggregates have both long range dipolar and short range Ising-like interactions. We study the ground state of a simple model with these competing interactions. We find that the competition between Ising-like and dipolar forces yield a periodic domain structure, which can be controlled by adjusting the force constants and film thickness. When the surface forces are included in the potential, the system exhibits a finite macroscopic polar order.

Production of a fungistatic substance by Pseudallescheria boydii isolated from soil amended with vegetable tissues and its significance.

PubMed

Ko, Wen-Hsiung; Tsou, Yi-Jung; Ju, Yu-Ming; Hsieh, Huei-Mei; Ann, Pao-Jen

2010-02-01

Four fungal isolates that were able to use vegetable tissues for multiplication in soil were isolated and identified as Pseudallescheria boydii based on morphological characteristics and ITS sequence similarity. When grown in broth prepared from the same vegetable tissues used in soil amendment, all these isolates of P. boydii produced a substance capable of reducing the disease incidence of black leaf spot of spoon cabbage caused by Alternaria brassicicola and inhibiting the germination of A. brassicicola conidia. The substance, which was fungistatic, was very stable under high temperature and high or low pH value. It was soluble in polar solvents and insoluble in non-polar solvents. Molecular weight estimation and ion exchange ability tests suggest that the fungistatic compound has a molecular weight between 500 and 1,000 and has no charge on its molecule. Results from this study suggest the possession of a strong competitive saprophytic ability by P. boydii, which in turn may explain the widespread occurrence of this human pathogen in soil. Production of a fungistatic substance when P. boydii was grown in broth prepared from vegetable tissues suggests the importance of antibiotic production in its competitive saprophytic colonization of organic matters in soil.

High-resolution internal state control of ultracold 23Na87Rb molecules

NASA Astrophysics Data System (ADS)

Guo, Mingyang; Ye, Xin; He, Junyu; Quéméner, Goulven; Wang, Dajun

2018-02-01

We report the full internal state control of ultracold 23Na87Rb molecules, including vibrational, rotational, and hyperfine degrees of freedom. Starting from a sample of weakly bound Feshbach molecules, we realize the creation of molecules in single hyperfine levels of both the rovibrational ground and excited states with a high-efficiency and high-resolution stimulated Raman adiabatic passage. This capability brings broad possibilities for investigating ultracold polar molecules with different chemical reactivities and interactions with a single molecular species. Moreover, starting from the rovibrational and hyperfine ground state, we achieve rotational and hyperfine control with one- and two-photon microwave spectroscopy to reach levels not accessible by the stimulated Raman transfer. The combination of these two techniques results in complete control over the internal state of ultracold polar molecules, which paves the way to study state-dependent molecular collisions and state-controlled chemical reactions.

Short communication: Conservation of Streptococcus uberis adhesion molecule and the sua gene in strains of Streptococcus uberis isolated from geographically diverse areas.

PubMed

Yuan, Ying; Dego, Oudessa Kerro; Chen, Xueyan; Abadin, Eurife; Chan, Shangfeng; Jory, Lauren; Kovacevic, Steven; Almeida, Raul A; Oliver, Stephen P

2014-12-01

The objective was to identify and sequence the sua gene (GenBank no. DQ232760; http://www.ncbi.nlm.nih.gov/genbank/) and detect Streptococcus uberis adhesion molecule (SUAM) expression by Western blot using serum from naturally S. uberis-infected cows in strains of S. uberis isolated in milk from cows with mastitis from geographically diverse areas of the world. All strains evaluated yielded a 4.4-kb sua-containing PCR fragment that was subsequently sequenced. Deduced SUAM AA sequences from those S. uberis strains evaluated shared >97% identity. The pepSUAM sequence located at the N terminus of SUAM was >99% identical among strains of S. uberis. Streptococcus uberis adhesion molecule expression was detected in all strains of S. uberis tested. These results suggest that sua is ubiquitous among strains of S. uberis isolated from diverse geographic locations and that SUAM is immunogenic. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Laser-induced emission spectroscopy of matrix-isolated carbon molecules: Experimental setup and new results on C3

NASA Astrophysics Data System (ADS)

Čermák, Ivo; Förderer, Markus; Čermáková, Iva; Kalhofer, Stefan; Stopka-Ebeler, Helmut; Monninger, Gerold; Krätschmer, Wolfgang

1998-06-01

We have studied small carbon molecules using a matrix-isolation technique. Our experimental setup is described in detail. The carbon clusters were produced by evaporating graphite and trapping the carbon-vapor molecules in solid argon, where molecular growth could be induced by controlled matrix annealing. To identify the produced molecules, absorption spectroscopy in the ultraviolet (UV)-visible and infrared (IR) spectral ranges was applied. Additional characterization of the excited and ground states of the molecules was obtained from emission and excitation spectra. The molecules were excited by a pulsed dye laser system and the emission spectra were recorded with a high-sensitivity photodiode-array spectrometer. We present our measurements on linear C3. The à 1Πu excited state of linear C3 was populated by the electronic transition à 1Πu←X˜ 1Σg+, and the corresponding excitation spectra of the C3 fluorescence (à 1Πu→X˜ 1Σg+) and phosphorescence (ã 3Πu→X˜ 1Σg+) were studied. Comparison of excitation and absorption spectra yielded information on site effects due to the matrix environment. Emission bands in the fluorescence and phosphorescence spectra up to vibrational energies of 8500 cm-1 could be observed. The radiation lifetime of the à 1Πu excited state of C3 in solid argon was found to be shorter than 10 ns. The phosphorescence transition ã 3Πu→X˜ 1Σg+ decays in about 10 ms and its rise indicates fast vibrational relaxation within the triplet system. Our data support a linear ground state geometry for C3 also in solid argon.

Dual-polarized feed antenna apparatus and method of use

NASA Technical Reports Server (NTRS)

Sarehraz, Mohammed (Inventor); Buckle, Kenneth A. (Inventor); Stefanakos, Elias (Inventor); Weller, Thomas (Inventor); Goswami, D. Yogi (Inventor)

2009-01-01

An antenna apparatus and method for the interception of randomly polarized electromagnetic waves utilizing a dual polarized antenna which is excited through a cross-slot aperture using two well-isolated orthogonal feeds.

Dual-polarized feed antenna apparatus and method of use

NASA Technical Reports Server (NTRS)

Sarehraz, Mohammad (Inventor); Buckle, Kenneth A. (Inventor); Stefanakos, Elias (Inventor); Weller, Thomas (Inventor); Goswami, D. Yogi (Inventor)

2008-01-01

An antenna apparatus and method for the interception of randomly polarized electromagnetic waves utilizing a dual polarized antenna which is excited through a cross-slot aperture using two well-isolated orthogonal feeds.

Salting-out effect in aqueous NaCl solutions: trends with size and polarity of solute molecules.

PubMed

Endo, Satoshi; Pfennigsdorff, Andrea; Goss, Kai-Uwe

2012-02-07

Salting-out in aqueous NaCl solutions is relevant for the environmental behavior of organic contaminants. In this study, Setschenow (or salting-out) coefficients (K(s) [M(-1)]) for 43 diverse neutral compounds in NaCl solutions were measured using a shared headspace passive dosing method and a negligible depletion solid phase microextraction technique. The results were used to calibrate and evaluate estimation models for K(s). The molar volume of the solute correlated only moderately with K(s) (R(2) = 0.49, SD = 0.052). The polyparameter linear free energy relationship (pp-LFER) model that uses five compound descriptors resulted in a more accurate fit to our data (R(2) = 0.83, SD = 0.031). The pp-LFER analysis revealed that Na(+) and Cl(-) in aqueous solutions increase the cavity formation energy cost and the polar interaction energies toward neutral organic solutes. Accordingly, the salting-out effect increases with the size and decreases with the polarity of the solute molecule. COSMO-RS, a quantum mechanics-based fully predictive model, generally overpredicted the experimental K(s), but the predicted values were moderately correlated with the experimental values (R(2) = 0.66, SD = 0.042). Literature data (n = 93) were predicted by the calibrated pp-LFER and COSMO-RS models with root mean squared errors of 0.047 and 0.050, respectively. This study offers prediction models to estimate K(s), allowing implementation of the salting-out effect in contaminant fate models, linkage of various partition coefficients (such as air-water, sediment-water, and extraction phase-water partition coefficients) measured for fresh water and seawater, and estimation of enhancement of extraction efficiency in analytical procedures.

Re-polarization of nuclear spins using selective SABRE-INEPT

NASA Astrophysics Data System (ADS)

Knecht, Stephan; Kiryutin, Alexey S.; Yurkovskaya, Alexandra V.; Ivanov, Konstantin L.

2018-02-01

A method is proposed for significant improvement of NMR pulse sequences used in high-field SABRE (Signal Amplification By Reversible Exchange) experiments. SABRE makes use of spin order transfer from parahydrogen (pH2, the H2 molecule in its singlet spin state) to a substrate in a transient organometallic Ir-based complex. The technique proposed here utilizes "re-polarization", i.e., multiple application of an NMR pulse sequence used for spin order transfer. During re-polarization only the form of the substrate, which is bound to the complex, is excited by selective NMR pulses and the resulting polarization is transferred to the free substrate via chemical exchange. Owing to the fact that (i) only a small fraction of the substrate molecules is in the bound form and (ii) spin relaxation of the free substrate is slow, the re-polarization scheme provides greatly improved NMR signal enhancement, ε . For instance, when pyridine is used as a substrate, single use of the SABRE-INEPT sequence provides ε ≈ 260 for 15N nuclei, whereas SABRE-INEPT with re-polarization yields ε > 2000 . We anticipate that the proposed method is useful for achieving maximal NMR enhancement with spin hyperpolarization techniques.

Interaction between perylene-derivated molecules observed by low temperature scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Vernisse, Loranne; Guillermet, Olivier; Gourdon, André; Coratger, Roland

2018-03-01

Derivative perylene molecules deposited on Ag(111) and on NaCl(001) ultrathin layers have been investigated using low temperature STM and NC-AFM. When the metallic substrate is held at ambient temperature during evaporation, the molecules form characteristic trimers on the Ag(111) surface and interact through their polar groups. Close to the steps, the molecules form linear structures and seems to stand side by side. On the other hand, after deposition on a substrate cooled at liquid helium temperature, single molecules are observed both on metal and on NaCl. On the ultrathin insulator layers, the STM images present characteristic contrasts related to the molecular orbitals which favors the localization of aldehyde groups. In this case, the lateral molecular interactions may induce the formation of small assemblies in which the electronic levels are slightly shifted. A possible interpretation of this phenomenon is to take into account polar interactions and charge transfer between neighboring molecules.

Multiport optical circulator by using polarizing beam splitter cubes as spatial walk-off polarizers.

PubMed

Chen, Jing-Heng; Chen, Kun-Huang; Lin, Jiun-You; Hsieh, Hsiang-Yung

2010-03-10

Optical circulators are necessary passive devices applied in optical communication systems. In the design of optical circulators, the implementation of the function of spatial walk-off polarizers is a key technique that significantly influences the performance and cost of a device. This paper proposes a design of a multiport optical circulator by using polarizing beam splitter cubes as spatial walk-off polarizers. To show the feasibility of the design, a prototype of a six-port optical circulator was fabricated. The insertion losses are 0.94-1.49 dB, the isolations are 25-51 dB, and return losses are 27.72 dB.

Polarity effects and apparent ion recombination in microionization chambers

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

Miller, Jessica R., E-mail: miller@humonc.wisc.edu; Hooten, Brian D.; Micka, John A.

Purpose: Microchambers demonstrate anomalous voltage-dependent polarity effects. Existing polarity and ion recombination correction factors do not account for these effects. As a result, many commercial microchamber models do not meet the specification of a reference-class ionization chamber as defined by the American Association of Physicists in Medicine. The purpose of this investigation is to determine the cause of these voltage-dependent polarity effects. Methods: A series of microchamber prototypes were produced to isolate the source of the voltage-dependent polarity effects. Parameters including ionization-chamber collecting-volume size, stem and cable irradiation, chamber assembly, contaminants, high-Z materials, and individual chamber components were investigated. Measurementsmore » were performed with electrodes coated with graphite to isolate electrode conductivity. Chamber response was measured as the potential bias of the guard electrode was altered with respect to the collecting electrode, through the integration of additional power supplies. Ionization chamber models were also simulated using COMSOL Multiphysics software to investigate the effect of a potential difference between electrodes on electric field lines and collecting volume definition. Results: Investigations with microchamber prototypes demonstrated that the significant source of the voltage-dependent polarity effects was a potential difference between the guard and collecting electrodes of the chambers. The voltage-dependent polarity effects for each prototype were primarily isolated to either the guard or collecting electrode. Polarity effects were reduced by coating the isolated electrode with a conductive layer of graphite. Polarity effects were increased by introducing a potential difference between the electrodes. COMSOL simulations further demonstrated that for a given potential difference between electrodes, the collecting volume of the chamber changed as the applied voltage was

Polarized light modulates light-dependent magnetic compass orientation in birds.

PubMed

Muheim, Rachel; Sjöberg, Sissel; Pinzon-Rodriguez, Atticus

2016-02-09

Magnetoreception of the light-dependent magnetic compass in birds is suggested to be mediated by a radical-pair mechanism taking place in the avian retina. Biophysical models on magnetic field effects on radical pairs generally assume that the light activating the magnetoreceptor molecules is nondirectional and unpolarized, and that light absorption is isotropic. However, natural skylight enters the avian retina unidirectionally, through the cornea and the lens, and is often partially polarized. In addition, cryptochromes, the putative magnetoreceptor molecules, absorb light anisotropically, i.e., they preferentially absorb light of a specific direction and polarization, implying that the light-dependent magnetic compass is intrinsically polarization sensitive. To test putative interactions between the avian magnetic compass and polarized light, we developed a spatial orientation assay and trained zebra finches to magnetic and/or overhead polarized light cues in a four-arm "plus" maze. The birds did not use overhead polarized light near the zenith for sky compass orientation. Instead, overhead polarized light modulated light-dependent magnetic compass orientation, i.e., how the birds perceive the magnetic field. Birds were well oriented when tested with the polarized light axis aligned parallel to the magnetic field. When the polarized light axis was aligned perpendicular to the magnetic field, the birds became disoriented. These findings are the first behavioral evidence to our knowledge for a direct interaction between polarized light and the light-dependent magnetic compass in an animal. They reveal a fundamentally new property of the radical pair-based magnetoreceptor with key implications for how birds and other animals perceive the Earth's magnetic field.

Helicity-Selective Enhancement and Polarization Control of Attosecond High Harmonic Waveforms Driven by Bichromatic Circularly Polarized Laser Fields.

PubMed

Dorney, Kevin M; Ellis, Jennifer L; Hernández-García, Carlos; Hickstein, Daniel D; Mancuso, Christopher A; Brooks, Nathan; Fan, Tingting; Fan, Guangyu; Zusin, Dmitriy; Gentry, Christian; Grychtol, Patrik; Kapteyn, Henry C; Murnane, Margaret M

2017-08-11

High harmonics driven by two-color counterrotating circularly polarized laser fields are a unique source of bright, circularly polarized, extreme ultraviolet, and soft x-ray beams, where the individual harmonics themselves are completely circularly polarized. Here, we demonstrate the ability to preferentially select either the right or left circularly polarized harmonics simply by adjusting the relative intensity ratio of the bichromatic circularly polarized driving laser field. In the frequency domain, this significantly enhances the harmonic orders that rotate in the same direction as the higher-intensity driving laser. In the time domain, this helicity-dependent enhancement corresponds to control over the polarization of the resulting attosecond waveforms. This helicity control enables the generation of circularly polarized high harmonics with a user-defined polarization of the underlying attosecond bursts. In the future, this technique should allow for the production of bright highly elliptical harmonic supercontinua as well as the generation of isolated elliptically polarized attosecond pulses.

MCSCF wave functions for excited states of polar molecules - Application to BeO. [Multi-Configuration Self-Consistent Field

NASA Technical Reports Server (NTRS)

Bauschlicher, C. W., Jr.; Yarkony, D. R.

1980-01-01

A previously reported multi-configuration self-consistent field (MCSCF) algorithm based on the generalized Brillouin theorem is extended in order to treat the excited states of polar molecules. In particular, the algorithm takes into account the proper treatment of nonorthogonality in the space of single excitations and invokes, when necessary, a constrained optimization procedure to prevent the variational collapse of excited states. In addition, a configuration selection scheme (suitable for use in conjunction with extended configuration interaction methods) is proposed for the MCSCF procedure. The algorithm is used to study the low-lying singlet states of BeO, a system which has not previously been studied using an MCSCF procedure. MCSCF wave functions are obtained for three 1 Sigma + and two 1 Pi states. The 1 Sigma + results are juxtaposed with comparable results for MgO in order to assess the generality of the description presented here.

Effects of climate change on polar bears.

PubMed

Wiig, Øystein; Aars, Jon; Born, Erik W

2008-01-01

In this article, we review the effects on polar bears of global warming that have already been observed, and try to evaluate what may happen to the polar bears in the future. Many researchers have predicted a wide range of impacts of climate change on polar bear demography and conditions. A predicted major reduction in sea ice habitat will reduce the availability of ice associated seals, the main prey of polar bears, and a loss and fragmentation of polar bear habitat will ultimately lead to large future reductions in most subpopulations. It is likely that polar bears will be lost from many areas where they are common today and also that the total population will change into a few more distinctly isolated populations.

Modulation of spatial spin polarization at organic spinterface by side groups

NASA Astrophysics Data System (ADS)

Qiu, Shuai; Zhang, Zhao; Miao, Yuan-yuan; Zhang, Guang-ping; Ren, Jun-feng; Wang, Chuan-kui; Hu, Gui-chao

2018-01-01

Spin polarization at benzene/Ni organic/ferromagnetic interface is investigated by applying different substituting side groups. Based on first-principle calculations, it is demonstrated that the spin polarization of the states may be tuned in magnitude and sign by the side groups, which depends on the type of side groups as well as their position in the aromatic ring. Especially, a spatial spin polarization modulation is realized at the surface with the utilization of electron donating group sbnd NH2 or electron accepting group sbnd NO2. The analysis of projected density of states onto the pz orbital of carbon atoms indicates that the side group reduces the structural symmetry of the molecule and changes the pz orbital of carbon atom at different position, which further modifies the pz-d orbital hybridization as well as the spin transfer between the molecule and the ferromagnet. This work indicates a feasible way to modulate the spatial spin polarization at organic spinterface by side groups, which deserves to be measured by spin-polarized scanning tunneling microscopy.

Predicting the Stability of Hypervalent Molecules

ERIC Educational Resources Information Center

Mitchell, Tracy A.; Finnocchio, Debbie; Kua, Jeremy

2007-01-01

An exercise is described which introduces students to using concepts in thermochemistry to predict relative stability of a hypervalent molecule. Students will compare the energies of formation for both fluoride and the hydride by calculations and they will also explore the issue of partial ionic character in polar covalent bonds.

Organic molecules in the polar ice: from chemical analysis to environmental proxies

NASA Astrophysics Data System (ADS)

Barbante, Carlo; Zennaro, Piero; Giorio, Chiara; Kehrwald, Natalie; Benton, Alisa K.; Wolff, Eric W.; Kalberer, Markus; Kirchgeorg, Torben; Zangrando, Roberta; Barbaro, Elena; Gambaro, Andrea

2015-04-01

The molecular and isotopic compositions of organic matter buried in ice contains information that helps reconstruct past environmental conditions, evaluate histories of climate change, and assess impacts of humans on ecosystems. In recent years novel analytical techniques were developed to quantify molecular compounds in ice cores. As an example, biomass burning markers, including monosaccharide anhydrides, lightweight carboxylic acids, lignin and resin pyrolysis products, black carbon, and charcoal records help in reconstructing past fire activity across seasonal to millennial time scales. Terrestrial biomarkers, such as plant waxes (e.g. long-chain n-alkanes) are also a promising paleo vegetation proxy in ice core studies. Polycyclic aromatic hydrocarbons are ubiquitous pollutants recently detected in ice cores. These hydrocarbons primarily originate from incomplete combustion of organic matter and fossil fuels (e.g. diesel engines, domestic heating, industrial combustion) and therefore can be tracers of past combustion activities. In order to be suitable for paloeclimate purposes, organic molecular markers detected in ice cores should include the following important features. Markers have to be stable under oxidizing atmospheric conditions, and ideally should not react with hydroxyl radicals, during their transport to polar regions. Organic markers must be released in large amounts in order to be detected at remote distances from the sources. Proxies must be specific, in order to differentiate them from other markers with multiple sources. The extraction of glaciochemical information from ice cores is challenging due to the low concentrations of some impurities, thereby demanding rigorous control of external contamination sources and sensitive analytical techniques. Here, we review the analysis and use of organic molecules in ice as proxies of important environmental and climatic processes.

Re-polarization of nuclear spins using selective SABRE-INEPT.

PubMed

Knecht, Stephan; Kiryutin, Alexey S; Yurkovskaya, Alexandra V; Ivanov, Konstantin L

2018-02-01

A method is proposed for significant improvement of NMR pulse sequences used in high-field SABRE (Signal Amplification By Reversible Exchange) experiments. SABRE makes use of spin order transfer from parahydrogen (pH 2 , the H 2 molecule in its singlet spin state) to a substrate in a transient organometallic Ir-based complex. The technique proposed here utilizes "re-polarization", i.e., multiple application of an NMR pulse sequence used for spin order transfer. During re-polarization only the form of the substrate, which is bound to the complex, is excited by selective NMR pulses and the resulting polarization is transferred to the free substrate via chemical exchange. Owing to the fact that (i) only a small fraction of the substrate molecules is in the bound form and (ii) spin relaxation of the free substrate is slow, the re-polarization scheme provides greatly improved NMR signal enhancement, ε. For instance, when pyridine is used as a substrate, single use of the SABRE-INEPT sequence provides ε≈260 for 15 N nuclei, whereas SABRE-INEPT with re-polarization yields ε>2000. We anticipate that the proposed method is useful for achieving maximal NMR enhancement with spin hyperpolarization techniques. Copyright © 2017 Elsevier Inc. All rights reserved.

Real-Time Description of the Electronic Dynamics for a Molecule Close to a Plasmonic Nanoparticle

PubMed Central

2016-01-01

The optical properties of molecules close to plasmonic nanostructures greatly differ from their isolated molecule counterparts. To theoretically investigate such systems from a quantum-chemistry perspective, one has to take into account that the plasmonic nanostructure (e.g., a metal nanoparticle–NP) is often too large to be treated atomistically. Therefore, a multiscale description, where the molecule is treated by an ab initio approach and the metal NP by a lower level description, is needed. Here we present an extension of one such multiscale model [Corni, S.; Tomasi, J. J. Chem. Phys.2001, 114, 3739], originally inspired by the polarizable continuum model, to a real-time description of the electronic dynamics of the molecule and of the NP. In particular, we adopt a time-dependent configuration interaction (TD CI) approach for the molecule, the metal NP is described as a continuous dielectric of complex shape characterized by a Drude–Lorentz dielectric function, and the molecule–NP electromagnetic coupling is treated by an equation-of-motion (EOM) extension of the quasi-static boundary element method (BEM). The model includes the effects of both the mutual molecule–NP time-dependent polarization and the modification of the probing electromagnetic field due to the plasmonic resonances of the NP. Finally, such an approach is applied to the investigation of the light absorption of a model chromophore, LiCN, in the presence of a metal–NP of complex shape. PMID:28035246

Photo-assisted intersystem crossing: The predominant triplet formation mechanism in some isolated polycyclic aromatic molecules excited with pulsed lasers

DOE PAGES

Johnson, Philip M.; Sears, Trevor J.

2015-07-28

Naphthalene, anthracene, and phenanthrene are shown to have very long-lived triplet lifetimes when the isolated molecules are excited with nanosecond pulsed lasers resonant with the lowest singlet state. For naphthalene, triplet state populations are created only during the laser pulse, excluding the possibility of normal intersystem crossing at the one photon level, and all molecules have triplet lifetimes greater than hundreds of microseconds, similar to the behavior previously reported for phenylacetylene. Although containing 7–12 thousand cm⁻¹ of vibrational energy, the triplet molecules have ionization thresholds appropriate to vibrationless T₁ states. The laser power dependences (slopes of log-log power plots) ofmore » the excited singlet and triplet populations are about 0.7 for naphthalene and about 0.5 for anthracene. Kinetic modeling of the power dependences successfully reproduces the experimental results and suggests that the triplet formation mechanism involves an enhanced spin orbit coupling caused by sigma character in states at the 2-photon level. Symmetry Adapted Cluster-Configuration Interaction calculations produced excited state absorption spectra to provide guidance for estimating kinetic rates and the sigma character present in higher electronic states. It is concluded that higher excited state populations are significant when larger molecules are excited with pulsed lasers and need to be taken into account whenever discussing the molecular photodynamics.« less

Polar Nature of Biomimetic Fluorapatite/Gelatin Composites: A Comparison of Bipolar Objects and the Polar State of Natural Tissue.

PubMed

Burgener, Matthias; Putzeys, Tristan; Gashti, Mazeyar Parvinzadeh; Busch, Susanne; Aboulfadl, Hanane; Wübbenhorst, Michael; Kniep, Rüdiger; Hulliger, Jürg

2015-09-14

The correspondence of the state of alignment of macromolecules in biomimetic materials and natural tissues is demonstrated by investigating a mechanism of electrical polarity formation: An in vitro grown biomimetic FAp/gelatin composite is investigated for its polar properties by second harmonic (SHGM) and scanning pyroelectric microscopy (SPEM). Hexagonal prismatic seed crystals formed in gelatin gels represent a monodomain polar state, due to aligned mineralized gelatin molecules. Later growth stages, showing dumbbell morphologies, develop into a bipolar state because of surface recognition by gelatin functionality: A reversal of the polar alignment of macromolecules, thus, takes place close to that basal plane of the seed. In natural hard tissues (teeth and bone investigated by SPEM) and the biomimetic FAp/gelatin composite, we find a surprising analogy in view of growth-induced states of polarity: The development of polarity in vivo and in vitro can be explained by a Markov-type mechanism of molecular recognition during the attachment of macromolecules.

Polarized light modulates light-dependent magnetic compass orientation in birds

PubMed Central

Muheim, Rachel; Sjöberg, Sissel; Pinzon-Rodriguez, Atticus

2016-01-01

Magnetoreception of the light-dependent magnetic compass in birds is suggested to be mediated by a radical-pair mechanism taking place in the avian retina. Biophysical models on magnetic field effects on radical pairs generally assume that the light activating the magnetoreceptor molecules is nondirectional and unpolarized, and that light absorption is isotropic. However, natural skylight enters the avian retina unidirectionally, through the cornea and the lens, and is often partially polarized. In addition, cryptochromes, the putative magnetoreceptor molecules, absorb light anisotropically, i.e., they preferentially absorb light of a specific direction and polarization, implying that the light-dependent magnetic compass is intrinsically polarization sensitive. To test putative interactions between the avian magnetic compass and polarized light, we developed a spatial orientation assay and trained zebra finches to magnetic and/or overhead polarized light cues in a four-arm “plus” maze. The birds did not use overhead polarized light near the zenith for sky compass orientation. Instead, overhead polarized light modulated light-dependent magnetic compass orientation, i.e., how the birds perceive the magnetic field. Birds were well oriented when tested with the polarized light axis aligned parallel to the magnetic field. When the polarized light axis was aligned perpendicular to the magnetic field, the birds became disoriented. These findings are the first behavioral evidence to our knowledge for a direct interaction between polarized light and the light-dependent magnetic compass in an animal. They reveal a fundamentally new property of the radical pair-based magnetoreceptor with key implications for how birds and other animals perceive the Earth’s magnetic field. PMID:26811473

Modeling molecule-plasmon interactions using quantized radiation fields within time-dependent electronic structure theory

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

Nascimento, Daniel R.; DePrince, A. Eugene, E-mail: deprince@chem.fsu.edu

2015-12-07

We present a combined cavity quantum electrodynamics/ab initio electronic structure approach for simulating plasmon-molecule interactions in the time domain. The simple Jaynes-Cummings-type model Hamiltonian typically utilized in such simulations is replaced with one in which the molecular component of the coupled system is treated in a fully ab initio way, resulting in a computationally efficient description of general plasmon-molecule interactions. Mutual polarization effects are easily incorporated within a standard ground-state Hartree-Fock computation, and time-dependent simulations carry the same formal computational scaling as real-time time-dependent Hartree-Fock theory. As a proof of principle, we apply this generalized method to the emergence ofmore » a Fano-like resonance in coupled molecule-plasmon systems; this feature is quite sensitive to the nanoparticle-molecule separation and the orientation of the molecule relative to the polarization of the external electric field.« less

Quantum Drude oscillator model of atoms and molecules: Many-body polarization and dispersion interactions for atomistic simulation

NASA Astrophysics Data System (ADS)

Jones, Andrew P.; Crain, Jason; Sokhan, Vlad P.; Whitfield, Troy W.; Martyna, Glenn J.

2013-04-01

Treating both many-body polarization and dispersion interactions is now recognized as a key element in achieving the level of atomistic modeling required to reveal novel physics in complex systems. The quantum Drude oscillator (QDO), a Gaussian-based, coarse grained electronic structure model, captures both many-body polarization and dispersion and has linear scale computational complexity with system size, hence it is a leading candidate next-generation simulation method. Here, we investigate the extent to which the QDO treatment reproduces the desired long-range atomic and molecular properties. We present closed form expressions for leading order polarizabilities and dispersion coefficients and derive invariant (parameter-free) scaling relationships among multipole polarizability and many-body dispersion coefficients that arise due to the Gaussian nature of the model. We show that these “combining rules” hold to within a few percent for noble gas atoms, alkali metals, and simple (first-row hydride) molecules such as water; this is consistent with the surprising success that models with underlying Gaussian statistics often exhibit in physics. We present a diagrammatic Jastrow-type perturbation theory tailored to the QDO model that serves to illustrate the rich types of responses that the QDO approach engenders. QDO models for neon, argon, krypton, and xenon, designed to reproduce gas phase properties, are constructed and their condensed phase properties explored via linear scale diffusion Monte Carlo (DMC) and path integral molecular dynamics (PIMD) simulations. Good agreement with experimental data for structure, cohesive energy, and bulk modulus is found, demonstrating a degree of transferability that cannot be achieved using current empirical models or fully ab initio descriptions.

Discrete microfluidics for the isolation of circulating tumor cell subpopulations targeting fibroblast activation protein alpha and epithelial cell adhesion molecule.

PubMed

Witek, Małgorzata A; Aufforth, Rachel D; Wang, Hong; Kamande, Joyce W; Jackson, Joshua M; Pullagurla, Swathi R; Hupert, Mateusz L; Usary, Jerry; Wysham, Weiya Z; Hilliard, Dawud; Montgomery, Stephanie; Bae-Jump, Victoria; Carey, Lisa A; Gehrig, Paola A; Milowsky, Matthew I; Perou, Charles M; Soper, John T; Whang, Young E; Yeh, Jen Jen; Martin, George; Soper, Steven A

2017-01-01

Circulating tumor cells consist of phenotypically distinct subpopulations that originate from the tumor microenvironment. We report a circulating tumor cell dual selection assay that uses discrete microfluidics to select circulating tumor cell subpopulations from a single blood sample; circulating tumor cells expressing the established marker epithelial cell adhesion molecule and a new marker, fibroblast activation protein alpha, were evaluated. Both circulating tumor cell subpopulations were detected in metastatic ovarian, colorectal, prostate, breast, and pancreatic cancer patients and 90% of the isolated circulating tumor cells did not co-express both antigens. Clinical sensitivities of 100% showed substantial improvement compared to epithelial cell adhesion molecule selection alone. Owing to high purity (>80%) of the selected circulating tumor cells, molecular analysis of both circulating tumor cell subpopulations was carried out in bulk, including next generation sequencing, mutation analysis, and gene expression. Results suggested fibroblast activation protein alpha and epithelial cell adhesion molecule circulating tumor cells are distinct subpopulations and the use of these in concert can provide information needed to navigate through cancer disease management challenges.

The interfacial energetics of the oil molecules interactions with shale media using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Zhang, Z.; Wang, J.

2017-12-01

Characterizing the behavior of oil molecules in nanopore is vital to the understanding of geochemistry of hydrocarbon-bearing fluid in ultra-tight source rocks, such as shale. The heterogeneous nature of hydrocarbon system of nanoscale complicates experimental studies of oil / shale interfacial interaction. Therefore, to gain mechanistic understanding of the interplay of oil molecules in rock nanopore, molecular dynamics simulations have been applied to study the interactions of polar and non-polar oil on both calcite and kerogen surfaces. The effect of surface wetting, oil polarity, and temperature on the Gibbs free energy of adsorption have been investigated. The free energy, entropy, and enthalpy profiles have been calculated using advanced molecular dynamics method: umbrella sampling. In agreement with experiment, 1) surface with adsorbed water layer significantly reduces the oil adsorption energy on kerogen and turns the calcite surface to highly oil-repellent; 2) polar oil has overall stronger adsorption free energy than that of non-polar oil on both non-wetted calcite and kerogen surface; 3) organic interface (e.g. kerogen) exhibits stronger adsorption of oil molecules compared to inorganic one (e.g. calcite). The finding of this study indicates that oil displacement in nanopores can be enhanced by promoting the water adsorption on surface and reducing the polarity of oil on both inorganic and organic interfaces.

The Identification of Complex Organic Molecules in the Interstellar Medium: Using Lasers and Matrix Isolation Spectroscopy to Simulate the Interstellar Environment

NASA Technical Reports Server (NTRS)

Stone, Bradley M.

1998-01-01

The Astrochemistry Group at NASA Ames Research Center is interested in the identification of large organic molecules in the interstellar medium Many smaller organic species (e.g. hydrocarbons, alcohols, etc.) have been previously identified by their radiofrequency signature due to molecular rotations. However, this becomes increasingly difficult to observe as the size of the molecule increases. Our group in interested in the identification of the carriers of the Diffuse Interstellar Bands (absorption features observed throughout the visible and near-infrared in the spectra of stars, due to species in the interstellar medium). Polycyclic Aromatic Hydrocarbons (PAHs) and related molecules are thought to be good candidates for these carriers. Laboratory experiments am performed at Ames to simulate the interstellar environment, and to compare spectra obtained from molecules in the laboratory to those derived astronomically. We are also interested in PAHs with respect to their possible connection to the UIR (Unidentified infrared) and ERE (Extended Red Emission) bands - emission features found to emanate from particular regions of our galaxy (e.g. Orion nebula, Red Rectangle, etc.). An old, "tried and proven spectroscopic technique, matrix isolation spectroscopy creates molecular conditions ideal for performing laboratory astrophysics.

Third-order-harmonic generation in coherently spinning molecules

NASA Astrophysics Data System (ADS)

Prost, E.; Zhang, H.; Hertz, E.; Billard, F.; Lavorel, B.; Bejot, P.; Zyss, Joseph; Averbukh, Ilya Sh.; Faucher, O.

2017-10-01

The rotational Doppler effect occurs when circularly polarized light interacts with a rotating anisotropic material. It is manifested by the appearance of a spectral shift ensuing from the transfer of angular momentum and energy between radiation and matter. Recently, we reported terahertz-range rotational Doppler shifts produced in third-order nonlinear optical conversion [O. Faucher et al., Phys. Rev. A 94, 051402(R) (2016), 10.1103/PhysRevA.94.051402]. The experiment was performed in an ensemble of coherently spinning molecules prepared by a short laser pulse exhibiting a twisted linear polarization. The present work provides an extensive analysis of the rotational Doppler effect in third-order-harmonic generation from spinning linear molecules. The underlying physics is investigated both experimentally and theoretically. The implication of the rotational Doppler effect in higher-order processes like high-order-harmonic generation is discussed.

A CMB polarization primer

NASA Astrophysics Data System (ADS)

Hu, Wayne; White, Martin

1997-10-01

We present a pedagogical and phenomenological introduction to the study of cosmic microwave background (CMB) polarization to build intuition about the prospects and challenges facing its detection. Thomson scattering of temperature anisotropies on the last scattering surface generates a linear polarization pattern on the sky that can be simply read off from their quadrupole moments. These in turn correspond directly to the fundamental scalar (compressional), vector (vortical), and tensor (gravitational wave) modes of cosmological perturbations. We explain the origin and phenomenology of the geometric distinction between these patterns in terms of the so-called electric and magnetic parity modes, as well as their correlation with the temperature pattern. By its isolation of the last scattering surface and the various perturbation modes, the polarization provides unique information for the phenomenological reconstruction of the cosmological model. Finally we comment on the comparison of theory with experimental data and prospects for the future detection of CMB polarization.

Confocal fluorescence detected linear dichroism imaging of isolated human amyloid fibrils. Role of supercoiling.

PubMed

Steinbach, Gábor; Pomozi, István; Jánosa, Dávid Péter; Makovitzky, Josef; Garab, Gyozo

2011-05-01

Amyloids are highly organized insoluble protein aggregates that are associated with a large variety of degenerative diseases. In this work, we investigated the anisotropic architecture of isolated human amyloid samples stained with Congo Red. This was performed by fluorescence detected linear dichroism (FDLD) imaging in a laser scanning confocal microscope that was equipped with a differential polarization attachment using high frequency modulation of the polarization state of the laser beam and a demodulation circuit. Two- and three-dimensional FDLD images of amyloids provided information on the orientation of the electric transition dipoles of the intercalated Congo Red molecules with unprecedented precision and spatial resolution. We show that, in accordance with linear dichroism imaging (Jin et al. Proc Natl Acad Sci USA 100:15294, 2003), amyloids exhibit strong anisotropy with preferential orientation of the dye molecules along the fibrils; estimations on the orientation angle, of around 45°, are given using a model calculation which takes into account the helical organization of the filaments and fibrils. Our data also show that FDLD images display large inhomogeneities, high local values with alternating signs and, in some regions, well identifiable µm-sized periodicities. These features of the anisotropic architecture are accounted for by supercoiling of helically organized amyloid fibrils. © Springer Science+Business Media, LLC 2010

Coherent Bichromatic Force Deflection of Molecules

NASA Astrophysics Data System (ADS)

Kozyryev, Ivan; Baum, Louis; Aldridge, Leland; Yu, Phelan; Eyler, Edward E.; Doyle, John M.

2018-02-01

We demonstrate the effect of the coherent optical bichromatic force on a molecule, the polar free radical strontium monohydroxide (SrOH). A dual-frequency retroreflected laser beam addressing the X˜2Σ+↔A˜2Π1 /2 electronic transition coherently imparts momentum onto a cryogenic beam of SrOH. This directional photon exchange creates a bichromatic force that transversely deflects the molecules. By adjusting the relative phase between the forward and counterpropagating laser beams we reverse the direction of the applied force. A momentum transfer of 70 ℏk is achieved with minimal loss of molecules to dark states. Modeling of the bichromatic force is performed via direct numerical solution of the time-dependent density matrix and is compared with experimental observations. Our results open the door to further coherent manipulation of molecular motion, including the efficient optical deceleration of diatomic and polyatomic molecules with complex level structures.

An experimental toolbox for the generation of cold and ultracold polar molecules

NASA Astrophysics Data System (ADS)

Zeppenfeld, Martin; Gantner, Thomas; Glöckner, Rosa; Ibrügger, Martin; Koller, Manuel; Prehn, Alexander; Wu, Xing; Chervenkov, Sotir; Rempe, Gerhard

2017-01-01

Cold and ultracold molecules enable fascinating applications in quantum science. We present our toolbox of techniques to generate the required molecule ensembles, including buffergas cooling, centrifuge deceleration and optoelectrical Sisyphus cooling. We obtain excellent control over both the motional and internal molecular degrees of freedom, allowing us to aim at various applications.

92 GHz dual-polarized integrated horn antennas

NASA Technical Reports Server (NTRS)

Ali-Ahmad, Walid Y.; Rebeiz, Gabriel M.

1991-01-01

A dual-polarized two-dimensional imaging array was designed for millimeter-wave applications. The dual-polarized design consists of two dipoles perpendicular to each other and suspended on the same membrane inside a pyramidal cavity etched in silicon. The dual-polarized antenna is fully monolithic with room available for processing electronics. The IF or video signals are taken out through a novel bias and feeding structure. The measured polarization isolation is better than 20 dB at 92 GHz, and the orthogonal channels show identical far-field patterns. The antenna is well suited for millimeter-wave polarimetric synthetic-aperture radars (SARs) and high-efficiency balanced-mixer receivers.

Roto-translational Raman spectra of pairs of hydrogen molecules from first principles.

PubMed

Gustafsson, Magnus; Frommhold, Lothar; Li, Xiaoping; Hunt, K L C

2009-04-28

We calculate the collision-induced, roto-translational, polarized, and depolarized Raman spectra of pairs of H(2) molecules. The Schrodinger equation of H(2)-H(2) scattering in the presence of a weak radiation field is integrated in the close-coupled scheme. This permits the accounting for the anisotropy of the intermolecular potential energy surface and thereby it includes mixing of polarizability components. The static polarizability invariants, trace and anisotropy, of two interacting H(2) molecules were obtained elsewhere [Li et al., J. Chem. Phys. 126, 214302 (2007)] from first principles. Here we report the associated spherical tensor components which, along with the potential surface, are input in the calculation of the supramolecular Raman spectra. Special attention is paid to the interferences in the wings of the rotational S(0)(0) and S(0)(1) lines of the H(2) molecule. The calculated Raman pair spectra show reasonable consistency with existing measurements of the polarized and depolarized Raman spectra of pairs of H(2) molecules.

Raman Optical Activity of Biological Molecules

NASA Astrophysics Data System (ADS)

Blanch, Ewan W.; Barron, Laurence D.

Now an incisive probe of biomolecular structure, Raman optical activity (ROA) measures a small difference in Raman scattering from chiral molecules in right- and left-circularly polarized light. As ROA spectra measure vibrational optical activity, they contain highly informative band structures sensitive to the secondary and tertiary structures of proteins, nucleic acids, viruses and carbohydrates as well as the absolute configurations of small molecules. In this review we present a survey of recent studies on biomolecular structure and dynamics using ROA and also a discussion of future applications of this powerful new technique in biomedical research.

Tunable Superfluidity and Quantum Magnetism with Ultracold Polar Molecules

DTIC Science & Technology

2011-09-08

generalization of the t-J model that we refer to as the anisotropic t-J-V-W model. Dipole-dipole interactions that give rise to this model are orders...controlled by the ratio between the Rabi frequency and the detuning of a þ-polarized microwave field acting on the j0i j1i tran- sition [27]. In 40K87Rb...field coupling jm0i and jm1i and performing an adiabatic passage from an easily accessible state to the desired ground state by tuning the Rabi

The signalling receptor MCAM coordinates apical-basal polarity and planar cell polarity during morphogenesis

PubMed Central

Gao, Qian; Zhang, Junfeng; Wang, Xiumei; Liu, Ying; He, Rongqiao; Liu, Xingfeng; Wang, Fei; Feng, Jing; Yang, Dongling; Wang, Zhaoqing; Meng, Anming; Yan, Xiyun

2017-01-01

The apical–basal (AB) polarity and planar cell polarity (PCP) provide an animal cell population with different phenotypes during morphogenesis. However, how cells couple these two patterning systems remains unclear. Here we provide in vivo evidence that melanoma cell adhesion molecule (MCAM) coordinates AB polarity-driven lumenogenesis and c-Jun N-terminal kinase (JNK)/PCP-dependent ciliogenesis. We identify that MCAM is an independent receptor of fibroblast growth factor 4 (FGF4), a membrane anchor of phospholipase C-γ (PLC-γ), an immediate upstream receptor of nuclear factor of activated T-cells (NFAT) and a constitutive activator of JNK. We find that MCAM-mediated vesicular trafficking towards FGF4, while generating a priority-grade transcriptional response of NFAT determines lumenogenesis. We demonstrate that MCAM plays indispensable roles in ciliogenesis through activating JNK independently of FGF signals. Furthermore, mcam-deficient zebrafish and Xenopus exhibit a global defect in left-right (LR) asymmetric establishment as a result of morphogenetic failure of their LR organizers. Therefore, MCAM coordination of AB polarity and PCP provides insight into the general mechanisms of morphogenesis. PMID:28589943

Rapid and accurate prediction and scoring of water molecules in protein binding sites.

PubMed

Ross, Gregory A; Morris, Garrett M; Biggin, Philip C

2012-01-01

Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97% of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.

Expanding signaling-molecule wavefront model of cell polarization in the Drosophila wing primordium.

PubMed

Wortman, Juliana C; Nahmad, Marcos; Zhang, Peng Cheng; Lander, Arthur D; Yu, Clare C

2017-07-01

In developing tissues, cell polarization and proliferation are regulated by morphogens and signaling pathways. Cells throughout the Drosophila wing primordium typically show subcellular localization of the unconventional myosin Dachs on the distal side of cells (nearest the center of the disc). Dachs localization depends on the spatial distribution of bonds between the protocadherins Fat (Ft) and Dachsous (Ds), which form heterodimers between adjacent cells; and the Golgi kinase Four-jointed (Fj), which affects the binding affinities of Ft and Ds. The Fj concentration forms a linear gradient while the Ds concentration is roughly uniform throughout most of the wing pouch with a steep transition region that propagates from the center to the edge of the pouch during the third larval instar. Although the Fj gradient is an important cue for polarization, it is unclear how the polarization is affected by cell division and the expanding Ds transition region, both of which can alter the distribution of Ft-Ds heterodimers around the cell periphery. We have developed a computational model to address these questions. In our model, the binding affinity of Ft and Ds depends on phosphorylation by Fj. We assume that the asymmetry of the Ft-Ds bond distribution around the cell periphery defines the polarization, with greater asymmetry promoting cell proliferation. Our model predicts that this asymmetry is greatest in the radially-expanding transition region that leaves polarized cells in its wake. These cells naturally retain their bond distribution asymmetry after division by rapidly replenishing Ft-Ds bonds at new cell-cell interfaces. Thus we predict that the distal localization of Dachs in cells throughout the pouch requires the movement of the Ds transition region and the simple presence, rather than any specific spatial pattern, of Fj.

Myosin conformational states determined by single fluorophore polarization

PubMed Central

Warshaw, David M.; Hayes, Eric; Gaffney, Donald; Lauzon, Anne-Marie; Wu, Junru; Kennedy, Guy; Trybus, Kathleen; Lowey, Susan; Berger, Christopher

1998-01-01

Muscle contraction is powered by the interaction of the molecular motor myosin with actin. With new techniques for single molecule manipulation and fluorescence detection, it is now possible to correlate, within the same molecule and in real time, conformational states and mechanical function of myosin. A spot-confocal microscope, capable of detecting single fluorophore polarization, was developed to measure orientational states in the smooth muscle myosin light chain domain during the process of motion generation. Fluorescently labeled turkey gizzard smooth muscle myosin was prepared by removal of endogenous regulatory light chain and re-addition of the light chain labeled at cysteine-108 with the 6-isomer of iodoacetamidotetramethylrhodamine (6-IATR). Single myosin molecule fluorescence polarization data, obtained in a motility assay, provide direct evidence that the myosin light chain domain adopts at least two orientational states during the cyclic interaction of myosin with actin, a randomly disordered state, most likely associated with myosin whereas weakly bound to actin, and an ordered state in which the light chain domain adopts a finite angular orientation whereas strongly bound after the powerstroke. PMID:9653135

Tuning spin-polarized transport in organic semiconductors

NASA Astrophysics Data System (ADS)

Mattana, Richard; Galbiati, Marta; Delprat, Sophie; Tatay, Sergio; Deranlot, Cyrile; Seneor, Pierre; Petroff, Frederic

Molecular spintronics is an emerging research field at the frontier between organic chemistry and the spintronics. Compared to traditional inorganic materials molecules are flexible and can be easily tailored by chemical synthesis. Due to their theoretically expected very long spin lifetime, they were first only seen as the ultimate media for spintronics devices. It was recently that new spintronics tailoring could arise from the chemical versatility brought by molecules. The hybridization between a ferromagnet and molecules induces a spin dependent broadening and energy shifting of the molecular orbitals leading to an induced spin polarization on the first molecular layer. This spin dependent hybridization can be used to tailor the spin dependent transport in organic spintronics devices. We have studied vertical Co/Alq3/Co organic spin valves. The negative magnetoresistance observed is the signature of different coupling strengths at the top and bottom interfaces. We have then inserted an inorganic tunnel barrier at the bottom interface in order to suppress the spin-dependent hybridization. In this case we restore a positive magnetoresistance. This demonstrates that at the bottom Co/Alq3 interface a stronger coupling occurs which induces an inversion of the spin polarization.

Polarization Sensitive Coherent Raman Measurements of DCVJ

NASA Astrophysics Data System (ADS)

Anderson, Josiah; Cooper, Nathan; Lawhead, Carlos; Shiver, Tegan; Ujj, Laszlo

2014-03-01

Coherent Raman spectroscopy which recently developed into coherent Raman microscopy has been used to produce label free imaging of thin layers of material and find the spatial distributions of certain chemicals within samples, e.g. cancer cells.(1) Not all aspects of coherent scattering have been used for imaging. Among those for example are special polarization sensitive measurements. Therefore we have investigated the properties of polarization sensitive CARS spectra of a highly fluorescent molecule, DCVJ.(2) Spectra has been recorded by using parallel polarized and perpendicular polarized excitations. A special polarization arrangement was developed to suppress the non-resonant background scattering from the sample. These results can be used to improve the imaging properties of a coherent Raman microscope in the future. This is the first time coherent Raman polarization sensitive measurements have been used to characterize the vibrational modes of DCVJ. 1: K. I. Gutkowski, et al., ``Fluorescence of dicyanovinyl julolidine in a room temperature ionic liquid '' Chemical Physics Letters 426 (2006) 329 - 333 2: Fouad El-Diasty, ``Coherent anti-Stokes Raman scattering: Spectroscopy and microscopy'' Vibrational Spectroscopy 55 (2011) 1-37

Design strategies to minimize the radiative efficiency of global warming molecules

PubMed Central

Bera, Partha P.; Francisco, Joseph S.; Lee, Timothy J.

2010-01-01

A strategy is devised to screen molecules based on their radiative efficiency. The methodology should be useful as one additional constraint when determining the best molecule to use for an industrial application. The strategy is based on the results of a recent study where we examined molecular properties of global warming molecules using ab initio electronic structure methods to determine which fundamental molecular properties are important in assessing the radiative efficiency of a molecule. Six classes of perfluorinated compounds are investigated. For similar numbers of fluorine atoms, their absorption of radiation in the IR window decreases according to perfluoroethers > perfluorothioethers ≈ sulfur/carbon compounds > perfluorocarbons > perfluoroolefins > carbon/nitrogen compounds. Perfluoroethers and hydrofluorethers are shown to possess a large absorption in the IR window due to (i) the C─O bonds are very polar, (ii) the C-O stretches fall within the IR window and have large IR intensity due to their polarity, and (iii) the IR intensity for C-F stretches in which the fluorine atom is bonded to the carbon that is bonded to the oxygen atom is enhanced due to a larger C─F bond polarity. Lengthening the carbon chain leads to a larger overall absorption in the IR window, though the IR intensity per bond is smaller. Finally, for a class of partially fluorinated compounds with a set number of electronegative atoms, the overall absorption in the IR window can vary significantly, as much as a factor of 2, depending on how the fluorine atoms are distributed within the molecule. PMID:20439762

Efficient spin-current injection in single-molecule magnet junctions

NASA Astrophysics Data System (ADS)

Xie, Haiqing; Xu, Fuming; Jiao, Hujun; Wang, Qiang; Liang, J.-Q.

2018-01-01

We study theoretically spin transport through a single-molecule magnet (SMM) in the sequential and cotunneling regimes, where the SMM is weakly coupled to one ferromagnetic and one normal-metallic leads. By a master-equation approach, it is found that the spin polarization injected from the ferromagnetic lead is amplified and highly polarized spin-current can be generated, due to the exchange coupling between the transport electron and the anisotropic spin of the SMM. Moreover, the spin-current polarization can be tuned by the gate or bias voltage, and thus an efficient spin injection device based on the SMM is proposed in molecular spintronics.

Imprint control of BaTiO 3 thin films via chemically induced surface polarization pinning

DOE PAGES

Lee, Hyungwoo; Kim, Tae Heon; Patzner, Jacob J.; ...

2016-02-22

Surface-adsorbed polar molecules can significantly alter the ferroelectric properties of oxide thin films. Thus, fundamental understanding and controlling the effect of surface adsorbates are crucial for the implementation of ferroelectric thin film devices, such as ferroelectric tunnel junctions. Herein, we report an imprint control of BaTiO 3 (BTO) thin films by chemically induced surface polarization pinning in the top few atomic layers of the water-exposed BTO films. Our studies based on synchrotron X-ray scattering and coherent Bragg rod analysis demonstrate that the chemically induced surface polarization is not switchable but reduces the polarization imprint and improves the bistability of ferroelectricmore » phase in BTO tunnel junctions. Here, we conclude that the chemical treatment of ferroelectric thin films with polar molecules may serve as a simple yet powerful strategy to enhance functional properties of ferroelectric tunnel junctions for their practical applications.« less

Electrical Deflection of Polar Liquid Streams: A Misunderstood Demonstration

NASA Astrophysics Data System (ADS)

Ziaei-Moayyed, Maryam; Goodman, Edward; Williams, Peter

2000-11-01

The electrical deflection of polar liquid streams, commonly used as a textbook illustration of the behavior of polar molecules, is shown to be due to the formation of electrically charged droplets in the polar liquid stream, induced by a nearby charged object, rather than any force exerted on molecular dipoles. Streams of water and polar organic liquids could be deflected in a uniform electric field, which could not have exerted any force on dipolar species. Water and polar organic liquid streams formed within a grounded, electrically screened region could not be deflected after exiting the screened region, demonstrating that there is no electrical force on uncharged polar liquid droplets. Induced charging was observed also in insulating polar organic liquids and is suggested to be due to ionic impurities. A weak deflection of a stream of a nonpolar liquid (tetrachloroethylene) was also observed, indicating that such impurity effects are quite general, even in nonpolar liquids.

Current progress in isolation and characterization of toxins isolated from Pfiesteria piscicida.

PubMed Central

Moeller, P D; Morton, S L; Mitchell, B A; Sivertsen, S K; Fairey, E R; Mikulski, T M; Glasgow, H; Deamer-Melia, N J; Burkholder, J M; Ramsdell, J S

2001-01-01

The isolation and partial purification of toxic substances derived from Pfiesteria piscicida Steidinger & Burkholder extracts is described. Four distinct bioassay systems were used to monitor bioactivity of the P. piscicida extracts, including a high throughput cell cytotoxicity assay and a reporter gene assay as well as assays using brine shrimp and fish. Using these bioassays to guide fractionation, we have isolated two distinct, active fractions from Pfiesteria culture medium and cell mass extracts on the basis of their solubility characteristics. We have identified and characterized a bioactive lipophilic substance from Pfiesteria-derived extracts as di(2-ethylhexyl)phthalate, a commonly used plasticizer. The source of this typically man-made substance has been identified as originating from Instant Ocean (Aquarium Systems, Mentor, OH, USA), a commercially available seawater salt mixture used to prepare our mass culture growth medium. We have developed chromatographic methodology to isolate a bioactive polar compound isolated from extracts of Pfiesteria culture and presently report the characterization of the activity of this substance. The molecular structural analysis of the polar active component(s) using mass spectrometry and nuclear magnetic resonance spectroscopy is currently under way. PMID:11677183

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.

PubMed

Cole, Daniel J; Vilseck, Jonah Z; Tirado-Rives, Julian; Payne, Mike C; Jorgensen, William L

2016-05-10

Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme.

A Strategy for Simultaneous Isolation of Less Polar Ginsenosides, Including a Pair of New 20-Methoxyl Isomers, from Flower Buds of Panax ginseng.

PubMed

Li, Sha-Sha; Li, Ke-Ke; Xu, Fei; Tao, Li; Yang, Li; Chen, Shu-Xiao; Gong, Xiao-Jie

2017-03-10

The present study was designed to simultaneously isolate the less polar ginsenosides from the flower buds of Panax ginseng (FBPG). Five ginsenosides, including a pair of new 20-methoxyl isomers, were extracted from FBPG and purified through a five-step integrated strategy, by combining ultrasonic extraction, Diaion Hp-20 macroporous resin column enrichment, solid phase extraction (SPE), reversed-phase high-performance liquid chromatography (RP-HPLC) analysis and preparation, and nuclear magnetic resonance (NMR) analysis. The quantification of the five ginsenosides was also discussed by a developed method with validations within acceptable limits. Ginsenoside Rg5 showed content of about 1% in FBPG. The results indicated that FBPG might have many different ginsenosides with diverse chemical structures, and the less polar ginsenosides were also important to the quality control and standardization of FBPG.

Spin Polarization Spectroscopy of Alkali-Noble Gas Interatomic Potentials

NASA Astrophysics Data System (ADS)

Mironov, Andrey E.; Goldshlag, William; Eden, J. Gary

2017-06-01

We report a new laser spectroscopic technique capable of detecting weak state-state interactions in diatomic molecules. Specifically, a weak interaction has been observed between the 6pσ antibonding orbital of the CsXe (B ^2Σ^+_{1/2}) state and a 5dσ MO associated with a 5dΛ (Λ = 0, 1) state. Thermal Cs-rare gas collision pairs are photoexcited by a circularly-polarized optical field having a wavelength within the B ^2Σ^+_{1/2} \\longleftarrow X ^2Σ^+_{1/2} (free\\longleftarrowfree) continuum. Subsequent dissociation of the B ^2Σ^+_{1/2} transient diatomic selectively populates the F= 4, 5 hyperfine levels of the Cs 6p ^2P_{3/2} state, and circularly-polarized (σ^+) amplified spontaneous emission (ASE) is generated on the Cs D_2 line. The dependence of Cs 6p spin polarization on the Cs(6p)-Xe internuclear separation (R), clearly shows an interaction between the CsXe(B ^2Σ^+_{1/2}) state and a 5dΛ (Λ = 0, 1) potential of the diatomic molecule.

Highly Polarized Fluorescent Illumination Using Liquid Crystal Phase.

PubMed

Gim, Min-Jun; Turlapati, Srikanth; Debnath, Somen; Rao, Nandiraju V S; Yoon, Dong Ki

2016-02-10

Liquid crystal (LC) materials are currently the dominant electronic materials in display technology because of the ease of control of molecular orientation using an electric field. However, this technology requires the fabrication of two polarizers to create operational displays, reducing light transmission efficiency below 10%. It is therefore desirable to develop new technologies to enhance the light efficiency while maintaining or improving other properties such as the modulation speed of the molecular orientation. Here we report a uniaxial-oriented B7 smectic liquid crystalline film, using fluorescent bent-core LC molecules, a chemically modified substrate, and an in-plane electric field. A LC droplet under homeotropic boundary conditions of air/LC as well as LC/substrate exhibits large focal conic like optical textures. The in-plane electric field induced uniaxial orientation of the LC molecules, in which molecular polar directors are aligned in the direction of the electric field. This highly oriented LC film exhibits linearly polarized luminescence and microsecond time-scale modulation characteristics. The resultant device is both cheap and easy to fabricate and thus has great potential for electro-optic applications, including LC displays, bioimaging systems, and optical communications.

Origin of the Strong Interaction between Polar Molecules and Copper(II) Paddle-Wheels in Metal Organic Frameworks

DOE PAGES

Ongari, Daniele; Tiana, Davide; Stoneburner, Samuel J.; ...

2017-06-27

The copper paddle-wheel is the building unit of many metal organic frameworks. Because of the ability of the copper cations to attract polar molecules, copper paddle-wheels are promising for carbon dioxide adsorption and separation. They have therefore been studied extensively, both experimentally and computationally. In this work we investigate the copper–CO 2 interaction in HKUST-1 and in two different cluster models of HKUST-1: monocopper Cu(formate) 2 and dicopper Cu 2(formate) 4. We show that density functional theory methods severely underestimate the interaction energy between copper paddle-wheels and CO 2, even including corrections for the dispersion forces. In contrast, a multireferencemore » wave function followed by perturbation theory to second order using the CASPT2 method correctly describes this interaction. The restricted open-shell Møller–Plesset 2 method (ROS-MP2, equivalent to (2,2) CASPT2) was also found to be adequate in describing the system and used to develop a novel force field. Our parametrization is able to predict the experimental CO 2 adsorption isotherms in HKUST-1, and it is shown to be transferable to other copper paddle-wheel systems.« less

Origin of the Strong Interaction between Polar Molecules and Copper(II) Paddle-Wheels in Metal Organic Frameworks.

PubMed

Ongari, Daniele; Tiana, Davide; Stoneburner, Samuel J; Gagliardi, Laura; Smit, Berend

2017-07-20

The copper paddle-wheel is the building unit of many metal organic frameworks. Because of the ability of the copper cations to attract polar molecules, copper paddle-wheels are promising for carbon dioxide adsorption and separation. They have therefore been studied extensively, both experimentally and computationally. In this work we investigate the copper-CO 2 interaction in HKUST-1 and in two different cluster models of HKUST-1: monocopper Cu(formate) 2 and dicopper Cu 2 (formate) 4 . We show that density functional theory methods severely underestimate the interaction energy between copper paddle-wheels and CO 2 , even including corrections for the dispersion forces. In contrast, a multireference wave function followed by perturbation theory to second order using the CASPT2 method correctly describes this interaction. The restricted open-shell Møller-Plesset 2 method (ROS-MP2, equivalent to (2,2) CASPT2) was also found to be adequate in describing the system and used to develop a novel force field. Our parametrization is able to predict the experimental CO 2 adsorption isotherms in HKUST-1, and it is shown to be transferable to other copper paddle-wheel systems.

Origin of the Strong Interaction between Polar Molecules and Copper(II) Paddle-Wheels in Metal Organic Frameworks

PubMed Central

2017-01-01

The copper paddle-wheel is the building unit of many metal organic frameworks. Because of the ability of the copper cations to attract polar molecules, copper paddle-wheels are promising for carbon dioxide adsorption and separation. They have therefore been studied extensively, both experimentally and computationally. In this work we investigate the copper–CO2 interaction in HKUST-1 and in two different cluster models of HKUST-1: monocopper Cu(formate)2 and dicopper Cu2(formate)4. We show that density functional theory methods severely underestimate the interaction energy between copper paddle-wheels and CO2, even including corrections for the dispersion forces. In contrast, a multireference wave function followed by perturbation theory to second order using the CASPT2 method correctly describes this interaction. The restricted open-shell Møller–Plesset 2 method (ROS-MP2, equivalent to (2,2) CASPT2) was also found to be adequate in describing the system and used to develop a novel force field. Our parametrization is able to predict the experimental CO2 adsorption isotherms in HKUST-1, and it is shown to be transferable to other copper paddle-wheel systems. PMID:28751926

Origin of the Strong Interaction between Polar Molecules and Copper(II) Paddle-Wheels in Metal Organic Frameworks

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

Ongari, Daniele; Tiana, Davide; Stoneburner, Samuel J.

The copper paddle-wheel is the building unit of many metal organic frameworks. Because of the ability of the copper cations to attract polar molecules, copper paddle-wheels are promising for carbon dioxide adsorption and separation. They have therefore been studied extensively, both experimentally and computationally. In this work we investigate the copper–CO 2 interaction in HKUST-1 and in two different cluster models of HKUST-1: monocopper Cu(formate) 2 and dicopper Cu 2(formate) 4. We show that density functional theory methods severely underestimate the interaction energy between copper paddle-wheels and CO 2, even including corrections for the dispersion forces. In contrast, a multireferencemore » wave function followed by perturbation theory to second order using the CASPT2 method correctly describes this interaction. The restricted open-shell Møller–Plesset 2 method (ROS-MP2, equivalent to (2,2) CASPT2) was also found to be adequate in describing the system and used to develop a novel force field. Our parametrization is able to predict the experimental CO 2 adsorption isotherms in HKUST-1, and it is shown to be transferable to other copper paddle-wheel systems.« less

Topological insulator infrared pseudo-bolometer with polarization sensitivity

DOEpatents

Sharma, Peter Anand

2017-10-25

Topological insulators can be utilized in a new type of infrared photodetector that is intrinsically sensitive to the polarization of incident light and static magnetic fields. The detector isolates single topological insulator surfaces and allows light collection and exposure to static magnetic fields. The wavelength range of interest is between 750 nm and about 100 microns. This detector eliminates the need for external polarization selective optics. Polarization sensitive infrared photodetectors are useful for optoelectronics applications, such as light detection in environments with low visibility in the visible wavelength regime.

Polarization of fluorescein fluorescence in single cells.

PubMed

Udkoff, R; Norman, A

1979-01-01

Measurement of fluorescence polarization (P) gives information about the immediate environment of the fluorescent molecule. We used a flow polarimeter to investigate the factors influencing P of fluorescein in mammalian cells to determine whether such measurements are useful for characterizing heterogeneous cell populations. Fluorescein was introduced into cells by incubation with FDA. Measurements of the intensity of fluorescence (TI) and polarization (P) revealed an unexpected dependence: P decreased with increasing intensity of fluorescence. This may be accounted for by the classical model of the binding of small molecules to protein in which P is dependent on the ratio bound to unbound molecules. We have been able to estimate the quenching due to binding and construct a Scatchard plot. We estimated a wavelength shift from in vitro data consistent with the dependence of P on wavelength seen in our cell work. Generally, the distributions of P are symmetrical. Photon statistics broadens the P distribution of dim cells. However, structure does develop in the P distribution when the cells are deprived of calcium or incubated in the cold. This appears as a shoulder on the P distribution or resolves into two peaks. Calcium deprivation may differentially affect a subpopulation of cells whose significance remains to be explored in various cell types.

Proteoform-specific protein binding of small molecules in complex matrices

USDA-ARS?s Scientific Manuscript database

Characterizing the specific binding between protein targets and small molecules is critically important for drug discovery. Conventional assays require isolation and purification of small molecules from complex matrices through multistep chromatographic fractionation, which may alter their original ...

The bound states of ultracold KRb molecules

NASA Astrophysics Data System (ADS)

Julienne, Paul; Hanna, Thomas

2009-03-01

Recently ultracold vibrational ground state ^40K^87Rb polar molecules have been made using magnetoassociation of two cold atoms to a weakly bound Feshbach molecule, followed by a two-color optical STIRAP process to transfer molecules to the molecular ground state [1]. We have used accurate potential energy curves for the singlet and triplet states of the KRb molecule [2] with coupled channels calculations to calculate all of the bound states of the ^40K^87Rb molecule as a function of magnetic field from the cold atom collision threshold to the v=0 ground state. We have also developed approximate models for understanding the changing properties of the molecular bound states as binding energy increases. Some overall conclusions from these calculations will be presented. [1] K.-K. Ni, S. Ospelkaus, M. H. G. de Miranda, A. Peer, B. Neyenhuis, J. J. Zirbel, S. Kotochigova, P. S. Julienne, D. S. Jin, and J. Ye, Science, 2008, 322, 231--235. [2] A. Pashov, O. Docenko, M. Tamanis, R. Ferber, H. Kn"ockel, and E. Tiemann, Phys. Rev. A, 2007, 76, 022511.

Exp6-polar thermodynamics of dense supercritical water

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

Bastea, S; Fried, L E

2007-12-13

We introduce a simple polar fluid model for the thermodynamics of dense supercritical water based on a Buckingham (exp-6) core and point dipole representation of the water molecule. The proposed exp6-polar thermodynamics, based on ideas originally applied to dipolar hard spheres, performs very well when tested against molecular dynamics simulations. Comparisons of the model predictions with experimental data available for supercritical water yield excellent agreement for the shock Hugoniot, isotherms and sound speeds, and are also quite good for the self-diffusion constant and relative dielectric constant. We expect the present approach to be also useful for other small polar moleculesmore » and their mixtures.« less

Ionization Study of Isomeric Molecules in Strong-field Laser Pulses

DOE PAGES

Zigo, Stefan; Le, Anh-Thu; Timilsina, Pratap; ...

2017-02-10

Through the use of the technique of time-of-flight mass spectroscopy, we obtain strong-field ionization yields for randomly oriented 1,2-dichloroethylene (1,2-DCE) (C 2H 2Cl 2) and 2-butene (C 4H 8). Here, we are interested in studying the effect of conformal structure in strong-field ionization and, in particular, the role of molecular polarity. That is, we can perform strong-field ionization studies in polar vs non-polar molecules that have the same chemical composition. Here, we report our findings through the ionization yields and the ratio (trans/cis) of each stereoisomer pair as a function of intensity.

Molecular density functional theory of water including density-polarization coupling.

PubMed

Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel

2016-06-22

We present a three-dimensional molecular density functional theory of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: (i) scalar density and vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and (ii) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities.

Deformation of DNA molecules by hydrodynamic focusing

NASA Astrophysics Data System (ADS)

Wong, Pak Kin; Lee, Yi-Kuen; Ho, Chih-Ming

2003-12-01

The motion of a DNA molecule in a solvent flow reflects the deformation of a nano/microscale flexible mass spring structure by the forces exerted by the fluid molecules. The dynamics of individual molecules can reveal both fundamental properties of the DNA and basic understanding of the complex rheological properties of long-chain molecules. In this study, we report the dynamics of isolated DNA molecules under homogeneous extensional flow. Hydrodynamic focusing generates homogeneous extensional flow with uniform velocity in the transverse direction. The deformation of individual DNA molecules in the flow was visualized with video fluorescence microscopy. A coil stretch transition was observed when the Deborah number (De) is larger than 0.8. With a sudden stopping of the flow, the DNA molecule relaxes and recoils. The longest relaxation time of T2 DNA was determined to be 0.63 s when scaling viscosity to 0.9 cP.

Experimental Realization of Efficient, Room Temperature Single-Photon Sources with Definite Circular and Linear Polarizations

NASA Astrophysics Data System (ADS)

Boutsidis, Christos

In this thesis I present experimental demonstrations of room-temperature, single-photon sources with definite linear and circular polarizations. Definite photon polarization increases the efficiency of quantum communication systems. In contrast with cryogenic-temperature single-photon sources based on epitaxial quantum dots requiring expensive MBE and nanofabrication, my method utilizes a mature liquid crystal technology, which I made consistent with single-emitter fluorescence microscopy. The structures I have prepared are planar-aligned cholesteric liquid crystals forming 1-D photonic bandgaps for circularly-polarized light, which were used to achieve definite circularly-polarized fluorescence of single emitters doped in this environment. I also used planar-aligned nematic liquid crystals to align single molecules with linear dipole moments and achieved definite linearly-polarized fluorescence. I used single nanocrystal quantum dots, single nanodiamond color-centers, rare-earth-doped nanocrystals, and single terrylene and DiIC18(3) dye molecules as emitters. For nanocrystal quantum dots I observed circular polarization dissymmetry factors as large as ge = --1.6. In addition, I observed circularly-polarized resonances in the fluorescence of emitters within a cholesteric microcavity, with cavity quality factors of up to Q ˜ 250. I also showed that the fluorescence of DiIC18(3) dye molecules in planar-aligned nematic cells exhibits definite linear polarization, with a degree of polarization of rho = --0.58 +/- 0.03. Distributed Bragg reflectors form another type of microcavity that can be used to realize a single-photon source. I characterized the fluorescence from nanocrystal quantum dots doped in the defect layers of such microcavites, both organic and inorganic. Finally, to demonstrate the single-photon properties of single-emitter-doped cholesteric and nematic liquid crystal structures and distributed Bragg reflector microcavities, I present observations of

Polar lipid composition of a new halobacterium

NASA Technical Reports Server (NTRS)

Tindall, B. J.; Tomlinson, G. A.; Hochstein, L. I.

1987-01-01

Investigations of the polar lipid composition of a new aerobic, extremely halophilic aracheabacterium capable of nitrate reduction have shown that this organism contains two previously unknown phospholycolipids derived from diphytanyl glycerol diethers. Comparison of the lipid pattern from this new isolate with other known strains indicate that this organism is novel. On the basis of the unique polar lipid pattern it can be concluded that this organism represents a new taxon, at least at the species level.

Laser Cooled YbF Molecules for Measuring the Electron's Electric Dipole Moment

NASA Astrophysics Data System (ADS)

Lim, J.; Almond, J. R.; Trigatzis, M. A.; Devlin, J. A.; Fitch, N. J.; Sauer, B. E.; Tarbutt, M. R.; Hinds, E. A.

2018-03-01

We demonstrate one-dimensional sub-Doppler laser cooling of a beam of YbF molecules to 100 μ K . This is a key step towards a measurement of the electron's electric dipole moment using ultracold molecules. We compare the effectiveness of magnetically assisted and polarization-gradient sub-Doppler cooling mechanisms. We model the experiment and find good agreement with our data.

Laser Cooled YbF Molecules for Measuring the Electron's Electric Dipole Moment.

PubMed

Lim, J; Almond, J R; Trigatzis, M A; Devlin, J A; Fitch, N J; Sauer, B E; Tarbutt, M R; Hinds, E A

2018-03-23

We demonstrate one-dimensional sub-Doppler laser cooling of a beam of YbF molecules to 100  μK. This is a key step towards a measurement of the electron's electric dipole moment using ultracold molecules. We compare the effectiveness of magnetically assisted and polarization-gradient sub-Doppler cooling mechanisms. We model the experiment and find good agreement with our data.

Polarized Continuum Radiation from Stellar Atmospheres

NASA Astrophysics Data System (ADS)

Harrington, J. Patrick

2015-10-01

Continuum scattering by free electrons can be significant in early type stars, while in late type stars Rayleigh scattering by hydrogen atoms or molecules may be important. Computer programs used to construct models of stellar atmospheres generally treat the scattering of the continuum radiation as isotropic and unpolarized, but this scattering has a dipole angular dependence and will produce polarization. We review an accurate method for evaluating the polarization and limb darkening of the radiation from model stellar atmospheres. We use this method to obtain results for: (i) Late type stars, based on the MARCS code models (Gustafsson et al. 2008), and (ii) Early type stars, based on the NLTE code TLUSTY (Lanz and Hubeny 2003). These results are tabulated at http://www.astro.umd.edu/~jph/Stellar_Polarization.html. While the net polarization vanishes for an unresolved spherical star, this symmetry is broken by rapid rotation or by the masking of part of the star by a binary companion or during the transit of an exoplanet. We give some numerical results for these last cases.

Molecular orbital imaging via above-threshold ionization with circularly polarized pulses.

PubMed

Zhu, Xiaosong; Zhang, Qingbin; Hong, Weiyi; Lu, Peixiang; Xu, Zhizhan

2011-07-18

Above-threshold ionization (ATI) for aligned or orientated linear molecules by circularly polarized laser pulsed is investigated. It is found that the all-round structural information of the molecular orbital is extracted with only one shot by the circularly polarized probe pulse rather than with multi-shot detections in a linearly polarized case. The obtained photoelectron momentum spectrum directly depicts the symmetry and electron distribution of the occupied molecular orbital, which results from the strong sensitivity of the ionization probability to these structural features. Our investigation indicates that the circularly polarized probe scheme would present a simple method to study the angle-dependent ionization and image the occupied electronic orbital.

Cloud-top height retrieval from polarizing remote sensor POLDER

NASA Astrophysics Data System (ADS)

He, Xianqiang; Pan, Delu; Yan, Bai; Mao, Zhihua

2006-10-01

A new cloud-top height retrieval method is proposed by using polarizing remote sensing. In cloudy conditions, it shows that, in purple and blue bands, linear polarizing radiance at the top-of-atmosphere (TOA) is mainly contributed by Rayleigh scattering of the atmosphere's molecules above cloud, and the contribution by cloud reflection and aerosol scattering can be neglected. With such characteristics, the basis principle and method of cloud-top height retrieval using polarizing remote sensing are presented in detail, and tested by the polarizing remote sensing data of POLDER. The satellite-derived cloud-top height product can not only show the distribution of global cloud-top height, but also obtain the cloud-top height distribution of moderate-scale meteorological phenomena like hurricanes and typhoons. This new method is promising to become the operational algorithm for cloud-top height retrieval for POLDER and the future polarizing remote sensing satellites.

New parameter-free polarization potentials in low-energy positron collisions

NASA Technical Reports Server (NTRS)

Jain, Ashok

1990-01-01

The polarization potential plays a decisive role in shaping up the cross sections in low energy positron collisions with atoms and molecules. However, its inclusion without involving any adjustable parameter, is still a challenge. Various other techniques employed so far for positron collisions are summarized, and a new, nonadjustable and very simple form of the polarization potential for positron-atom (molecule) collisions below the threshold of positronium formation is discussed. This new recently proposed potential is based on the correlation energy of a single positron in a homogeneous electron gas. The correlation energy was calculated by solving the Schrodinger equation of the positron-electron system and fitted to an analytical form in various ranges of the density parameter. In the outside region, the correlation energy is joined smoothly with the correct asymptotic form. This new positron correlation polarization (PCOP) potential was tested on several atomic and molecular targets such as the Ar, CO, and CH4. The results on the total and differential cross sections on these targets are shown along with the experimental data where available.

W-Band Circularly Polarized TE11 Mode Transducer

NASA Astrophysics Data System (ADS)

Zhan, Mingzhou; He, Wangdong; Wang, Lei

2018-06-01

This paper presents a balanced sidewall exciting approach to realize the circularly polarized TE11 mode transducer. We used a voltage vector transfer matrix to establish the relationship between input and output vectors, then we analyzed amplitude and phase errors to estimate the isolation of degenerate mode. A mode transducer with a sidewall exciter was designed based on the results. In the 88-100 GHz frequency range, the simulated axial ratio is less than 1.05 and the isolation of linearly polarization TE11 mode is higher than 30 dBc. In back-to-back measurements, the return loss is generally greater than 20 dB with a typical insertion loss of 1.2 dB. Back-to-back transmission measurements are in excellent agreement with simulations.

W-Band Circularly Polarized TE11 Mode Transducer

NASA Astrophysics Data System (ADS)

Zhan, Mingzhou; He, Wangdong; Wang, Lei

2018-04-01

This paper presents a balanced sidewall exciting approach to realize the circularly polarized TE11 mode transducer. We used a voltage vector transfer matrix to establish the relationship between input and output vectors, then we analyzed amplitude and phase errors to estimate the isolation of degenerate mode. A mode transducer with a sidewall exciter was designed based on the results. In the 88-100 GHz frequency range, the simulated axial ratio is less than 1.05 and the isolation of linearly polarization TE11 mode is higher than 30 dBc. In back-to-back measurements, the return loss is generally greater than 20 dB with a typical insertion loss of 1.2 dB. Back-to-back transmission measurements are in excellent agreement with simulations.

Dual polarized receiving steering antenna array for measurement of ultrawideband pulse polarization structure

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

Balzovsky, E. V.; Buyanov, Yu. I.; Koshelev, V. I., E-mail: koshelev@lhfe.hcei.tsc.ru

To measure simultaneously two orthogonal components of the electromagnetic field of nano- and subnano-second duration, an antenna array has been developed. The antenna elements of the array are the crossed dipoles of dimension 5 × 5 cm. The arms of the dipoles are connected to the active four-pole devices to compensate the frequency response variations of a short dipole in the frequency band ranging from 0.4 to 4 GHz. The dipoles have superimposed phase centers allowing measuring the polarization structure of the field in different directions. The developed antenna array is the linear one containing four elements. The pattern maximummore » position is controlled by means of the switched ultrawideband true time delay lines. Discrete steering in seven directions in the range from −40° to +40° has been realized. The error at setting the pattern maximum position is less than 4°. The isolation of the polarization exceeds 29 dB in the direction orthogonal to the array axis and in the whole steering range it exceeds 23 dB. Measurement results of the polarization structure of radiated and scattered pulses with different polarization are presented as well.« less

Polarized fluorescence in NADH under two-photon excitation with femtosecond laser pulses

NASA Astrophysics Data System (ADS)

Vasyutinskii, O. S.; Smolin, A. G.; Oswald, C.; Gericke, K. H.

2017-04-01

Polarized fluorescence decay in NADH molecules in aqueous solution under two-photon excitation by femtosecond laser pulses has been studied. The excitation was carried out by linear and circularly polarized radiation at four wavelengths: 720, 730, 740, and 750 nm. Time-dependent polarized fluorescence signals were recorded as a function of the excitation light polarization and used for determination of a set of molecular parameters, two lifetimes characterizing the molecular excited states, and the rotation correlation time τrot. The results obtained can be used to create and prove theoretical models describing the intensity and polarization of fluorescence in NADH involved in the regulation of the redox reactions in cells and tissues of living organisms.

How many molecular layers of polar solvent molecules control chemistry? The concept of compensating dipoles.

PubMed

Langhals, Heinz; Braun, Patricia; Dietl, Christian; Mayer, Peter

2013-09-27

The extension of the solvent influence of the shell into the volume of a polar medium was examined by means of anti-collinear dipoles on the basis of the E(T)(30) solvent polarity scale (i.e., the molar energy of excitation of a pyridinium-N-phenolatebetaine dye; generally: E(T) =28,591 nm kcal mol(-1)/λmax) where no compensation effects were found. As a consequence, solvent polarity effects are concentrated to a very thin layer of a few thousand picometres around the solute where extensions into the bulk solvent become unimportant. A parallelism to the thin surface layer of water to the gas phase is discussed. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Polarization patterns of the twilight sky

NASA Astrophysics Data System (ADS)

Cronin, Thomas W.; Warrant, Eric J.; Greiner, Birgit

2005-08-01

Although natural light sources produce depolarized light, patterns of partially linearly polarized light appear in the sky due to scattering from air molecules, dust, and aerosols. Many animals, including bees and ants, orient themselves to patterns of polarization that are present in daytime skies, when the intensity is high and skylight polarization is strong and predictable. The halicitid bee Megalopta genalis inhabits rainforests in Central America. Unlike typical bees, it forages before sunrise and after sunset, when light intensities under the forest canopy are very low, and must find its way to food sources and return to its nest in visually challenging circumstances. An important cue for the orientation could be patterns of polarization in the twilight sky. Therefore, we used a calibrated digital camera to image skylight polarization in an overhead patch of sky, 87.6° across, before dawn on Barro Colorado Island in Panama, where the bees are found. We simultaneously measured the spectral properties of polarized light in a cloudless patch of sky 15° across centered on the zenith. We also performed full-sky imaging of polarization before dawn and after dusk on Lizard Island in Australia, another tropical island. During twilight, celestial polarized light occurs in a wide band stretching perpendicular to the location of the hidden sun and reaching typical degrees of polarization near 80% at wavelengths >600 nm. This pattern appears about 45 minutes before local sunrise or disappears 45 minutes after local sunset (about 20 minutes after the onset of astronomical twilight at dawn, or before its end at dusk) and extends with little change through the entire twilight period. Such a strong and reliable orientation cue could be used for flight orientation by any animal with polarization sensitivity that navigates during twilight.

The spontaneous synchronized dance of pairs of water molecules

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

Roncaratti, Luiz F.; Instituto de Física, Universidade de Brasília, 70910-900 Brasília; Cappelletti, David, E-mail: david.cappelletti@unipg.it

2014-03-28

Molecular beam scattering experiments have been performed to study the effect of long-range anisotropic forces on the collision dynamics of two small polar molecules. The main focus of this paper is on water, but also ammonia and hydrogen sulphide molecules have been investigated, and some results will be anticipated. The intermolecular distances mainly probed are of the order of 1 nm and therefore much larger than the molecular dimensions. In particular, we have found that the natural electric field gradient, generated by different spatial orientations of the permanent electric dipoles, is able to promote the transformation of free rotations into coupledmore » pendular states, letting the molecular partners involved in the collision complex swinging to and fro around the field direction. This long-ranged concerted motion manifested itself as large increases of the magnitude of the total integral cross section. The experimental findings and the theoretical treatment developed to shed light on the details of the process suggest that the transformation from free rotations to pendular states depends on the rotational level of both molecules, on the impact parameter, on the relative collision velocity, on the dipole moment product and occurs in the time scale of picoseconds. The consequences of this intriguing phenomenon may be important for the interpretation and, in perspective, for the control of elementary chemical and biological processes, given by polar molecules, ions, and free radicals, occurring in several environments under various conditions.« less

The spontaneous synchronized dance of pairs of water molecules

NASA Astrophysics Data System (ADS)

Roncaratti, Luiz F.; Cappelletti, David; Pirani, Fernando

2014-03-01

Molecular beam scattering experiments have been performed to study the effect of long-range anisotropic forces on the collision dynamics of two small polar molecules. The main focus of this paper is on water, but also ammonia and hydrogen sulphide molecules have been investigated, and some results will be anticipated. The intermolecular distances mainly probed are of the order of 1 nm and therefore much larger than the molecular dimensions. In particular, we have found that the natural electric field gradient, generated by different spatial orientations of the permanent electric dipoles, is able to promote the transformation of free rotations into coupled pendular states, letting the molecular partners involved in the collision complex swinging to and fro around the field direction. This long-ranged concerted motion manifested itself as large increases of the magnitude of the total integral cross section. The experimental findings and the theoretical treatment developed to shed light on the details of the process suggest that the transformation from free rotations to pendular states depends on the rotational level of both molecules, on the impact parameter, on the relative collision velocity, on the dipole moment product and occurs in the time scale of picoseconds. The consequences of this intriguing phenomenon may be important for the interpretation and, in perspective, for the control of elementary chemical and biological processes, given by polar molecules, ions, and free radicals, occurring in several environments under various conditions.

Investigation of fingerprints for small polar molecules by using a tunable monochromatic THz source

NASA Astrophysics Data System (ADS)

Sun, Hongqian

Over the past 20 years, considerable efforts have been dedicated to the generation and the application of electromagnetic waves in the Terahertz (THz) regime. Among all of the proposed applications, the THz spectroscopy is probably the most mature and promising one. According to the previous reports, the THz spectroscopy has been extensively applied into many analysis fields, including the investigation of vibrational modes for the crystalline solids, the characterization of electron transport in the condense matters and the identification of explosive materials at a standoff distance. More interestingly, since most gas phase chemicals exhibit unique transition peaks in the THz spectra, one could in principle achieve highly accurate molecular fingerprinting and chemical sensing as well. However, all of the practical THz spectroscopy applications were still greatly hampered by the lack of suitable sources and detectors. In this thesis, a unique approach to measure the THz spectrum is developed based on a novel tunable narrowband source. Unlike the previous THz systems, high power THz pulses were generated by the difference frequency generation processes between two collinearly propagated near infrared laser beams. To tune the output THz signal frequency, one can simply adjust one of the incident beam frequencies. Therefore, based on a convenient wavelength tuning scheme, the transmission spectra can be measured for a series of polar gases with either similar or distinct molecular structures. According to the measured spectra, it is found that the obtained transition frequencies, absorption intensities and molecular constants are all in good agreement with the theoretical results tabulated in the molecular spectroscopic databases, such as the HITRAN database. By further analyzing the transition frequencies, it is also discovered that one can confidently identify each polar molecule and differentiate between various isotopic variants based on their characteristic

Dielectric relaxation of guest molecules in a clathrate structure of syndiotactic polystyrene.

PubMed

Urakawa, Osamu; Kaneko, Fumitoshi; Kobayashi, Hideo

2012-12-13

Structure and dynamics of semicrystalline polymer films composed of syndiotactic polystyrene (sPS) and 2-butanone were examined through X-ray diffraction, polarized FTIR, and dielectric relaxation measurements. The X-ray and FTIR measurements revealed its crystal structure to be δ-clathrate containing 2-butanone molecules inside. The carbonyl group of 2-butanone in the crystal was found to orient preferentially parallel to the ac plane of the crystal through the polarized ATR FTIR measurements. Dielectric measurements were also conducted on these film samples to see only the relaxation dynamics of 2-butanone thanks to the high dielectric intensity of 2-butanone compared to sPS. Two relaxation modes denoted by slow and fast modes appeared. The former was assigned to the motion of 2-butanone molecules entrapped in the cavities of the crystalline (δ-form) and the latter to those in the amorphous region. We focused on the slow mode in order to elucidate the specific dynamics of the guest molecule confined in the crystalline region. The relaxation time of the slow mode was about 4 orders of magnitude longer than that of liquid 2-butanone. This suggests that the dynamics of guest molecules is highly restricted due to the high barrier to conformational and/or orientational change of the guest molecule in the cavity of δ-crystal. Furthermore, the dielectric intensity Δε of the slow mode was much smaller than the one calculated from that of bulk liquid 2-butanone and the guest concentration in the crystalline region (the intensity was only 10% of the estimated value from the bulk liquid data). This result also indicates that the free rotational motion of 2-butanone molecules is restricted inside the crystal. This will be consistently related to the weak uniplanar orientation of the carbonyl group of 2-butanone parallel to the ac plane revealed by the X-ray and polarized ATR FTIR measurements.

Excited state electronic polarization and reappraisal of the n ← π∗ emission of acetone in water

NASA Astrophysics Data System (ADS)

Orozco-González, Yoelvis; Coutinho, Kaline; Canuto, Sylvio

2010-10-01

Electronic polarization of the acetone molecule in the excited n → π∗ state is considered and its influence on the solvent shift in the emission spectrum is analyzed. Using an iterative procedure the electronic polarizations of both the ground and the excited states are included and compared with previous results obtained with Car-Parrinello dynamics. Analysis of the emission transition obtained using CIS(D)/aug-cc-pVDZ on statistically uncorrelated solute-solvent structures, composed of acetone and twelve explicit water molecules embedded in the electrostatic field of remaining 263 water molecules, corroborates that the solvent effect is mild, calculated here between 80 and 380 cm -1.

Polarization Spectroscopy and Collisions in NaK

NASA Astrophysics Data System (ADS)

Wolfe, C. M.; Ashman, S.; Huennekens, J.; Beser, B.; Bai, J.; Lyyra, A. M.

2009-05-01

We report current work to study transfer of population and orientation in collisions of NaK molecules with argon and potassium atoms using polarization labeling (PL) and laser-induced fluorescence (LIF) spectroscopy. In the PL experiment, a circularly polarized pump laser excites a specific NaK A^1&+circ;(v=16, J) <- X^1&+circ;(v=0, J±1) transition, creating an orientation (non-uniform MJ level distribution) in both levels. The linear polarized probe laser is scanned over various 3^1π(v=8, J' ±1) <- A^1&+circ;(v=16, J') transitions. The probe laser passes through a crossed linear polarizer before detection, and signal is recorded if the probe laser polarization has been modified by the vapor (which occurs when it comes into resonance with an oriented level). In addition to strong direct transitions (J' = J), we also observe weak collisional satellite lines (J' = J±n with n = 1, 2, 3, ...) indicating that orientation is transferred to adjacent rotational levels during a collision. An LIF experiment (with linear polarized pump and probe beams) gives information on the collisional transfer of population. From these data, cross sections for both processes can be determined. We experimentally distinguish collisions of NaK with argon atoms from collisions with alkali atoms.

Submillikelvin Dipolar Molecules in a Radio-Frequency Magneto-Optical Trap.

PubMed

Norrgard, E B; McCarron, D J; Steinecker, M H; Tarbutt, M R; DeMille, D

2016-02-12

We demonstrate a scheme for magneto-optically trapping strontium monofluoride (SrF) molecules at temperatures one order of magnitude lower and phase space densities 3 orders of magnitude higher than obtained previously with laser-cooled molecules. In our trap, optical dark states are destabilized by rapidly and synchronously reversing the trapping laser polarizations and the applied magnetic field gradient. The number of molecules and trap lifetime are also significantly improved from previous work by loading the trap with high laser power and then reducing the power for long-term trapping. With this procedure, temperatures as low as 400  μK are achieved.

Communication: Potentials of mean force study of ionic liquid ion pair aggregation in polar covalent molecule solvents

NASA Astrophysics Data System (ADS)

Bandlamudi, Santosh Rathan Paul; Benjamin, Kenneth M.

2018-05-01

Molecular dynamics (MD) simulations were conducted for 1-ethyl-3-methylimidazolium methylsulfate [EMIM][MeSO4] dissolved in six polar covalent molecules [acetic acid, acetone, chloroform, dimethyl sulfoxide (DMSO), isopropyl alcohol, and methanol] to understand the free energies of ionic liquid (IL) ion pairing/aggregation in the limit of infinite dilution. Free energy landscapes or potentials of mean force (PMF) were computed using umbrella sampling and the weighted histogram analysis method. The PMF studies showed the strongest IL ion pairing in chloroform, and the strength of IL ion pairing decreases in the order of chloroform, acetone, propanol, acetic acid, DMSO, and methanol. In the limit of infinite dilution, the free energy curves for IL ion aggregation in co-solvents were characterized by two distinct minima [global (˜3.6 Å) and local (˜5.7 Å)], while free energy values at these minima differed significantly for IL in each co-solvent. The PMF studies were extended for determining the free energy of IL ion aggregation as a function of concentration of methanol. Studies showed that as the concentration of methanol increased, the free energy of ion aggregation decreased, suggesting greater ion pair stability, in agreement with previously reported MD clustering and radial distribution function data.

SiO maser polarization in evolved stars: magnetic field

NASA Astrophysics Data System (ADS)

Herpin, F.; Baudry, A.; Thum, C.; Morris, D.; Wiesemeyer, H.

The maser theory still needs to be improved, in particular in terms of polarization. The study of the maser geometry inside the circumstellar envelopes can also be achieved through polarization studies (e.g., VLBI observations). But the most exciting point is the determination of the magnetic field that can be made from polarization measurements: this is definitively a new field of investigation for these evolved objects. The magnetic field probably plays an important role in the AGB star's life and can be a major factor (magnetic rotator theory) on the origin of the high mass loss rates observed in evolved objects. Measurement of the magnetic field is thus essential to study the mass loss mechanisms and also the Alfven waves. During its transition most quasi spherical AGB stars (i.e. envelopes) become complicated aspherical objects. This shaping is well explained by the Interacting Stellar Winds theory (Kwok works), but the ISW model fails to reproduce very complicated structures with jets and ansae. A new model (Magnetized Wind Blown Bubble theory) was thus developed by Blackman et al. (2001) and A. Franck: a weak toroidal magnetic field, embedded in the stellar wind, acts as a collimating agent (cf. Garcia-Segura 1997) and can produce such structures. Three molecules can show polarized maser emission in the circumstellar envelopes: - OH traces the envelope far from the central star (1000-10000 AU) - H2O at intermediate distances (a few 100 AU) - SiO in the inner circumstellar layers (5-10 AU) Measurement of the polarization rate of the maser radiation emitted by these molecules can give us the averaged value B// of the magnetic field along the line of sight (for a single dish observation). We present here the first complete study of the SiO maser polarization in a large sample of evolved stars (more than 100). The 4 Stokes parameters I, U, Q, V were simultaneously measured with the polarimeter on the IRAM-30m telescope. From the Stokes parameters values we

Identification of Quorum-Sensing Signal Molecules and a Biosynthetic Gene in Alicycliphilus sp. Isolated from Activated Sludge

PubMed Central

Morohoshi, Tomohiro; Okutsu, Noriya; Xie, Xiaonan; Ikeda, Tsukasa

2016-01-01

Activated sludge is a complicated mixture of various microorganisms that is used to treat sewage and industrial wastewater. Many bacteria produce N-acylhomoserine lactone (AHL) as a quorum-sensing signal molecule to regulate the expression of the exoenzymes used for wastewater treatment. Here, we isolated an AHL-producing bacteria from an activated sludge sample collected from an electronic component factory, which we named Alicycliphilus sp. B1. Clone library analysis revealed that Alicycliphilus was a subdominant genus in this sample. When we screened the activated sludge sample for AHL-producing strains, 12 of 14 the AHL-producing isolates were assigned to the genus Alicycliphilus. A putative AHL-synthase gene, ALISP_0667, was cloned from the genome of B1 and transformed into Escherichia coli DH5α. The AHLs were extracted from the culture supernatants of the B1 strain and E. coli DH5α cells harboring the ALISP_0667 gene and were identified by liquid chromatography-mass spectrometry as N-(3-hydroxydecanoyl)-l-homoserine lactone and N-(3-hydroxydodecanoyl)-l-homoserine lactone. The results of comparative genomic analysis suggested that the quorum-sensing genes in the B1 strain might have been acquired by horizontal gene transfer within activated sludge. PMID:27490553

Redistribution of Lunar Polar Water to Mid-latitudes and Its Role in Forming an OH Veneer

NASA Technical Reports Server (NTRS)

Farrell, William M.; Hurley, D. M.; Hodges, R. R.; Killen, R. M.; Halekas, J. S.; Zimmerman, M. I.; Delory, G. T.

2013-01-01

We suggest that energization processes like ion sputtering and impact vaporization can eject/release polar water molecules residing within cold trapped regions with sufficient velocity to allow their redistribution to mid-latitudes. We consider the possibility that these polar-ejected molecules can contribution to the water/OH veneer observed as a 3 micrometer IR absorption feature at mid-latitudes by Chandrayaan-1, Cassini, and EPOXI. We find this source cannot fully account for the observed IR feature, but could be a low intensity additional source.

Polymer physics experiments with single DNA molecules

NASA Astrophysics Data System (ADS)

Smith, Douglas E.

1999-11-01

Bacteriophage DNA molecules were taken as a model flexible polymer chain for the experimental study of polymer dynamics at the single molecule level. Video fluorescence microscopy was used to directly observe the conformational dynamics of fluorescently labeled molecules, optical tweezers were used to manipulate individual molecules, and micro-fabricated flow cells were used to apply controlled hydrodynamic strain to molecules. These techniques constitute a powerful new experimental approach in the study of basic polymer physics questions. I have used these techniques to study the diffusion and relaxation of isolated and entangled polymer molecules and the hydrodynamic deformation of polymers in elongational and shear flows. These studies revealed a rich, and previously unobserved, ``molecular individualism'' in the dynamical behavior of single molecules. Individual measurements on ensembles of identical molecules allowed the average conformation to be determined as well as the underlying probability distributions for molecular conformation. Scaling laws, that predict the dependence of properties on chain length and concentration, were also tested. The basic assumptions of the reptation model were directly confirmed by visualizing the dynamics of entangled chains.

Cell biochemistry studied by single-molecule imaging.

PubMed

Mashanov, G I; Nenasheva, T A; Peckham, M; Molloy, J E

2006-11-01

Over the last decade, there have been remarkable developments in live-cell imaging. We can now readily observe individual protein molecules within living cells and this should contribute to a systems level understanding of biological pathways. Direct observation of single fluorophores enables several types of molecular information to be gathered. Temporal and spatial trajectories enable diffusion constants and binding kinetics to be deduced, while analyses of fluorescence lifetime, intensity, polarization or spectra give chemical and conformational information about molecules in their cellular context. By recording the spatial trajectories of pairs of interacting molecules, formation of larger molecular complexes can be studied. In the future, multicolour and multiparameter imaging of single molecules in live cells will be a powerful analytical tool for systems biology. Here, we discuss measurements of single-molecule mobility and residency at the plasma membrane of live cells. Analysis of diffusional paths at the plasma membrane gives information about its physical properties and measurement of temporal trajectories enables rates of binding and dissociation to be derived. Meanwhile, close scrutiny of individual fluorophore trajectories enables ideas about molecular dimerization and oligomerization related to function to be tested directly.

The Origins and Evolution of Molecules in Icy Solids

NASA Technical Reports Server (NTRS)

Hudson, Reggie L.; Moore, Marla H.

2010-01-01

Astronomical observations of the past few decades have revealed the existence of a variety of molecules in extraterrestrial ices. These molecules include H2O, CO, and CO2, and organics such as CH4, CH30H, and C2H6. Some ices are dominated by polar molecules, while non-polar species appear to dominate others. Observations, mainly in the radio and IR regions, have allowed the inference of other solid-phase molecules whose formation remains difficult to explain by gas-phase chemistry alone. Several laboratory research groups have reported on extensive experiments on the solid-phase reaction chemistry of icy materials, generally as initiated by either ionizing radiation or vacuum-UV photons. These experiments not only permit molecular identifications to be made from astronomical observations, but also allow predictions of yet unidentified molecules. This laboratory approach has evolved over more than 30 years with much of the earliest work focusing on complex mixtures thought to represent either cometary or interstellar ices. Although those early experiments documented a rich solid-state photo- and radiation chemistry, they revealed few details of reactions for particular molecules, partly due to the multi-component nature of the samples. Since then, model systems have been examined that allow the chemistry of individual species and specific reactions to be probed. Reactions involving most of the smaller astronomical molecules have now been studied and specific processes identified. Current laboratory work suggests that a variety of reactions occur in extraterrestrial ices, including acid-base processes, radical dimerizations, proton transfers, oxidations, reductions, and isomerizations. This workshop presentation will focus on chemical reactions relevant to solar system and interstellar ices. While most of the work will be drawn from that to which the speaker has contributed, results from other laboratories also will be included. Suggestions for future studies will be

Small molecule fluoride toxicity agonists.

PubMed

Nelson, James W; Plummer, Mark S; Blount, Kenneth F; Ames, Tyler D; Breaker, Ronald R

2015-04-23

Fluoride is a ubiquitous anion that inhibits a wide variety of metabolic processes. Here, we report the identification of a series of compounds that enhance fluoride toxicity in Escherichia coli and Streptococcus mutans. These molecules were isolated by using a high-throughput screen (HTS) for compounds that increase intracellular fluoride levels as determined via a fluoride riboswitch reporter fusion construct. A series of derivatives were synthesized to examine structure-activity relationships, leading to the identification of compounds with improved activity. Thus, we demonstrate that small molecule fluoride toxicity agonists can be identified by HTS from existing chemical libraries by exploiting a natural fluoride riboswitch. In addition, our findings suggest that some molecules might be further optimized to function as binary antibacterial agents when combined with fluoride. Copyright © 2015 Elsevier Ltd. All rights reserved.

Small Molecule Fluoride Toxicity Agonists

PubMed Central

Nelson1, James W.; Plummer, Mark S.; Blount, Kenneth F.; Ames, Tyler D.; Breaker, Ronald R.

2015-01-01

SUMMARY Fluoride is a ubiquitous anion that inhibits a wide variety of metabolic processes. Here we report the identification of a series of compounds that enhance fluoride toxicity in Escherichia coli and Streptococcus mutans. These molecules were isolated by using a high-throughput screen (HTS) for compounds that increase intracellular fluoride levels as determined via a fluoride riboswitch-reporter fusion construct. A series of derivatives were synthesized to examine structure-activity relationships, leading to the identification of compounds with improved activity. Thus, we demonstrate that small molecule fluoride toxicity agonists can be identified by HTS from existing chemical libraries by exploiting a natural fluoride riboswitch. In addition, our findings suggest that some molecules might be further optimized to function as binary antibacterial agents when combined with fluoride. PMID:25910244

Superradiance Effects in the Linear and Nonlinear Optical Response of Quantum Dot Molecules

NASA Astrophysics Data System (ADS)

Sitek, A.; Machnikowski, P.

2008-11-01

We calculate the linear optical response from a single quantum dot molecule and the nonlinear, four-wave-mixing response from an inhomogeneously broadened ensemble of such molecules. We show that both optical signals are affected by the coupling-dependent superradiance effect and by optical interference between the two polarizations. As a result, the linear and nonlinear responses are not identical.

Theoretical investigation of polarization effects in solution: Importance of solvent collective motions

NASA Astrophysics Data System (ADS)

Ishida, Tateki

2015-01-01

Recent theoretical studies on interesting topics related to polarization effects in solutions are presented. As one of interesting topics, ionic liquids (ILs) solvents are focused on. The collective dynamics of electronic polarizability through interionic dynamics and the effect of polarization in ILs, 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]), are studied with molecular dynamics simulation. Also, the time-dependent polarization effect on the probe betaine dye molecule, pyridinium N-phenoxide, in water is investigated by a time-dependent reference interaction site model self-consistent field (time-dependent RISM-SCF) approach. The importance of considering polarization effects on solution systems related to solvent collective motions is shown.

Theoretical investigation of polarization effects in solution: Importance of solvent collective motions

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

Ishida, Tateki

2015-01-22

Recent theoretical studies on interesting topics related to polarization effects in solutions are presented. As one of interesting topics, ionic liquids (ILs) solvents are focused on. The collective dynamics of electronic polarizability through interionic dynamics and the effect of polarization in ILs, 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF{sub 6}]), are studied with molecular dynamics simulation. Also, the time-dependent polarization effect on the probe betaine dye molecule, pyridinium N-phenoxide, in water is investigated by a time-dependent reference interaction site model self-consistent field (time-dependent RISM-SCF) approach. The importance of considering polarization effects on solution systems related to solvent collective motions is shown.

Sampling and Analysis of Organic Molecules in the Plumes of Enceladus

NASA Astrophysics Data System (ADS)

Monroe, A. A.; Williams, P.; Anbar, A. D.; Tsou, P.

2012-12-01

The recent detection of organic molecules in the plumes of Enceladus, which also contain water and nitrogen (Waite et al., 2006; Matson et al., 2007), suggests that the geologically active South polar region contains habitable, subsurface water (McKay et al., 2008). Characterizing these molecules will be a high priority for any future mission to Enceladus. Sample return is highly desirable, but can it capture useful samples at Enceladus? Using Stardust mission parameters for comparison, we consider the survival of complex organic molecules during collection to assess the feasibility of one aspect of a sample return mission. A successful sample return mission must include the capability to capture and recover intact or partly intact molecules of particular astrobiological interest: lipids, amino and nucleic acids, polypeptides, and polynucleotides. The Stardust mission to comet Wild 2 successfully captured amino acids, amines, and PAHs using a combination of aerogel and Al foil (Sandford et al., 2006, 2010). For larger and more fragile molecules, particularly polypeptides and polynucleotides, low collisional damage is achieved by impact on low molecular weight surfaces. A particularly intriguing possibility is a capture surface pre-coated with organic matrices identified as ideal for analysis of various biomolecules using MALDI-MS (matrix-assisted laser desorption/ionization mass spectrometry) (Hillenkamp and Karas, 2007). MALDI is a standard technique with attomole sensitivity, exceptional mass resolution, and (bio)molecular specificity (Vestal, 2011). Capture surfaces appropriate for MALDI-MS analysis could be analyzed directly without post-return manipulation, minimizing post-capture damage to these molecules and the risk of contamination during handling. A hypothetical sample collection encounter speed of ~ 5 km/s corresponds to ~0.13 eV kinetic energy per amu. Studies of molecule survival and fragmentation exist for free hexapeptides impacting hydrocarbon

Mapping of all polarization-singularity C-point morphologies

NASA Astrophysics Data System (ADS)

Galvez, E. J.; Rojec, B. L.; Beach, K.

2014-02-01

We present theoretical descriptions and measurements of optical beams carrying isolated polarization-singularity C-points. Our analysis covers all types of C-points, including asymmetric lemons, stars and monstars. They are formed by the superposition of a circularly polarized mode carrying an optical vortex and a fundamental Gaussian mode in the opposite state of polarization. The type of C-point can be controlled experimentally by varying two parameters controlling the asymmetry of the optical vortex. This was implemented via a superposition of modes with singly charged optical vortices of opposite sign, and varying the relative amplitude and phase. The results are in excellent agreement with the predictions.

Measurement of Single Macromolecule Orientation by Total Internal Reflection Fluorescence Polarization Microscopy

PubMed Central

Forkey, Joseph N.; Quinlan, Margot E.; Goldman, Yale E.

2005-01-01

A new approach is presented for measuring the three-dimensional orientation of individual macromolecules using single molecule fluorescence polarization (SMFP) microscopy. The technique uses the unique polarizations of evanescent waves generated by total internal reflection to excite the dipole moment of individual fluorophores. To evaluate the new SMFP technique, single molecule orientation measurements from sparsely labeled F-actin are compared to ensemble-averaged orientation data from similarly prepared densely labeled F-actin. Standard deviations of the SMFP measurements taken at 40 ms time intervals indicate that the uncertainty for individual measurements of axial and azimuthal angles is ∼10° at 40 ms time resolution. Comparison with ensemble data shows there are no substantial systematic errors associated with the single molecule measurements. In addition to evaluating the technique, the data also provide a new measurement of the torsional rigidity of F-actin. These measurements support the smaller of two values of the torsional rigidity of F-actin previously reported. PMID:15894632

Maintained expression of the planar cell polarity molecule Vangl2 and reformation of hair cell orientation in the regenerating inner ear.

PubMed

Warchol, Mark E; Montcouquiol, Mireille

2010-09-01

The avian inner ear possesses a remarkable ability to regenerate sensory hair cells after ototoxic injury. Regenerated hair cells possess phenotypes and innervation that are similar to those found in the undamaged ear, but little is known about the signaling pathways that guide hair cell differentiation during the regenerative process. The aim of the present study was to examine the factors that specify the orientation of hair cell stereocilia bundles during regeneration. Using organ cultures of the chick utricle, we show that hair cells are properly oriented after having regenerated entirely in vitro and that orientation is not affected by surgical removal of the striolar reversal zone. These results suggest that the orientation of regenerating stereocilia is not guided by the release of a diffusible morphogen from the striolar reversal zone but is specified locally within the regenerating sensory organ. In order to determine the nature of the reorientation cues, we examined the expression patterns of the core planar cell polarity molecule Vangl2 in the normal and regenerating utricle. We found that Vangl2 is asymmetrically expressed on cells within the sensory epithelium and that this expression pattern is maintained after ototoxic injury and throughout regeneration. Notably, treatment with a small molecule inhibitor of c-Jun-N-terminal kinase disrupted the orientation of regenerated hair cells. Both of these results are consistent with the hypothesis that noncanonical Wnt signaling guides hair cell orientation during regeneration.

Bose-Einstein condensate of rigid rotor molecules

NASA Astrophysics Data System (ADS)

Jones, Evan; Smith, Joseph; Rittenhouse, Seth; Peden, Brandon; Wilson, Ryan

2017-04-01

We study the ground state phases of a quasi-two-dimensional Bose-Einstein condensate (BEC) of dipolar rigid rotor molecules subject to a DC electric field. In the high-field limit, this system acquires the properties of the fully polarized dipolar BEC, which exhibits a roton-maxon excitation spectrum, and has been thoroughly studied in the theoretical literature. In the weak-field limit, however, qualitatively new physics emerges due to the competition between the (weak) applied field and internal electric fields, which are produced by the molecules themselves. We characterize the ground states of this system, and study its unique dielectric properties. We gratefully acknowledge support from the National Science Foundation under Grant No. PHYS-1516421.

Intrinsic Polarization and Tunable Color of Electroluminescence from Organic Single Crystal-based Light-Emitting Devices

PubMed Central

Ding, Ran; Feng, Jing; Zhou, Wei; Zhang, Xu-Lin; Fang, Hong-Hua; Yang, Tong; Wang, Hai-Yu; Hotta, Shu; Sun, Hong-Bo

2015-01-01

A single crystal-based organic light-emitting device (OLED) with intrinsically polarized and color-tunable electroluminescence (EL) has been demonstrated without any subsequent treatment. The polarization ratio of 5:1 for the transversal-electric (TE) and transversal-magnetic (TM) polarization at the emission peak of 575 nm, and 4.7:1 for the TM to TE polarization at the emission peak of 635 nm, respectively, have been obtained. The emitting color is tunable between yellow, yellow-green and orange by changing the polarization angle. The polarized EL and the polarization-induced color tunability can be attributed to the anisotropic microcavity formed by the BP3T crystal with uniaxial alignment of the molecules. PMID:26207723

A charge-polarized porous metal-organic framework for gas chromatographic separation of alcohols from water.

PubMed

Sun, Jian-Ke; Ji, Min; Chen, Cheng; Wang, Wu-Gen; Wang, Peng; Chen, Rui-Ping; Zhang, Jie

2013-02-25

A bipyridinium ligand with a charge separated skeleton has been introduced into a metal-organic framework to yield a porous material with charge-polarized pore space, which exhibits selective adsorption for polar guest molecules and can be further used in gas chromatography for the separation of alcohol-water mixtures.

Micro-scale temperature measurement method using fluorescence polarization

NASA Astrophysics Data System (ADS)

Tatsumi, K.; Hsu, C.-H.; Suzuki, A.; Nakabe, K.

2016-09-01

A novel method that can measure the fluid temperature in microscopic scale by measuring the fluorescence polarization is described in this paper. The measurement technique is not influenced by the quenching effects which appears in conventional LIF methods and is believed to show a higher reliability in temperature measurements. Experiment was performed using a microchannel flow and fluorescent molecule probes, and the effects of the fluid temperature, fluid viscosity, measurement time, and pH of the solution on the measured fluorescence polarization degree are discussed to understand the basic characteristics of the present method. The results showed that fluorescence polarization is considerably less sensible to these quenching factors. A good correlation with the fluid temperature, on the other hand, was obtained and agreed well with the theoretical values confirming the feasibility of the method.

Isolation of rotational isomers and developments derived therefrom

PubMed Central

ŌKI, Michinori

2010-01-01

Isolation of rotational isomer models of ethane-type molecules is described. We could experimentally prove that, if rotational isomers whose molecular shape was chiral, the molecule could be optically active, even though it did not carry an asymmetric carbon atom. As an extension, other types of stereochemically fundamental and optically active molecules were isolated and their absolute stereochemistry was determined. One example is the model of meso-tartaric acid, for which optical inactivity had been attributed to internal compensation but is now explained as follows. On dissolution of meso-tartaric acid in a solvent, the molecule gives two kinds of conformers, one of which is a Ci molecule and the other is a C1 molecule. Although the latter is intrinsically optically active, the optical activity is cancelled by its enantiomer. The theory of internal compensation is recommended to be abandoned. As an extension to another area, some reactions of conformers are also discussed. PMID:21084771

Simulation of Titan's atmospheric photochemistry. Formation of non-volatile residue from polar nitrile ices

NASA Astrophysics Data System (ADS)

Couturier-Tamburelli, Isabelle; Piétri, Nathalie; Gudipati, Murthy S.

2015-06-01

We studied the photochemistry of frozen ice of a polar Titan's atmospheric molecule cyanodiacetylene (HC5N) to determine the possible contribution of this compound to the lower altitude photochemistry of haze layers found on Titan. We used infrared analysis to examine the residue produced by irradiation of solid HC5N at λ > 300 nm. The resulting polymer is orange-brown in color. Based on theoretical analysis and the general tendency of HC5N and C4N2 to undergo similar ice photochemistry at longer wavelengths accessible in Titan's lower atmosphere, we conclude that Titan's lower atmosphere is photochemically active in the regions of cloud, ice, and aerosol formation. C4N2is a symmetric molecule with no net dipole moment whereas, HC5N has a large dipole moment of ~4 D. Consequently, though both these molecules have very similar molecular weight and size, their sublimation temperatures are different, HC5N subliming around 170 K compared to 160 K for C4N2. Based on our studies we conclude that in Titan's atmosphere the cyanoacetylene class of molecules (HCN, HC3N, HC5N, etc.) would condense first followed by the dicyanoacetylenes (C2N2, C4N2, C6N2, etc.), leading to fractionation of different class of molecules. From the fluxes used in the laboratory and depletion of the original HC5N signals, we estimate Titan's haze ice photochemistry involving polar nitriles to be significant and very similar to their non-polar counterparts.

Quantitative analyses of bifunctional molecules.

PubMed

Braun, Patrick D; Wandless, Thomas J

2004-05-11

Small molecules can be discovered or engineered to bind tightly to biologically relevant proteins, and these molecules have proven to be powerful tools for both basic research and therapeutic applications. In many cases, detailed biophysical analyses of the intermolecular binding events are essential for improving the activity of the small molecules. These interactions can often be characterized as straightforward bimolecular binding events, and a variety of experimental and analytical techniques have been developed and refined to facilitate these analyses. Several investigators have recently synthesized heterodimeric molecules that are designed to bind simultaneously with two different proteins to form ternary complexes. These heterodimeric molecules often display compelling biological activity; however, they are difficult to characterize. The bimolecular interaction between one protein and the heterodimeric ligand (primary dissociation constant) can be determined by a number of methods. However, the interaction between that protein-ligand complex and the second protein (secondary dissociation constant) is more difficult to measure due to the noncovalent nature of the original protein-ligand complex. Consequently, these heterodimeric compounds are often characterized in terms of their activity, which is an experimentally dependent metric. We have developed a general quantitative mathematical model that can be used to measure both the primary (protein + ligand) and secondary (protein-ligand + protein) dissociation constants for heterodimeric small molecules. These values are largely independent of the experimental technique used and furthermore provide a direct measure of the thermodynamic stability of the ternary complexes that are formed. Fluorescence polarization and this model were used to characterize the heterodimeric molecule, SLFpYEEI, which binds to both FKBP12 and the Fyn SH2 domain, demonstrating that the model is useful for both predictive as well as ex

The microbe-mineral environment and gypsum neogenesis in a weathered polar evaporite.

PubMed

Cockell, C S; Osinski, G R; Banerjee, N R; Howard, K T; Gilmour, I; Watson, J S

2010-09-01

Evaporitic deposits are a globally widespread habitat for micro-organisms. The microbe-mineral environment in weathered and remobilized gypsum from exposed mid-Ordovician marine evaporite beds in the polar desert of Devon Island, Nunavut, Canadian High Arctic was examined. The gypsum is characterized by internal green zones of cyanobacterial colonization (dominated by Gloeocapsa/Aphanothece and Chroococcidiopsis spp. morphotypes) and abundant black zones, visible from the surface, that contain pigmented cyanobacteria and fungi. Bioessential elements in the gypsum are primarily provided by allochthonous material from the present-day polar desert. The disruption, uplift and rotation of the evaporite beds by the Haughton meteorite impact 39 Ma have facilitated gypsum weathering and its accessibility as a habitat. No cultured cyanobacteria, bacteria and fungi were halophilic consistent with the expectation that halophily is not required to persist in gypsum habitats. Heterotrophic bacteria from the evaporite were slightly or moderately halotolerant, as were heterotrophs isolated from soil near the gypsum outcrop showing that halotolerance is common in arctic bacteria in this location. Psychrotolerant Arthrobacter species were isolated. No psychrophilic organisms were isolated. Two Arthrobacter isolates from the evaporite were used to mediate gypsum neogenesis in the laboratory, demonstrating a potential role for microbial biomineralization processes in polar environments.

Magnetically-induced electric polarization in an organo-metallic magnet

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

Zapf, W S; Fabris, F W; Balakirev, F F

2009-01-01

The coupling between magnetic order and ferroelectricity has been under intense investigation in a wide range of transition metal oxides. The strongest coupling is obtained in so-called magnetically induced multiferroics where ferroelectricity arises directly from magnetic order that breaks inversion symmetry. However, it has been difficult to find non-oxide based materials in which these effects occur. Here we present a study of copper dimethyl sulfoxide dichloride (CDC), an organometallic quantum magnet containing S =1/1 Cu spins, in which a switchable electric polarization arises from field-tuned magnetic order. Fast magnetic field pulses allow us to perform sensitive measurements of the electricmore » polarization and demonstrate that the electric state is present only if the magnetic order is non-collinear. Furthermore, we show that the electric polarization can be switched in a stunning hysteretic fashion. Because the magnetic order in CDC is mediated by large organic molecules, our study shows that magnetoelectric interactions can exist in this important class of materials, opening the road to designing magnetoelectrics and multiferroics using large molecules as building blocks. Further, we demonstrate that CDC undergoes a magnetoelectric quantum phase transition -the first of its kind, where both ferroelectric and magnetic order emerge simultaneously as a function of magnetic field at very low temperatures.« less

Coherent Control of Ground State NaK Molecules

NASA Astrophysics Data System (ADS)

Yan, Zoe; Park, Jee Woo; Loh, Huanqian; Will, Sebastian; Zwierlein, Martin

2016-05-01

Ultracold dipolar molecules exhibit anisotropic, tunable, long-range interactions, making them attractive for the study of novel states of matter and quantum information processing. We demonstrate the creation and control of 23 Na40 K molecules in their rovibronic and hyperfine ground state. By applying microwaves, we drive coherent Rabi oscillations of spin-polarized molecules between the rotational ground state (J=0) and J=1. The control afforded by microwave manipulation allows us to pursue engineered dipolar interactions via microwave dressing. By driving a two-photon transition, we are also able to observe Ramsey fringes between different J=0 hyperfine states, with coherence times as long as 0.5s. The realization of long coherence times between different molecular states is crucial for applications in quantum information processing. NSF, AFOSR- MURI, Alfred P. Sloan Foundation, DARPA-OLE

Adsorption Study of a Water Molecule on Vacancy-Defected Nonpolar CdS Surfaces

PubMed Central

2017-01-01

A detailed understanding of the water–semiconductor interface is of major importance for elucidating the molecular interactions at the photocatalyst’s surface. Here, we studied the effect of vacancy defects on the adsorption of a water molecule on the (101̅0) and (112̅0) CdS surfaces, using spin-polarized density functional theory. We observed that the local spin polarization did not persist for most of the cationic vacancies on the surfaces, unlike in bulk, owing to surface reconstructions caused by displaced S atoms. This result suggests that cationic vacancies on these surfaces may not be the leading cause of the experimentally observed magnetism in CdS nanostructures. The surface vacancies are predominantly nonmagnetic except for one case, where a magnetic cationic vacancy is relatively stable due to constraints posed by the (101̅0) surface geometry. At this particular magnetic defect site, we found a very strong interaction with the H2O molecule leading to a case of chemisorption, where the local spin polarization vanishes concurrently. At the same defect site, adsorption of an O2 molecule was also simulated, and the results were found to be consistent with experimental electron paramagnetic resonance findings for powdered CdS. The anion vacancies on these surfaces were always found to be nonmagnetic and did not affect the water adsorption at these surfaces. PMID:28539988

Single-Molecule and Superresolution Imaging in Live Bacteria Cells

PubMed Central

Biteen, Julie S.; Moerner, W.E.

2010-01-01

Single-molecule imaging enables biophysical measurements devoid of ensemble averaging, gives enhanced spatial resolution beyond the diffraction limit, and permits superresolution reconstructions. Here, single-molecule and superresolution imaging are applied to the study of proteins in live Caulobacter crescentus cells to illustrate the power of these methods in bacterial imaging. Based on these techniques, the diffusion coefficient and dynamics of the histidine protein kinase PleC, the localization behavior of the polar protein PopZ, and the treadmilling behavior and protein superstructure of the structural protein MreB are investigated with sub-40-nm spatial resolution, all in live cells. PMID:20300204

The impacts of surface polarity on the solubility of nanoparticle

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

Zhu, Jianzhuo; Su, Jiguo, E-mail: jiguosu@ysu.edu.cn; Ou, Xinwen

In order to study the dependence of water solubility and hydration behavior of nanoparticles on their surface polarity, we designed polar nanoparticles with varying surface polarity by assigning atomic partial charge to the surface of C60. The water solubility of the nanoparticle is enhanced by several orders of magnitude after the introduction of surface polarity. Nevertheless, when the atomic partial charge grows beyond a certain value (q{sub M}), the solubility continuously decreases to the level of nonpolar nanoparticle. It should be noted that such q{sub M} is comparable with atomic partial charge of a variety of functional groups. The hydrationmore » behaviors of nanoparticles were then studied to investigate the non-monotonic dependence of solubility on the surface polarity. The interaction between the polar nanoparticle and the hydration water is stronger than the nonpolar counterpart, which should facilitate the dissolution of the nanoparticles. On the other hand, the surface polarity also reduces the interaction of hydration water with the other water molecules and enhances the interaction between the nanoparticles which may hinder their dispersion. Besides, the introduction of surface polarity disturbs and even rearranges the hydration structure of nonpolar nanoparticle. Interestingly, the polar nanoparticle with less ordered hydration structure tends to have higher water solubility.« less

Polar frost formation on Ganymede

NASA Technical Reports Server (NTRS)

Johnson, R. E.

1985-01-01

Voyager photographs have shown the presence of polar frost on Ganymede, a satellite of Jupiter. A number of models have been proposed for the formation of this feature. The models are based on the transport of material from the equatorial to the polar regions. The present paper is concerned with a model regarding the origin and appearance of the Ganymede caps which does not depend on such a transport. The model is based on observations of the surficial changes produced by ion bombardment. It is pointed out that experiments on ion and electron bombardment of water ice at low temperatures have shown that these particles sputter significant quantities of water molecules. In addition, they also change the visual characteristics of the surface significantly. Ion bombardment competing with thermal reprocessing may be sufficient to explain the latitudinal differences observed on Ganymede.

Complete magnetic field dependence of SABRE-derived polarization.

PubMed

Kiryutin, Alexey S; Yurkovskaya, Alexandra V; Zimmermann, Herbert; Vieth, Hans-Martin; Ivanov, Konstantin L

2018-07-01

Signal amplification by reversible exchange (SABRE) is a promising hyperpolarization technique, which makes use of spin-order transfer from parahydrogen (the H 2 molecule in its singlet spin state) to a to-be-polarized substrate in a transient organometallic complex, termed the SABRE complex. In this work, we present an experimental method for measuring the magnetic field dependence of the SABRE effect over an ultrawide field range, namely, from 10 nT to 10 T. This approach gives a way to determine the complete magnetic field dependence of SABRE-derived polarization. Here, we focus on SABRE polarization of spin-1/2 hetero-nuclei, such as 13 C and 15 N and measure their polarization in the entire accessible field range; experimental studies are supported by calculations of polarization. Features of the field dependence of polarization can be attributed to level anticrossings in the spin system of the SABRE complex. Features at magnetic fields of the order of 100 nT-1 μT correspond to "strong coupling" of protons and hetero-nuclei, whereas features found in the mT field range stem from "strong coupling" of the proton system. Our approach gives a way to measuring and analyzing the complete SABRE field dependence, to probing NMR parameters of SABRE complexes and to optimizing the polarization value. Copyright © 2017 John Wiley & Sons, Ltd.

Stokes-attenuated tunneling ionization of molecules

NASA Astrophysics Data System (ADS)

Kornev, Aleksei S.; Zon, Boris A.

2018-03-01

We set forth the quantum theory of ionic vibrational-level population by means of tunneling ionization of a molecule. Specific calculations are carried out for the H2 molecule. The results are in qualitative agreement with the experimental data [X. Urbain et al., Phys. Rev. Lett. 92, 163004 (2004), 10.1103/PhysRevLett.92.163004]. Our account for the excited vibrational levels reveals an interplay of two tendencies which contribute to the ionization rate: (i) It decreases due to additional energy absorption needed to populate these states and (ii) it increases together with the Franck-Condon factors which are large for these states. We show that these two tendencies practically compensate each other. The average quantitative disagreement between the theory and experiment amounts to ˜30 %. The same disagreement takes place when using the frozen approximation for the description of the nuclei motion. We demonstrated that the light-dressing effect for H2 leads to the dependence of the ionization rate on the angle between the molecule axis and the polarization vector of the radiation.

Formation of intermediate products during the resonance stepwise polarization of dibenzyl ketone and benzil molecules

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

Polevoi, A.V.; Matyuk, V.M.; Grigor'eva, G.A.

1987-07-01

The processes resulting in the intramolecular redistribution of energy in electronically excited S/sub ..pi pi..*/ states of dibenzyl ketone and benzil molecules have been investigated by laser mass spectrometry. The decisive role of dissociation under the conditions of the resonance stepwise photoionization of these molecules upon excitation by radiation with lambda = 266 nm has been demonstrated. The ionization potentials of the molecules and the appearance potentials of fragment ions from dibenzyl ketone and benzil have been determined on the basis of an analysis of photoionization efficiency curves.

Impact of molecular packing on electronic polarization in organic crystals: the case of pentacene vs TIPS-pentacene.

PubMed

Ryno, Sean M; Risko, Chad; Brédas, Jean-Luc

2014-04-30

Polarization energy corresponds to the stabilization of the cation or anion state of an atom or molecule when going from the gas phase to the solid state. The decrease in ionization energy and increase in electron affinity in the solid state are related to the (electronic and nuclear) polarization of the surrounding atoms and molecules in the presence of a charged entity. Here, through a combination of molecular mechanics and quantum mechanics calculations, we evaluate the polarization energies in two prototypical organic semiconductors, pentacene and 6,13-bis(2-(tri-isopropylsilyl)ethynyl)pentacene (TIPS-pentacene). Comparison of the results for the two systems reveals the critical role played by the molecular packing configurations in the determination of the polarization energies and provides physical insight into the experimental data reported by Lichtenberger and co-workers (J. Amer. Chem. Soc. 2010, 132, 580; J. Phys. Chem. C 2010, 114, 13838). Our results underline that the impact of packing configurations, well established in the case of the charge-transport properties, also extends to the polarization properties of π-conjugated materials.

Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins

NASA Astrophysics Data System (ADS)

Poornima, C. S.; Dean, P. M.

1995-12-01

Water molecules are known to play an important rôle in mediating protein-ligand interactions. If water molecules are conserved at the ligand-binding sites of homologous proteins, such a finding may suggest the structural importance of water molecules in ligand binding. Structurally conserved water molecules change the conventional definition of `binding sites' by changing the shape and complementarity of these sites. Such conserved water molecules can be important for site-directed ligand/drug design. Therefore, five different sets of homologous protein/protein-ligand complexes have been examined to identify the conserved water molecules at the ligand-binding sites. Our analysis reveals that there are as many as 16 conserved water molecules at the FAD binding site of glutathione reductase between the crystal structures obtained from human and E. coli. In the remaining four sets of high-resolution crystal structures, 2-4 water molecules have been found to be conserved at the ligand-binding sites. The majority of these conserved water molecules are either bound in deep grooves at the protein-ligand interface or completely buried in cavities between the protein and the ligand. All these water molecules, conserved between the protein/protein-ligand complexes from different species, have identical or similar apolar and polar interactions in a given set. The site residues interacting with the conserved water molecules at the ligand-binding sites have been found to be highly conserved among proteins from different species; they are more conserved compared to the other site residues interacting with the ligand. These water molecules, in general, make multiple polar contacts with protein-site residues.

Effect of polarization forces on carbon deposition on a non-spherical nanoparticle. Monte Carlo simulations [Effect of polarization forces on atom deposition on a non-spherical nanoparticle. Monte Carlo simulations

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

Nemchinsky, V.; Khrabry, A.

Trajectories of a polarizable species (atoms or molecules) in the vicinity of a negatively charged nanoparticle (at a floating potential) are considered. The atoms are pulled into regions of strong electric field by polarization forces. The polarization increases the deposition rate of the atoms and molecules at the nanoparticle. The effect of the non-spherical shape of the nanoparticle is investigated by the Monte Carlo method. The shape of the non-spherical nanoparticle is approximated by an ellipsoid. The total deposition rate and its flux density distribution along the nanoparticle surface are calculated. As a result, it is shown that the fluxmore » density is not uniform along the surface. It is maximal at the nanoparticle tips.« less

Effect of polarization forces on carbon deposition on a non-spherical nanoparticle. Monte Carlo simulations [Effect of polarization forces on atom deposition on a non-spherical nanoparticle. Monte Carlo simulations

DOE PAGES

Nemchinsky, V.; Khrabry, A.

2018-02-01

Trajectories of a polarizable species (atoms or molecules) in the vicinity of a negatively charged nanoparticle (at a floating potential) are considered. The atoms are pulled into regions of strong electric field by polarization forces. The polarization increases the deposition rate of the atoms and molecules at the nanoparticle. The effect of the non-spherical shape of the nanoparticle is investigated by the Monte Carlo method. The shape of the non-spherical nanoparticle is approximated by an ellipsoid. The total deposition rate and its flux density distribution along the nanoparticle surface are calculated. As a result, it is shown that the fluxmore » density is not uniform along the surface. It is maximal at the nanoparticle tips.« less

Magnetic field manipulation of spin current in a single-molecule magnet tunnel junction with two-electron Coulomb interaction

NASA Astrophysics Data System (ADS)

Zhang, Chao; Yao, Hui; Nie, Yi-Hang; Liang, Jiu-Qing; Niu, Peng-Bin

2018-04-01

In this work, we study the generation of spin-current in a single-molecule magnet (SMM) tunnel junction with Coulomb interaction of transport electrons and external magnetic field. In the absence of field the spin-up and -down currents are symmetric with respect to the initial polarizations of molecule. The existence of magnetic field breaks the time-reversal symmetry, which leads to unsymmetrical spin currents of parallel and antiparallel polarizations. Both the amplitude and polarization direction of spin current can be controlled by the applied magnetic field. Particularly when the magnetic field increases to a certain value the spin-current with antiparallel polarization is reversed along with the magnetization reversal of the SMM. The two-electron occupation indeed enhances the transport current compared with the single-electron process. However the increase of Coulomb interaction results in the suppression of spin-current amplitude at the electron-hole symmetry point. We propose a scheme to compensate the suppression with the magnetic field.

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains.

PubMed

Makowski, Mariusz; Liwo, Adam; Scheraga, Harold A

2017-01-19

The physics-based potentials of side-chain-side-chain interactions corresponding to pairs composed of charged and polar, polar and polar, charged and hydrophobic, and hydrophobic and hydrophobic side chains have been determined. A total of 144 four-dimensional potentials of mean force (PMFs) of all possible pairs of molecules modeling these pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expressions were then fitted to the PMFs. Depending on the type of interacting sites, the analytical approximation to the PMF is a sum of terms corresponding to van der Waals interactions and cavity-creation involving the nonpolar sections of the side chains and van der Waals, cavity-creation, and electrostatic (charge-dipole or dipole-dipole) interaction energies and polarization energies involving the charged or polar sections of the side chains. The model used in this work reproduces all features of the interacting pairs. The UNited RESidue force field with the new side-chain-side-chain interaction potentials was preliminarily tested with the N-terminal part of the B-domain of staphylococcal protein A (PDBL 1BDD ; a three-α-helix bundle) and UPF0291 protein YnzC from Bacillus subtilis (PDB: 2HEP ; an α-helical hairpin).

Independent Controls of Differently-Polarized Reflected Waves by Anisotropic Metasurfaces

PubMed Central

Ma, Hui Feng; Wang, Gui Zhen; Kong, Gu Sheng; Cui, Tie Jun

2015-01-01

We propose a kind of anisotropic planar metasurface, which has capacity to manipulate the orthogonally-polarized electromagnetic waves independently in the reflection mode. The metasurface is composed of orthogonally I-shaped structures and a metal-grounded plane spaced by a dielectric isolator, with the thickness of about 1/15 wavelength. The normally incident linear-polarized waves will be totally reflected by the metal plane, but the reflected phases of x- and y-polarized waves can be controlled independently by the orthogonally I-shaped structures. Based on this principle, we design four functional devices using the anisotropic metasurfaces to realize polarization beam splitting, beam deflection, and linear-to-circular polarization conversion with a deflection angle, respectively. Good performances have been observed from both simulation and measurement results, which show good capacity of the anisotropic metasurfaces to manipulate the x- and y-polarized reflected waves independently. PMID:25873323

The adsorption, stability and properties of Mn6Cr Single-Molecule-Magnets studied by means of nc-AFM, STM, XAS and Spin-resolved Photoelectron Spectroscopy

NASA Astrophysics Data System (ADS)

Heinzmann, U.; Gryzia, A.; Helmstedt, A.; Dohmeier, N.; Predatsch, H.; Brechling, A.; Müller, N.; Sacher, M.; Hoeke, V.; Krickemeyer, E.; Glaser, T.; Bouvron, S.; Fonin, M.; Neumann, M.

2012-11-01

The ionic single-molecule-magnet [MnIII6CrIII]3 with corresponding three counterions has been deposited on different surfaces and studied with respect to its structure and its electronic and magnetic properties. This is the first time that spin polarization of photoelectrons ejected by means of circularly polarized synchrotron radiation has been measured in a single-molecule-magnet.

Study of open systems with molecules in isotropic liquids

NASA Astrophysics Data System (ADS)

Kondo, Yasushi; Matsuzaki, Masayuki

2018-05-01

We are interested in dynamics of a system in an environment, or an open system. Such phenomena as crossover from Markovian to non-Markovian relaxation and thermal equilibration are of our interest. Open systems have experimentally been studied with ultra cold atoms, ions in traps, optics, and cold electric circuits because well-isolated systems can be prepared here and thus the effects of environments can be controlled. We point out that some molecules solved in isotropic liquid are well isolated and thus they can also be employed for studying open systems in Nuclear Magnetic Resonance (NMR) experiments. First, we provide a short review on related phenomena of open systems that helps readers to understand our motivation. We, then, present two experiments as examples of our approach with molecules in isotropic liquids. Crossover from Markovian to non-Markovian relaxation was realized in one NMR experiment, while relaxation-like phenomena were observed in approximately isolated systems in the other.

Polarization Of Light In The Natural Environment

NASA Astrophysics Data System (ADS)

Coulson, Kinsell L.

1990-01-01

This paper provides a characterization of the fields of light polarization with which the optical designer or user of optical devices in the natural environment must be concerned. After a brief historical outline of the principal developments in polarization theory and observations during the last two centuries, the main emphasis is on the two primary processes responsible for the polarization of light in nature--scattering of light by particles of the atmosphere and reflection from soils, vegetation, snow, and water at the earth's surface. Finally, a seven minute film on polarization effects which can be seen in everyday surroundings will be shown. Scattering by atmospheric particles is responsible for high values of polarization in various atmospheric conditions and at certain scattering geometries. Such scattering particles include molecules of the atmospheric gases, aerosols of dust, haze, and air pollution, water droplets of fog and clouds, and the ice crystals of cirrus. It is seen that development of the theory of scattering by such particles has outstripped the measurements necessary for validation of the theory, a fact which points up the importance of symposia such as the present one. The reverse is true, however, for the polarizing properties of natural surfaces. Only in the case of still water is the theory of reflection adequate to characterize in a quantitative fashion the polarizing effects produced by the reflection of light from such natural surfaces. Polarization of light by reflection from vegetation is of prime importance in a remote sensing context, but much further work is needed to characterize vegetative reflectance for the purpose. The short film on polarization effects provides a good visualization technique and training aid for students interested in the field.

A bioassay-guided fractionation system to identify endogenous small molecules that activate plasma membrane H+-ATPase activity in Arabidopsis.

PubMed

Han, Xiuli; Yang, Yongqing; Wu, Yujiao; Liu, Xiaohui; Lei, Xiaoguang; Guo, Yan

2017-05-17

Plasma membrane (PM) H+-ATPase is essential for plant growth and development. Various environmental stimuli regulate its activity, a process that involves many protein cofactors. However, whether endogenous small molecules play a role in this regulation remains unknown. Here, we describe a bio-guided isolation method to identify endogenous small molecules that regulate PM H+-ATPase activity. We obtained crude extracts from Arabidopsis seedlings with or without salt treatment and then purified them into fractions based on polarity and molecular mass by repeated column chromatography. By evaluating the effect of each fraction on PM H+-ATPase activity, we found that fractions containing the endogenous, free unsaturated fatty acids oleic acid (C18:1), linoleic acid (C18:2), and linolenic acid (C18:3) extracted from salt-treated seedlings stimulate PM H+-ATPase activity. These results were further confirmed by the addition of exogenous C18:1, C18:2, or C18:3 in the activity assay. The ssi2 mutant, with reduced levels of C18:1, C18:2, and C18:3, displayed reduced PM H+-ATPase activity. Furthermore, C18:1, C18:2, and C18:3 directly bound to the C-terminus of the PM H+-ATPase AHA2. Collectively, our results demonstrate that the binding of free unsaturated fatty acids to the C-terminus of PM H+-ATPase is required for its activation under salt stress. The bio-guided isolation model described in this study could enable the identification of new endogenous small molecules that modulate essential protein functions, as well as signal transduction, in plants. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Mechanism and energetics of O and O{sub 2} adsorption on polar and non-polar ZnO surfaces

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

Gorai, Prashun; Seebauer, Edmund G.; Ertekin, Elif, E-mail: ertekin@illinois.edu

2016-05-14

Polar surfaces of semiconducting metal oxides can exhibit structures and chemical reactivities that are distinct from their non-polar surfaces. Using first-principles calculations, we examine O adatom and O{sub 2} molecule adsorption on 8 different known ZnO reconstructions including Zn-terminated (Zn–ZnO) and O-terminated (O–ZnO) polar surfaces, and non-polar surfaces. We find that adsorption tendencies are largely governed by the thermodynamic environment, but exhibit variations due to the different surface chemistries of various reconstructions. The Zn–ZnO surface reconstructions which appear under O-rich and H-poor environments are found to be most amenable to O and O{sub 2} adsorption. We attribute this to themore » fact that on Zn–ZnO, the O-rich environments that promote O adsorption also simultaneously favor reconstructions that involve adsorbed O species. On these Zn–ZnO surfaces, O{sub 2} dissociatively adsorbs to form O adatoms. By contrast, on O–ZnO surfaces, the O-rich conditions required for O or O{sub 2} adsorption tend to promote reconstructions involving adsorbed H species, making further O species adsorption more difficult. These insights about O{sub 2} adsorption on ZnO surfaces suggest possible design rules to understand the adsorption properties of semiconductor polar surfaces.« less

How polarity shapes the destiny of T cells.

PubMed

Russell, Sarah

2008-01-15

The differentiation, activation and expansion of T cells are dictated by their integrated response to a complex array of extracellular signals. Recent studies provide insight into how these signals are integrated and demonstrate a key role for cell shape in many aspects of T-cell signalling. T cells polarise during migration, antigen presentation and cell division to give rise to daughter cells that can have different cell fates. In each case, the polarity of the T cell facilitates this activity. This raises the possibility that adoption of a polarised state acts as a positive feedback mechanism to enhance responses to specific signals. Similarly, in asymmetric division of other cell types, the distribution of different molecules into each daughter can have profound consequences for proliferation, death and differentiation. The mechanisms of polarity regulation are far better understood in cells such as epithelial cells, neurons and neuronal precursors, and the fertilised zygote. With the emerging parallels between polarity in these cells and T cells, we should now be able to elucidate how polarity affects signalling and cell fate determination in T cells.

Isolation of antioxidative phenolic glucosides from lemon juice and their suppressive effect on the expression of blood adhesion molecules.

PubMed

Miyake, Yoshiaki; Mochizuki, Mika; Okada, Miki; Hiramitsu, Masanori; Morimitsu, Yasujiro; Osawa, Toshihiko

2007-08-01

Phenolic glucosides having radical scavenging activity were examined from the fraction eluted with 20% methanol on Amberlite XAD-2 resin applied to lemon (Citrus limon) juice by using reversed phase chromatography. Four phenolic glucosides were identified as 1-feruloyl-beta-D-glucopyranoside, 1-sinapoyl-beta-D-glucopyranoside, 6,8-di-C-glucosylapigenin and 6,8-di-C-glucosyldiosmetin by (1)H-NMR, (13)C-NMR, and MS analyses. They exhibited radical scavenging activity for 1,1-diphenyl-2-picrylhydrazyl (DPPH) and superoxide, although the activity was low in comparison with eriocitrin, a potent antioxidant in lemon fruit, and the eriodictyol of its aglycone. The phenolic compounds in lemon juice were examined for their suppressive effect on the expression of blood adhesion molecules by measuring the expression of intercellular adhesion molecule-1 (ICAM-1) in human umbilical vein endothelial cells (HUVECs) induced by necrosis factor-alpha (TNF-alpha). 6,8-Di-C-glucosylapigenin, apigenin, and diosmentin of the flavones were found to significantly suppress the expression of ICAM-1 at 10 muM (P<0.05). The phenolic glucosides isolated in this study were contained in comparative abundance in daidai (Citrus aurantium) and niihime (Citrus unshiu x Citrus tachibana) among the sour citrus juices.

Polar plot representation of time-resolved fluorescence.

PubMed

Eichorst, John Paul; Wen Teng, Kai; Clegg, Robert M

2014-01-01

Measuring changes in a molecule's fluorescence emission is a common technique to study complex biological systems such as cells and tissues. Although the steady-state fluorescence intensity is frequently used, measuring the average amount of time that a molecule spends in the excited state (the fluorescence lifetime) reveals more detailed information about its local environment. The lifetime is measured in the time domain by detecting directly the decay of fluorescence following excitation by short pulse of light. The lifetime can also be measured in the frequency domain by recording the phase and amplitude of oscillation in the emitted fluorescence of the sample in response to repetitively modulated excitation light. In either the time or frequency domain, the analysis of data to extract lifetimes can be computationally intensive. For example, a variety of iterative fitting algorithms already exist to determine lifetimes from samples that contain multiple fluorescing species. However, recently a method of analysis referred to as the polar plot (or phasor plot) is a graphical tool that projects the time-dependent features of the sample's fluorescence in either the time or frequency domain into the Cartesian plane to characterize the sample's lifetime. The coordinate transformations of the polar plot require only the raw data, and hence, there are no uncertainties from extensive corrections or time-consuming fitting in this analysis. In this chapter, the history and mathematical background of the polar plot will be presented along with examples that highlight how it can be used in both cuvette-based and imaging applications.

Frequency-tunable circular polarization beam splitter using a graphene-dielectric sub-wavelength film.

PubMed

Chen, Tuo; He, Sailing

2014-08-11

Manipulating the circular polarization of light is of great importance in chemistry and biology, as chiral molecules exhibit different physiological properties when exposed to different circularly polarized waves. Here we suggest a graphene/dielectric-stacked structure, which has both the properties of an epsilon-near-zero material and the high Hall conductivity of graphene. The proposed sub-wavelength structure demonstrates efficient manipulation of circular polarization properties of light. In a quite broad frequency range and at a large oblique incidence angle, the present magnetically active structure is transparent for one circularly polarized wave, and opaque for another. Such an effect can be further tuned by changing the magnitude of the applied magnetic field and chemical potential of graphene.

A dual-polarized broadband planar antenna and channelizing filter bank for millimeter wavelengths

NASA Astrophysics Data System (ADS)

O'Brient, Roger; Ade, Peter; Arnold, Kam; Edwards, Jennifer; Engargiola, Greg; Holzapfel, William L.; Lee, Adrian T.; Myers, Michael J.; Quealy, Erin; Rebeiz, Gabriel; Richards, Paul; Suzuki, Aritoki

2013-02-01

We describe the design, fabrication, and testing of a broadband log-periodic antenna coupled to multiple cryogenic bolometers. This detector architecture, optimized here for astrophysical observations, simultaneously receives two linear polarizations with two octaves of bandwidth at millimeter wavelengths. The broad bandwidth signal received by the antenna is divided into sub-bands with integrated in-line frequency-selective filters. We demonstrate two such filter banks: a diplexer with two sub-bands and a log-periodic channelizer with seven contiguous sub-bands. These detectors have receiver efficiencies of 20%-40% and percent level polarization isolation. Superconducting transition-edge sensor bolometers detect the power in each sub-band and polarization. We demonstrate circularly symmetric beam patterns, high polarization isolation, accurately positioned bands, and high optical efficiency. The pixel design is applicable to astronomical observations of intensity and polarization at millimeter through sub-millimeter wavelengths. As compared with an imaging array of pixels measuring only one band, simultaneous measurements of multiple bands in each pixel has the potential to result in a higher signal-to-noise measurement while also providing spectral information. This development facilitates compact systems with high mapping speeds for observations that require information in multiple frequency bands.

Nuclear Spin Locking and Extended Two-Electron Spin Decoherence Time in an InAs Quantum Dot Molecule

NASA Astrophysics Data System (ADS)

Chow, Colin; Ross, Aaron; Steel, Duncan; Sham, L. J.; Bracker, Allan; Gammon, Daniel

2015-03-01

The spin eigenstates for two electrons confined in a self-assembled InAs quantum dot molecule (QDM) consist of the spin singlet state, S, with J = 0 and the triplet states T-, T0 and T+, with J = 1. When a transverse magnetic field (Voigt geometry) is applied, the two-electron system can be initialized to the different states with appropriate laser excitation. Under the excitation of a weak probe laser, non-Lorentzian lineshapes are obtained when the system is initialized to either T- or T+, where T- results in a ``resonance locking'' lineshape while T+ gives a ``resonance avoiding '' lineshape: two different manifestations of hysteresis showing the importance of memory in the system. These observations signify dynamic nuclear spin polarization (DNSP) arising from a feedback mechanism involving hyperfine interaction between lattice nuclei and delocalized electron spins, and Overhauser shift due to nuclear spin polarization. Using pump configurations that generate coherent population trapping, the isolation of the electron spin from the optical excitation shows the stabilization of the nuclear spin ensemble. The dark-state lineshape measures the lengthened electron spin decoherence time, from 1 ns to 1 μs. Our detailed spectra highlight the potential of QDM for realizing a two-qubit gate. This work is supported by NSF, ARO, AFOSR, DARPA, and ONR.

Rationalizing the permeation of polar antibiotics into Gram-negative bacteria.

PubMed

Scorciapino, Mariano Andrea; Acosta-Gutierrez, Silvia; Benkerrou, Dehbia; D'Agostino, Tommaso; Malloci, Giuliano; Samanta, Susruta; Bodrenko, Igor; Ceccarelli, Matteo

2017-03-22

The increasing level of antibiotic resistance in Gram-negative bacteria, together with the lack of new potential drug scaffolds in the pipeline, make the problem of infectious diseases a global challenge for modern medicine. The main reason that Gram-negative bacteria are particularly challenging is the presence of an outer cell-protecting membrane, which is not present in Gram-positive species. Such an asymmetric bilayer is a highly effective barrier for polar molecules. Several protein systems are expressed in the outer membrane to control the internal concentration of both nutrients and noxious species, in particular: (i) water-filled channels that modulate the permeation of polar molecules and ions according to concentration gradients, and (ii) efflux pumps to actively expel toxic compounds. Thus, besides expressing specific enzymes for drugs degradation, Gram-negative bacteria can also resist by modulating the influx and efflux of antibiotics, keeping the internal concentration low. However, there are no direct and robust experimental methods capable of measuring the permeability of small molecules, thus severely limiting our knowledge of the molecular mechanisms that ultimately control the permeation of antibiotics through the outer membrane. This is the innovation gap to be filled for Gram-negative bacteria. This review is focused on the permeation of small molecules through porins, considered the main path for the entry of polar antibiotics into Gram-negative bacteria. A fundamental understanding of how these proteins are able to filter small molecules is a prerequisite to design/optimize antibacterials with improved permeation. The level of sophistication of modern molecular modeling algorithms and the advances in new computer hardware has made the simulation of such complex processes possible at the molecular level. In this work we aim to share our experience and perspectives in the context of a multidisciplinary extended collaboration within the IMI

Rationalizing the permeation of polar antibiotics into Gram-negative bacteria

NASA Astrophysics Data System (ADS)

Scorciapino, Mariano Andrea; Acosta-Gutierrez, Silvia; Benkerrou, Dehbia; D'Agostino, Tommaso; Malloci, Giuliano; Samanta, Susruta; Bodrenko, Igor; Ceccarelli, Matteo

2017-03-01

The increasing level of antibiotic resistance in Gram-negative bacteria, together with the lack of new potential drug scaffolds in the pipeline, make the problem of infectious diseases a global challenge for modern medicine. The main reason that Gram-negative bacteria are particularly challenging is the presence of an outer cell-protecting membrane, which is not present in Gram-positive species. Such an asymmetric bilayer is a highly effective barrier for polar molecules. Several protein systems are expressed in the outer membrane to control the internal concentration of both nutrients and noxious species, in particular: (i) water-filled channels that modulate the permeation of polar molecules and ions according to concentration gradients, and (ii) efflux pumps to actively expel toxic compounds. Thus, besides expressing specific enzymes for drugs degradation, Gram-negative bacteria can also resist by modulating the influx and efflux of antibiotics, keeping the internal concentration low. However, there are no direct and robust experimental methods capable of measuring the permeability of small molecules, thus severely limiting our knowledge of the molecular mechanisms that ultimately control the permeation of antibiotics through the outer membrane. This is the innovation gap to be filled for Gram-negative bacteria. This review is focused on the permeation of small molecules through porins, considered the main path for the entry of polar antibiotics into Gram-negative bacteria. A fundamental understanding of how these proteins are able to filter small molecules is a prerequisite to design/optimize antibacterials with improved permeation. The level of sophistication of modern molecular modeling algorithms and the advances in new computer hardware has made the simulation of such complex processes possible at the molecular level. In this work we aim to share our experience and perspectives in the context of a multidisciplinary extended collaboration within the IMI

Reliable energy level alignment at physisorbed molecule-metal interfaces from density functional theory.

PubMed

Egger, David A; Liu, Zhen-Fei; Neaton, Jeffrey B; Kronik, Leeor

2015-04-08

A key quantity for molecule-metal interfaces is the energy level alignment of molecular electronic states with the metallic Fermi level. We develop and apply an efficient theoretical method, based on density functional theory (DFT) that can yield quantitatively accurate energy level alignment information for physisorbed metal-molecule interfaces. The method builds on the "DFT+Σ" approach, grounded in many-body perturbation theory, which introduces an approximate electron self-energy that corrects the level alignment obtained from conventional DFT for missing exchange and correlation effects associated with the gas-phase molecule and substrate polarization. Here, we extend the DFT+Σ approach in two important ways: first, we employ optimally tuned range-separated hybrid functionals to compute the gas-phase term, rather than rely on GW or total energy differences as in prior work; second, we use a nonclassical DFT-determined image-charge plane of the metallic surface to compute the substrate polarization term, rather than the classical DFT-derived image plane used previously. We validate this new approach by a detailed comparison with experimental and theoretical reference data for several prototypical molecule-metal interfaces, where excellent agreement with experiment is achieved: benzene on graphite (0001), and 1,4-benzenediamine, Cu-phthalocyanine, and 3,4,9,10-perylene-tetracarboxylic-dianhydride on Au(111). In particular, we show that the method correctly captures level alignment trends across chemical systems and that it retains its accuracy even for molecules for which conventional DFT suffers from severe self-interaction errors.

Time-dependent analysis of the mixed-field orientation of molecules without rotational symmetry

NASA Astrophysics Data System (ADS)

Thesing, Linda V.; Küpper, Jochen; González-Férez, Rosario

2017-06-01

We present a theoretical study of the mixed-field orientation of molecules without rotational symmetry. The time-dependent one-dimensional and three-dimensional orientation of a thermal ensemble of 6-chloropyridazine-3-carbonitrile molecules in combined linearly or elliptically polarized laser fields and tilted dc electric fields is computed. The results are in good agreement with recent experimental results of one-dimensional orientation for weak dc electric fields [J. L. Hansen, J. Chem. Phys. 139, 234313 (2013)]. Moreover, they predict that using elliptically polarized laser fields or strong dc fields, three-dimensional orientation is obtained. The field-dressed dynamics of excited rotational states is characterized by highly non-adiabatic effects. We analyze the sources of these non-adiabatic effects and investigate their impact on the mixed-field orientation for different field configurations in mixed-field-orientation experiments.

[Exploring New Drug Targets through the Identification of Target Molecules of Bioactive Natural Products].

PubMed

Arai, Masayoshi

2016-01-01

With the development of cell biology and microbiology, it has become easy to culture many types of animal cells and microbes, and they are frequently used for phenotypic screening to explore medicinal seeds. On the other hand, it is recognized that cells and pathogenic microbes present in pathologic sites and infected regions of the human body display unique properties different from those under general culture conditions. We isolated several bioactive compounds from marine medicinal resources using constructed bioassay-guided separation focusing on the unique changes in the characteristics of cells and pathogenic microbes (Mycobacterium spp.) in the human body under disease conditions. In addition, we also carried out identification studies of target molecules of the bioactive compounds by methods utilizing the gene expression profile, transformants of cells or microbes, synthetic probe molecules of the isolated compounds, etc., since bioactive compounds isolated from the phenotypic screening system often target new molecules. This review presents our phenotypic screening systems, isolation of bioactive compounds from marine medicinal resources, and target identification of bioactive compounds.

Genetic structure of the world's polar bear populations.

PubMed

Paetkau, D; Amstrup, S C; Born, E W; Calvert, W; Derocher, A E; Garner, G W; Messier, F; Stirling, I; Taylor, M K; Wiig, O; Strobeck, C

1999-10-01

We studied genetic structure in polar bear (Ursus maritimus) populations by typing a sample of 473 individuals spanning the species distribution at 16 highly variable microsatellite loci. No genetic discontinuities were found that would be consistent with evolutionarily significant periods of isolation between groups. Direct comparison of movement data and genetic data from the Canadian Arctic revealed a highly significant correlation. Genetic data generally supported existing population (management unit) designations, although there were two cases where genetic data failed to differentiate between pairs of populations previously resolved by movement data. A sharp contrast was found between the minimal genetic structure observed among populations surrounding the polar basin and the presence of several marked genetic discontinuities in the Canadian Arctic. The discontinuities in the Canadian Arctic caused the appearance of four genetic clusters of polar bear populations. These clusters vary in total estimated population size from 100 to over 10 000, and the smallest may merit a relatively conservative management strategy in consideration of its apparent isolation. We suggest that the observed pattern of genetic discontinuities has developed in response to differences in the seasonal distribution and pattern of sea ice habitat and the effects of these differences on the distribution and abundance of seals.

Genetic structure of the world's polar bear populations

USGS Publications Warehouse

Paetkau, David; Amstrup, Steven C.; Born, E.W.; Calvert, W.; Derocher, A.E.; Garner, G.W.; Messier, F.; Stirling, I.; Taylor, M.K.; Wiig, O.; Strobeck, C.

1999-01-01

We studied genetic structure in polar bear (Ursus maritimus) populations by typing a sample of 473 individuals spanning the species distribution at 16 highly variable microsatellite loci. No genetic discontinuities were found that would be consistent with evolutionarily significant periods of isolation between groups. Direct comparison of movement data and genetic data from the Canadian Arctic revealed a highly significant correlation. Genetic data generally supported existing population (management unit) designations, although there were two cases where genetic data failed to differentiate between pairs of populations previously resolved by movement data. A sharp contrast was found between the minimal genetic structure observed among populations surrounding the polar basin and the presence of several marked genetic discontinuities in the Canadian Arctic. The discontinuities in the Canadian Arctic caused the appearance of four genetic clusters of polar bear populations. These clusters vary in total estimated population size from 100 to over 10 000, and the smallest may merit a relatively conservative management strategy in consideration of its apparent isolation. We suggest that the observed pattern of genetic discontinuities has developed in response to differences in the seasonal distribution and pattern of sea ice habitat and the effects of these differences on the distribution and abundance of seals.

Polarization effects in above-threshold ionization with a mid-infrared strong laser field

NASA Astrophysics Data System (ADS)

Kang, Hui-Peng; Xu, Song-Po; Wang, Yan-Lan; Yu, Shao-Gang; Zhao, Xiao-Yun; Hao, Xiao-Lei; Lai, Xuan-Yang; Pfeifer, Thomas; Liu, Xiao-Jun; Chen, Jing; Cheng, Ya; Xu, Zhi-Zhan

2018-05-01

Using a semiclassical approach, we theoretically study the above-threshold ionization of magnesium by intense, mid-infrared laser pulses. The formation of low-energy structures in the photoelectron spectrum is found to be enhanced by comparing with a calculation based on the single-active electron approximation. By performing electron trajectory and recollision-time distribution analysis, we demonstrate that this phenomenon is due to the laser-induced ionic core polarization effects on the recolliding electrons. We also show that the polarization effects should be experimentally detectable. Our finding provides new insight into ultrafast control of strong-field photoionization and imaging of polar molecules.

Optical-Fiber Fluorosensors With Polarized Light Sources

NASA Technical Reports Server (NTRS)

Egalon, Claudio O.; Rogowski, Robert S.

1995-01-01

Chemiluminescent and/or fluorescent molecules in optical-fiber fluorosensors oriented with light-emitting dipoles along transverse axis. Sensor of proposed type captures greater fraction of chemiluminescence or fluorescence and transmits it to photodetector. Transverse polarization increases sensitivity. Basic principles of optical-fiber fluorosensors described in "Making Optical-Fiber Chemical Sensors More Sensitive" (LAR-14525), "Improved Optical-Fiber Chemical Sensors" (LAR-14607), and "Improved Optical-Fiber Temperature Sensors" (LAR-14647).

Long-range interactions between polar bialkali ground-state molecules in arbitrary vibrational levels

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

Vexiau, R.; Lepers, M., E-mail: maxence.lepers@u-psud.fr; Aymar, M.

2015-06-07

We have calculated the isotropic C{sub 6} coefficients characterizing the long-range van der Waals interaction between two identical heteronuclear alkali-metal diatomic molecules in the same arbitrary vibrational level of their ground electronic state X{sup 1}Σ{sup +}. We consider the ten species made up of {sup 7}Li, {sup 23}Na, {sup 39}K, {sup 87}Rb, and {sup 133}Cs. Following our previous work [Lepers et al., Phys. Rev. A 88, 032709 (2013)], we use the sum-over-state formula inherent to the second-order perturbation theory, composed of the contributions from the transitions within the ground state levels, from the transition between ground-state and excited state levels,more » and from a crossed term. These calculations involve a combination of experimental and quantum-chemical data for potential energy curves and transition dipole moments. We also investigate the case where the two molecules are in different vibrational levels and we show that the Moelwyn-Hughes approximation is valid provided that it is applied for each of the three contributions to the sum-over-state formula. Our results are particularly relevant in the context of inelastic and reactive collisions between ultracold bialkali molecules in deeply bound or in Feshbach levels.« less

Mechanism of spontaneous polarization transfer in high-field SABRE experiments

NASA Astrophysics Data System (ADS)

Knecht, Stephan; Kiryutin, Alexey S.; Yurkovskaya, Alexandra V.; Ivanov, Konstantin L.

2018-02-01

We propose an explanation of the previously reported SABRE (Signal Amplification By Reversible Exchange) effect at high magnetic fields, observed in the absence of RF-excitation and relying only on "spontaneous" polarization transfer from parahydrogen (pH2, the H2 molecule in its nuclear singlet spin state) to a SABRE substrate. We propose a detailed mechanism for spontaneous polarization transfer and show that it is comprised of three steps: (i) Generation of the anti-phase Î1zÎ2z spin order of catalyst-bound H2; (ii) spin order conversion Î1zÎ2z → (Î1z +Î2z) due to cross-correlated relaxation, leading to net polarization of H2; (iii) polarization transfer to the SABRE substrate, occurring due to NOE. Formation of anti-phase polarization is due to singlet-to-T0 mixing in the catalyst-bound form of H2, while cross-correlated relaxation originates from fluctuations of dipole-dipole interactions and chemical shift anisotropy. The proposed mechanism is supported by a theoretical treatment, magnetic field-dependent studies and high-field NMR measurements with both pH2 and thermally polarized H2.

Redistribution of Lunar Polar Water to Mid-latitudes and its Role in Forming an OH veneer - Revisited

NASA Technical Reports Server (NTRS)

Farrell, W. M.; Killen, R. M.; Hurley, D. M.; Hodges, R. R.; Halekas, J. S.; Delory, G. T.

2012-01-01

We suggest that energization processes like ion sputtering and impact vaporization can eject/release polar water molecules residing within lunar cold trapped regions with sufficient velocity to allow their redistribution to mid-latitudes. We consider the possibility that these polar-ejected molecules can be an additional (but not dominant) contribution to the water/OH veneer observed as a 3 micron absorption feature at mid-latitudes by Chandrayaan-I, Cassini, and EPOXI. Taking the conservative case that polar water is ejected only from the floor of polar craters with an 0.1 % icy regolith then overall source rates are near 10(exp 18) H20s/s. This outflow amounts to approx 10(exp -7) kg/s of water to be ejected from each pole and is a water source rate that is 10(exp .5 lower than the overall exospheric source rate for all species. Hence, the out-flowing polar water is a perturbation in the overall exosphere composition & dynamics. This polar water 'fountain' model may not fully account for the relatively high concentrations in the mid-latitude water veneer observed in the IR (approx 10-1000 ppm). However, it may account for some part of the veneer. We note that the polar water fountain source rates scale linearly with ice concentration, and larger mass fractions of polar crater water should provide correspondingly larger fractions of water emission out of the poles which then 'spills' on to mid-latitude surfaces.

Solvent dependence of the activation energy of attachment determined by single molecule observations of surfactant adsorption.

PubMed

Honciuc, Andrei; Baptiste, Denver Jn; Campbell, Ian P; Schwartz, Daniel K

2009-07-07

Single-molecule total internal reflection fluorescence microscopy was used to obtain real-time images of fluorescently labeled hexadecanoic (palmitic) acid molecules as they adsorbed at the interface between fused silica and three different solvents: hexadecane (HD), tetrahydrofuran (THF), and water. These solvents were chosen to explore the effect of solvent polarity on the activation energy associated with the attachment rate, i.e., the rate at which molecules were transferred to the surface from the near-surface layer. Direct counting of single-molecule events, made under steady-state conditions at extremely low coverage, provided direct, model-independent measurements of this attachment rate, in contrast with conventional ensemble-averaged methods, which are influenced by bulk transport and competing detachment processes. We found that the attachment rate increased with increasing temperature for all solvents. Arrhenius analyses gave activation energies of 5+/-2 kJ/mol for adsorption from HD, 10+/-2 kJ/mol for adsorption from THF, and 19+/-2 kJ/mol for adsorption from water. These energies increased systematically with the solvent polarity and, therefore, with the expected strength of the solvent-substrate interaction. We hypothesize that the adsorption of amphiphilic solute molecules from solution can be regarded as a competitive exchange between solute molecules and surface-bound solvent. In this scenario, adsorption is an activated process, and the activation energy for attachment is associated with the solvent-substrate interaction energy.

Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells

PubMed Central

McQuilken, Molly; La Riviere, Patrick J.; Occhipinti, Patricia; Verma, Amitabh; Oldenbourg, Rudolf; Gladfelter, Amy S.; Tani, Tomomi

2016-01-01

Regulation of order, such as orientation and conformation, drives the function of most molecular assemblies in living cells but remains difficult to measure accurately through space and time. We built an instantaneous fluorescence polarization microscope, which simultaneously images position and orientation of fluorophores in living cells with single-molecule sensitivity and a time resolution of 100 ms. We developed image acquisition and analysis methods to track single particles that interact with higher-order assemblies of molecules. We tracked the fluctuations in position and orientation of molecules from the level of an ensemble of fluorophores down to single fluorophores. We tested our system in vitro using fluorescently labeled DNA and F-actin, in which the ensemble orientation of polarized fluorescence is known. We then tracked the orientation of sparsely labeled F-actin network at the leading edge of migrating human keratinocytes, revealing the anisotropic distribution of actin filaments relative to the local retrograde flow of the F-actin network. Additionally, we analyzed the position and orientation of septin-GFP molecules incorporated in septin bundles in growing hyphae of a filamentous fungus. Our data indicate that septin-GFP molecules undergo positional fluctuations within ∼350 nm of the binding site and angular fluctuations within ∼30° of the central orientation of the bundle. By reporting position and orientation of molecules while they form dynamic higher-order structures, our approach can provide insights into how micrometer-scale ordered assemblies emerge from nanoscale molecules in living cells. PMID:27679846

Breaking the polar-nonpolar division in solvation free energy prediction.

PubMed

Wang, Bao; Wang, Chengzhang; Wu, Kedi; Wei, Guo-Wei

2018-02-05

Implicit solvent models divide solvation free energies into polar and nonpolar additive contributions, whereas polar and nonpolar interactions are inseparable and nonadditive. We present a feature functional theory (FFT) framework to break this ad hoc division. The essential ideas of FFT are as follows: (i) representability assumption: there exists a microscopic feature vector that can uniquely characterize and distinguish one molecule from another; (ii) feature-function relationship assumption: the macroscopic features, including solvation free energy, of a molecule is a functional of microscopic feature vectors; and (iii) similarity assumption: molecules with similar microscopic features have similar macroscopic properties, such as solvation free energies. Based on these assumptions, solvation free energy prediction is carried out in the following protocol. First, we construct a molecular microscopic feature vector that is efficient in characterizing the solvation process using quantum mechanics and Poisson-Boltzmann theory. Microscopic feature vectors are combined with macroscopic features, that is, physical observable, to form extended feature vectors. Additionally, we partition a solvation dataset into queries according to molecular compositions. Moreover, for each target molecule, we adopt a machine learning algorithm for its nearest neighbor search, based on the selected microscopic feature vectors. Finally, from the extended feature vectors of obtained nearest neighbors, we construct a functional of solvation free energy, which is employed to predict the solvation free energy of the target molecule. The proposed FFT model has been extensively validated via a large dataset of 668 molecules. The leave-one-out test gives an optimal root-mean-square error (RMSE) of 1.05 kcal/mol. FFT predictions of SAMPL0, SAMPL1, SAMPL2, SAMPL3, and SAMPL4 challenge sets deliver the RMSEs of 0.61, 1.86, 1.64, 0.86, and 1.14 kcal/mol, respectively. Using a test set of 94

Pore Polarity and Charge Determine Differential Block of Kir1.1 and Kir7.1 Potassium Channels by Small-Molecule Inhibitor VU590.

PubMed

Kharade, Sujay V; Sheehan, Jonathan H; Figueroa, Eric E; Meiler, Jens; Denton, Jerod S

2017-09-01

VU590 was the first publicly disclosed, submicromolar-affinity (IC 50 = 0.2 μ M), small-molecule inhibitor of the inward rectifier potassium (Kir) channel and diuretic target, Kir1.1. VU590 also inhibits Kir7.1 (IC 50 ∼ 8 μ M), and has been used to reveal new roles for Kir7.1 in regulation of myometrial contractility and melanocortin signaling. Here, we employed molecular modeling, mutagenesis, and patch clamp electrophysiology to elucidate the molecular mechanisms underlying VU590 inhibition of Kir1.1 and Kir7.1. Block of both channels is voltage- and K + -dependent, suggesting the VU590 binding site is located within the pore. Mutagenesis analysis in Kir1.1 revealed that asparagine 171 (N171) is the only pore-lining residue required for high-affinity block, and that substituting negatively charged residues (N171D, N171E) at this position dramatically weakens block. In contrast, substituting a negatively charged residue at the equivalent position in Kir7.1 enhances block by VU590, suggesting the VU590 binding mode is different. Interestingly, mutations of threonine 153 (T153) in Kir7.1 that reduce constrained polarity at this site (T153C, T153V, T153S) make wild-type and binding-site mutants (E149Q, A150S) more sensitive to block by VU590. The Kir7.1-T153C mutation enhances block by the structurally unrelated inhibitor VU714 but not by a higher-affinity analog ML418, suggesting that the polar side chain of T153 creates a barrier to low-affinity ligands that interact with E149 and A150. Reverse mutations in Kir1.1 suggest that this mechanism is conserved in other Kir channels. This study reveals a previously unappreciated role of membrane pore polarity in determination of Kir channel inhibitor pharmacology. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

In vitro characterization of multivalent adhesion molecule 7-based inhibition of multidrug-resistant bacteria isolated from wounded military personnel.

PubMed

Krachler, Anne Marie; Mende, Katrin; Murray, Clinton; Orth, Kim

2012-07-01

Treatment of wounded military personnel at military medical centers is often complicated by colonization and infection of wounds with pathogenic bacteria. These include nosocomially transmitted, often multidrug-resistant pathogens such as Acinetobacter baumannii-calcoaceticus complex, Pseudomonas aeruginosa and extended spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae. We analyzed the efficacy of multivalent adhesion molecule (MAM) 7-based anti-adhesion treatment of host cells against aforementioned pathogens in a tissue culture infection model. Herein, we observed that a correlation between two important hallmarks of virulence, attachment and cytotoxicity, could serve as a useful predictor for the success of MAM7-based inhibition against bacterial infections. Initially, we characterized 20 patient isolates (five from each pathogen mentioned above) in terms of genotypic diversity, antimicrobial susceptibility and important hallmarks of pathogenicity (biofilm formation, attachment to and cytotoxicity toward cultured host cells). All isolates displayed a high degree of genotypic diversity, which was also reflected by large strain-to-strain variability in terms of biofilm formation, attachment and cytotoxicity within each group of pathogen. Using non-pathogenic bacteria expressing MAM7 or latex beads coated with recombinant MAM7 for anti-adhesion treatment, we showed a decrease in cytotoxicity, indicating that MAM7 has potential as a prophylactic agent to attenuate infection by multidrug-resistant bacterial pathogens.

Effect of the dynamic core-electron polarization of CO molecules on high-order harmonic generation

NASA Astrophysics Data System (ADS)

Le, Cam-Tu; Hoang, Van-Hung; Tran, Lan-Phuong; Le, Van-Hoang

2018-04-01

We theoretically investigate the influence of dynamic core-electron polarization (DCeP) of CO molecules on high-order harmonic generation (HHG) by solving the time-dependent Schrödinger equation (TDSE) within the single-active-electron (SAE) approximation. The effect of DCeP is shown to depend strongly on the molecular orientation angle θ . Particularly, compared to the calculations without DCeP, the inclusion of this effect gives rise to an enhancement of harmonic intensity at θ =0° when the electric field aligns along the O-C direction and to a suppression at θ =180° when the field heads in the opposite direction. Meanwhile, when the electric field is perpendicular to the molecular axis, the effect is almost insignificant. The phenomenon is thought to be linked to the ionization process. However, this picture is not completed yet. By solving the TDSE within the SAE approximation and conducting a classical simulation, we are able to obtain the ionization probability as well as the ionization rate and prove that HHG, in fact, receives a major contribution from electrons ionized at only a certain time interval, rather than throughout the whole pulse propagation. Including DCeP, the variation of the ionization rate in this interval highly correlates to that of the HHG intensity. To better demonstrate the origin of this manifestation, we also show the alternation DCeP makes on the effective potential that corresponds to the observed change in the ionization rate and consequently the HHG intensity. Our results confirm previous studies' observations and, more importantly, provide the missing physical explanation. With the role of DCeP now better understood for the entire range of the orientation angle, this effect can be handled more conveniently for calculating the HHG of other targets.

Polarity governed selective amplification of through plane proton shuttling in proton exchange membrane fuel cells.

PubMed

Gautam, Manu; Chattanahalli Devendrachari, Mruthyunjayachari; Thimmappa, Ravikumar; Raja Kottaichamy, Alagar; Pottachola Shafi, Shahid; Gaikwad, Pramod; Makri Nimbegondi Kotresh, Harish; Ottakam Thotiyl, Musthafa

2017-03-15

Graphene oxide (GO) anisotropically conducts protons with directional dominance of in plane ionic transport (σ IP) over the through plane (σ TP). In a typical H 2 -O 2 fuel cell, since the proton conduction occurs through the plane during its generation at the fuel electrode, it is indeed inevitable to selectively accelerate GO's σ TP for advancement towards a potential fuel cell membrane. We successfully achieved ∼7 times selective amplification of GO's σ TP by tuning the polarity of the dopant molecule in its nanoporous matrix. The coexistence of strongly non-polar and polar domains in the dopant demonstrated a synergistic effect towards σ TP with the former decreasing the number of water molecules coordinated to protons by ∼3 times, diminishing the effects of electroosmotic drag exerted on ionic movements, and the latter selectively accelerating σ TP across the catalytic layers by bridging the individual GO planes via extensive host guest H-bonding interactions. When they are decoupled, the dopant with mainly non-polar or polar features only marginally enhances the σ TP, revealing that polarity factors contribute to fuel cell relevant transport properties of GO membranes only when they coexist. Fuel cell polarization and kinetic analyses revealed that these multitask dopants increased the fuel cell performance metrics of the power and current densities by ∼3 times compared to the pure GO membranes, suggesting that the functional group factors of the dopants are of utmost importance in GO-based proton exchange membrane fuel cells.

From isolated light-harvesting complexes to the thylakoid membrane: a single-molecule perspective

NASA Astrophysics Data System (ADS)

Gruber, J. Michael; Malý, Pavel; Krüger, Tjaart P. J.; Grondelle, Rienk van

2018-01-01

The conversion of solar radiation to chemical energy in plants and green algae takes place in the thylakoid membrane. This amphiphilic environment hosts a complex arrangement of light-harvesting pigment-protein complexes that absorb light and transfer the excitation energy to photochemically active reaction centers. This efficient light-harvesting capacity is moreover tightly regulated by a photoprotective mechanism called non-photochemical quenching to avoid the stress-induced destruction of the catalytic reaction center. In this review we provide an overview of single-molecule fluorescence measurements on plant light-harvesting complexes (LHCs) of varying sizes with the aim of bridging the gap between the smallest isolated complexes, which have been well-characterized, and the native photosystem. The smallest complexes contain only a small number (10-20) of interacting chlorophylls, while the native photosystem contains dozens of protein subunits and many hundreds of connected pigments. We discuss the functional significance of conformational dynamics, the lipid environment, and the structural arrangement of this fascinating nano-machinery. The described experimental results can be utilized to build mathematical-physical models in a bottom-up approach, which can then be tested on larger in vivo systems. The results also clearly showcase the general property of biological systems to utilize the same system properties for different purposes. In this case it is the regulated conformational flexibility that allows LHCs to switch between efficient light-harvesting and a photoprotective function.

Isolated Polynucleotides and Methods of Promoting a Morphology in a Fungus

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

Lasure, Linda L; Dai, Ziyu

2008-10-21

The invention includes isolated polynucleotide molecules that are differentially expressed in a native fungus exhibiting a first morphology relative to the native fungus exhibiting a second morphology. The invention includes a method of enhancing a bioprocess utilizing a fungus. A transformed fungus is produced by transforming a fungus with a recombinant polynucleotide molecule. The recombinant polynucleotide molecule contains an isolated polynucleotide sequence linked operably to a promoter. The polynucleotide sequence is expressed to promote a first morphology. The first morphology of the transformed fungus enhances a bioprocess relative to the bioprocess utilizing a second morphology.

Novel nuclear magnetic resonance techniques for studying biological molecules

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

Laws, David Douglas

2000-06-01

Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. Inmore » this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone (Φ/Ψ) dihedral angles by comparing experimentally determined 13C a, chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized xenon are discussed, as well as the prospects for using optically pumped xenon as a polarizing solvent. In addition, a detailed study of the structure of PrP 89-143 is presented. PrP 89-143 is a 54 residue fragment of the prion proteins which, upon mutation and aggregation, can induce prion diseases in transgenic mice. Whereas the structure of the wild-type PrP 89-143 is a generally unstructured mixture of α-helical and β-sheet conformers in the solid state, the aggregates formed from the PrP 89-143 mutants appear to be mostly β-sheet.« less

Isolation of Protein-Associated Circular DNA from Healthy Cattle Serum

PubMed Central

Funk, Mathis; Gunst, Karin; Lucansky, Vincent; Müller, Hermann; zur Hausen, Harald

2014-01-01

Three replication-competent single-stranded DNA molecules sharing nucleotide similarity to transmissible spongiform encephalopathy (TSE)-associated isolate Sphinx 2.36 were isolated from healthy bovine serum. PMID:25169856

Development of a surface isolation estimation technique suitable for application of polar orbiting satellite data

NASA Technical Reports Server (NTRS)

Davis, P. A.; Penn, L. M. (Principal Investigator)

1981-01-01

A technique is developed for the estimation of total daily insolation on the basis of data derivable from operational polar-orbiting satellites. Although surface insolation and meteorological observations are used in the development, the algorithm is constrained in application by the infrequent daytime polar-orbiter coverage.

Characterization and origin of polar dissolved organic matter from the Great Salt Lake

USGS Publications Warehouse

Leenheer, J.A.; Noyes, T.I.; Rostad, C.E.; Davisson, M.L.

2004-01-01

Polar dissolved organic matter (DOM) was isolated from a surface-water sample from the Great Salt Lake by separating it from colloidal organic matter by membrane dialysis, from less-polar DOM fractions by resin sorbents, and from inorganic salts by a combination of sodium cation exchange followed by precipitation of sodium salts by acetic acid during evaporative concentration. Polar DOM was the most abundant DOM fraction, accounting for 56% of the isolated DOM. Colloidal organic matter was 14C-age dated to be about 100% modern carbon and all of the DOM fractions were 14C-age dated to be between 94 and 95% modern carbon. Average structural models of each DOM fraction were derived that incorporated quantitative elemental and infrared, 13C-NMR, and electrospray/mass spectrometric data. The polar DOM model consisted of open-chain N-acetyl hydroxy carboxylic acids likely derived from N-acetyl heteropolysaccharides that constituted the colloidal organic matter. The less polar DOM fraction models consisted of aliphatic alicyclic ring structures substituted with carboxyl, hydroxyl, ether, ester, and methyl groups. These ring structures had characteristics similar to terpenoid precursors. All DOM fractions in the Great Salt Lake are derived from algae and bacteria that dominate DOM inputs in this lake.

Receptor clustering drives polarized assembly of ankyrin.

PubMed

Jefford, G; Dubreuil, R R

2000-09-08

Expression of the L1 family cell adhesion molecule neuroglian in Drosophila S2 cells leads to cell aggregation and polarized ankyrin accumulation at sites of cell-cell contact. Thus neuroglian adhesion generates a spatial cue for polarized assembly of ankyrin and the spectrin cytoskeleton. Here we characterized a chimera of the extracellular and transmembrane domains of rat CD2 fused to the cytoplasmic domain of neuroglian. The chimera was used to test the hypothesis that clustering of neuroglian at sites of adhesion generates the signal that activates ankyrin binding. Abundant expression of the chimera at the plasma membrane was not a sufficient cue to drive ankyrin assembly, since ankyrin remained diffusely distributed throughout the cytoplasm of CD2-neuroglian-expressing cells. However, ankyrin became highly enriched at sites of antibody-induced capping of CD2-neuroglian. Spectrin codistributed with ankyrin at capped sites. A green fluorescent protein-tagged ankyrin was used to monitor ankyrin distribution in living cells. Enhanced green fluorescent protein-ankyrin behaved identically to antibody-stained endogenous ankyrin, proving that the polarized accumulation of ankyrin was not an artifact of fixing and staining cells. We propose a model in which clustering of neuroglian induces a conformational change in the cytoplasmic domain that drives polarized assembly of the spectrin cytoskeleton.

Inducing electric polarization in ultrathin insulating layers

NASA Astrophysics Data System (ADS)

Martinez-Castro, Jose; Piantek, Marten; Persson, Mats; Serrate, David; Hirjibehedin, Cyrus F.

Studies of ultrathin polar oxide films have attracted the interest of researchers for a long time due to their different properties compared to bulk materials. However they present several challenges such as the difficulty in the stabilization of the polar surfaces and the limited success in tailoring their properties. Moreover, recently developed Van der Waals materials have shown that the stacking of 2D-layers trigger new collective states thanks to the interaction between layers. Similarly, interface phenomena emerge in polar oxides, like induced ferroelectricity. This represents a promising way for the creation of new materials with customized properties that differ from those of the isolated layers. Here we present a new approach for the fabrication and study of atomically thin insulating films. We show that the properties of insulating polar layers of sodium chloride (NaCl) can be engineered when they are placed on top of a charge modulated template of copper nitride (Cu2N). STM studies carried out in ultra-high vacuum and at low temperatures over NaCl/Cu2N/Cu(001) show that we are able to build up and stabilize interfaces of polar surface at the limit of one atomic layer showing new properties not present before at the atomic scale.

Polarization Catastrophe Contributing to Rotation and Tornadic Motion in Cumulo-Nimbus Clouds

NASA Astrophysics Data System (ADS)

Handel, P. H.

2007-05-01

When the concentration of sub-micron ice particles in a cloud exceeds 2.5E21 per cubic cm, divided by the squared average number of water molecules per crystallite, the polarization catastrophe occurs. Then all ice crystallites nucleated on aerosol dust particles align their dipole moments in the same direction, and a large polarization vector field is generated in the cloud. Often this vector field has a radial component directed away from the vertical axis of the cloud. It is induced by the pre-existing electric field caused by the charged screening layers at the cloud surface, the screening shell of the cloud. The presence of a vertical component of the magnetic field of the earth creates a density of linear momentum G=DxB in the azimuthal direction, where D=eE+P is the electric displacement vector and e is the vacuum permittivity. This linear momentum density yields an angular momentum density vector directed upward in the nordic hemisphere, if the polarization vector points away from the vertical axis of the cloud. When the cloud becomes colloidally unstable, the crystallites grow beyond the size limit at which they still could carry a large ferroelectric saturation dipole moment, and the polarization vector quickly disappears. Then the cloud begins to rotate with an angular momentum that has the same direction. Due to the large average number of water molecules in a crystallite, the polarization catastrophe (PC) is present in practically all clouds, and is compensated by masking charges. In cumulo-nimbus (thunder-) clouds the collapse of the PC is rapid, and the masking charges lead to lightning, and in the upper atmosphere also to sprites, elves, and blue jets. In stratus clouds, however, the collapse is slow, and only leads to reverse polarity in dissipating clouds (minus on the bottom), as compared with growing clouds (plus on the bottom, because of the excess polarization charge). References: P.H. Handel: "Polarization Catastrophe Theory of Cloud

Contracted or uncontracted polarization functions? Comment on Dunning's correlation-consistent basis sets

NASA Astrophysics Data System (ADS)

Hashimoto, Tomohiro; Hirao, Kimihiko; Tatewaki, Hiroshi

1997-07-01

For the sake of computational economy, the polarization functions given by Dunning are contracted by multiconfigurational SCF calculations for H, B, C, N, O, F and Ne atoms. For the first-row atoms, B through Ne, the generated contracted polarization functions are ( 2 d/1 d) and ( 3 d/2 d) and for H they are ( 2 p/1 p), ( 3 p/1 p), and ( 3 p/2 p) where the numbers before and after the slash are the numbers of uncontracted and contracted polarization functions. Numerical examples on some diatomic molecules and benzene illustrate a large improvement in going from ( 1 d/1 dto ( 2 d/1 d) for various molecular properties.

Indistinguishable near-infrared single photons from an individual organic molecule

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

Trebbia, Jean-Baptiste; Tamarat, Philippe; Lounis, Brahim

2010-12-15

By using the zero-phonon line emission of an individual organic molecule, we realized a source of indistinguishable single photons in the near infrared. A Hong-Ou-Mandel interference experiment is performed and a two-photon coalescence probability higher than 50% at 2 K is obtained. The contribution of the temperature-dependent dephasing processes to the two-photon interference contrast is studied. We show that the molecule delivers nearly ideal indistinguishable single photons at the lowest temperatures when the dephasing is nearly lifetime limited. This source is used to generate postselected polarization-entangled photon pairs as a test bench for applications in quantum information.

Dual band metamaterial perfect absorber based on artificial dielectric "molecules".

PubMed

Liu, Xiaoming; Lan, Chuwen; Li, Bo; Zhao, Qian; Zhou, Ji

2016-07-13

Dual band metamaterial perfect absorbers with two absorption bands are highly desirable because of their potential application areas such as detectors, transceiver system, and spectroscopic imagers. However, most of these dual band metamaterial absorbers proposed were based on resonances of metal patterns. Here, we numerically and experimentally demonstrate a dual band metamaterial perfect absorber composed of artificial dielectric "molecules" with high symmetry. The artificial dielectric "molecule" consists of four "atoms" of two different sizes corresponding to two absorption bands with near unity absorptivity. Numerical and experimental absorptivity verify that the dual-band metamaterial absorber is polarization insensitive and can operate in wide-angle incidence.

Non-equilibrium transport and spin dynamics in single-molecule magnets

NASA Astrophysics Data System (ADS)

Moldoveanu, V.; Dinu, I. V.; Tanatar, B.

2015-11-01

The time-dependent transport through single-molecule magnets (SMM) coupled to magnetic or non-magnetic electrodes is studied in the framework of the generalized Master equation (GME) method. We calculate the transient currents which develop when the molecule is smoothly coupled to the source and drain electrodes. The signature of the electrically induced magnetic switching on these transient currents is investigated. Our simulations show that the magnetic switching of the molecular spin can be read indirectly from the transient currents if one lead is magnetic and it is much faster if the leads have opposite spin polarizations. We identify effects of the transverse anisotropy on the dynamics of molecular states.

Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling

PubMed Central

Wabnik, Krzysztof; Kleine-Vehn, Jürgen; Balla, Jozef; Sauer, Michael; Naramoto, Satoshi; Reinöhl, Vilém; Merks, Roeland M H; Govaerts, Willy; Friml, Jiří

2010-01-01

Plant development is exceptionally flexible as manifested by its potential for organogenesis and regeneration, which are processes involving rearrangements of tissue polarities. Fundamental questions concern how individual cells can polarize in a coordinated manner to integrate into the multicellular context. In canalization models, the signaling molecule auxin acts as a polarizing cue, and feedback on the intercellular auxin flow is key for synchronized polarity rearrangements. We provide a novel mechanistic framework for canalization, based on up-to-date experimental data and minimal, biologically plausible assumptions. Our model combines the intracellular auxin signaling for expression of PINFORMED (PIN) auxin transporters and the theoretical postulation of extracellular auxin signaling for modulation of PIN subcellular dynamics. Computer simulations faithfully and robustly recapitulated the experimentally observed patterns of tissue polarity and asymmetric auxin distribution during formation and regeneration of vascular systems and during the competitive regulation of shoot branching by apical dominance. Additionally, our model generated new predictions that could be experimentally validated, highlighting a mechanistically conceivable explanation for the PIN polarization and canalization of the auxin flow in plants. PMID:21179019

Live Cell Genomics: RNA Exon-Specific RNA-Binding Protein Isolation.

PubMed

Bell, Thomas J; Eberwine, James

2015-01-01

RNA-binding proteins (RBPs) are essential regulatory proteins that control all modes of RNA processing and regulation. New experimental approaches to isolate these indispensable proteins under in vivo conditions are needed to advance the field of RBP biology. Historically, in vitro biochemical approaches to isolate RBP complexes have been useful and productive, but biological relevance of the identified RBP complexes can be imprecise or erroneous. Here we review an inventive experimental to isolate RBPs under the in vivo conditions. The method is called peptide nucleic acid (PNA)-assisted identification of RBP (PAIR) technology and it uses cell-penetrating peptides (CPPs) to deliver photo-activatible RBP-capture molecule to the cytoplasm of the live cells. The PAIR methodology provides two significant advantages over the most commonly used approaches: (1) it overcomes the in vitro limitation of standard biochemical approaches and (2) the PAIR RBP-capture molecule is highly selective and adaptable which allows investigators to isolate exon-specific RBP complexes. Most importantly, the in vivo capture conditions and selectivity of the RBP-capture molecule yield biologically accurate and relevant RBP data.

Influence of polarity of solvents on IR absorption and Raman spectra of ascorbic acid

NASA Astrophysics Data System (ADS)

Kutsenko, S. A.; Danyaeva, Y. S.; Maximova, S. V.

2018-04-01

The results of numerical calculations of IR absorption and Raman spectra of ascorbic acid in polar and nonpolar solutions are presented. The dependence of the change in the total energy and the dipole moment of the molecule on the characteristics of the solvents was investigated using the two solvation models. Spectral bands and the corresponding structural groups of the molecule are found, the characteristics of which are most vulnerable to solvents.

Protein distribution in lupin protein isolates from Lupinus angustifolius L. prepared by various isolation techniques.

PubMed

Muranyi, Isabel S; Volke, Daniela; Hoffmann, Ralf; Eisner, Peter; Herfellner, Thomas; Brunnbauer, Markus; Koehler, Peter; Schweiggert-Weisz, Ute

2016-09-15

Differences in the protein distribution of various protein isolates from Lupinus angustifolius L. Vitabor were identified as affected by the isolation procedure (alkaline and/or salt-induced extraction followed by isoelectric and/or dilutive precipitation). Protein isolates extracted in alkaline solution showed higher protein yields (26.4-31.7%) compared to salt-induced extraction (19.8-30.0%) or combined alkaline and salt-induced extraction (23.3-25.6%). Chemical variations among the protein isolates especially occurred within the albumins. Protein isolates precipitated isoelectrically showed the highest contents, whereas protein isolates precipitated by dilutive showed the lowest contents of conglutin δ. Furthermore, the alkaline subunits of conglutin α and conglutin γ decreased during alkaline extraction compared to salt-induced extraction. A decrease in protein-bound polar and basic amino acids was shown after protein isolation. In contrast, the amounts of nonpolar, aliphatic, aromatic, hydroxylated and sulfur-rich amino acids were higher in the lupin protein isolates compared to the lupin flakes. However, the functional side chains could not be related to the specific molecular arrangements of the protein isolates, as a similar amino acid composition was found among the protein isolates. Copyright © 2016 Elsevier Ltd. All rights reserved.

Using elaborative interrogation to induce characteristics of polar and nonpolar solvents from animations of their molecular structures

NASA Astrophysics Data System (ADS)

Ems-Wilson, Janice

This study concerned (a) how general chemistry students learn to classify solvent polarity from animated molecules, (b) whether peer interaction increases the number of correct classifications, and (c) whether language, academic ability, logical thinking ability, or prior knowledge interact with rate of learning or posttest performance. Two types of interaction were compared, group discussion and elaborative interrogation. The study rested on three assumptions: (a) animated molecules are appropriate for learning the concept of solvent polarity, (b) question stems and a guided interrogation enhance learning of a visual concept, (c) general chemistry students can induce the concept of solvent polarity from animated molecules when no guiding cues, either visual or verbal, are given. After a review of molecular geometry and bonding theories, students were presented with four trials of ten animated molecular structures. Ten three-to-five minute discussions were distributed among the four trials. Prior to the trials the experimental group received a 45-minute training session on elaborative interrogation; the topic was what happens on the molecular level when a carbonated beverage is opened. The control group received a 45-minute expository lecture on the same carbonated beverage topic. Participants were given a four-part posttest immediately following the trials. Results of the study suggest that most students tend to classify the solvent polarity of animated molecules based on certain structural features using a prototype or feature-frequency categorization strategy. Elaborative interrogation did not show a significant effect on the rate of learning or on the performance of learners on posttest measures of recall and comprehension. The experimental group noted a significantly greater number and range of types of features, and offered higher quality generalizations and explanations of their polarity classification procedure. Finally, the results implied that learning

Vibrational cross sections for positron scattering by nitrogen molecules

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

Mazon, K. T.; Tenfen, W.; Michelin, S. E.

2010-09-15

We present a systematic study of low-energy positron collision with nitrogen molecules. Vibrational elastic and excitation cross sections are calculated using the multichannel version of the continued fractions method in the close-coupling scheme for the positron incident energy up to 20 eV. The interaction potential is treated within the static-correlation-polarization approximation. The comparison of our calculated data with existing theoretical and experimental results is encouraging.

Mechanism of spontaneous polarization transfer in high-field SABRE experiments.

PubMed

Knecht, Stephan; Kiryutin, Alexey S; Yurkovskaya, Alexandra V; Ivanov, Konstantin L

2018-02-01

We propose an explanation of the previously reported SABRE (Signal Amplification By Reversible Exchange) effect at high magnetic fields, observed in the absence of RF-excitation and relying only on "spontaneous" polarization transfer from parahydrogen (pH 2 , the H 2 molecule in its nuclear singlet spin state) to a SABRE substrate. We propose a detailed mechanism for spontaneous polarization transfer and show that it is comprised of three steps: (i) Generation of the anti-phase Î 1z Î 2z spin order of catalyst-bound H 2 ; (ii) spin order conversion Î 1z Î 2z →(Î 1z +Î 2z ) due to cross-correlated relaxation, leading to net polarization of H 2 ; (iii) polarization transfer to the SABRE substrate, occurring due to NOE. Formation of anti-phase polarization is due to singlet-to-T 0 mixing in the catalyst-bound form of H 2 , while cross-correlated relaxation originates from fluctuations of dipole-dipole interactions and chemical shift anisotropy. The proposed mechanism is supported by a theoretical treatment, magnetic field-dependent studies and high-field NMR measurements with both pH 2 and thermally polarized H 2 . Copyright © 2017 Elsevier Inc. All rights reserved.

Ultra-Wideband, Dual-Polarized, Beam-Steering P-Band Array Antenna

NASA Technical Reports Server (NTRS)

duToit, Cornelis

2014-01-01

A dual-polarized, wide-bandwidth (200 MHz for one polarization, 100 MHz for the orthogonal polarization) antenna array at P-band was designed to be driven by NASA's EcoSAR digital beam former. EcoSAR requires two wide P-band antenna arrays mounted on the wings of an aircraft, each capable of steering its main beam up to 35deg off-boresight, allowing the twin radar beams to be steered at angles to the flight path. The science requirements are mainly for dual-polarization capability and a wide bandwidth of operation of up to 200 MHz if possible, but at least 100 MHz with high polarization port isolation and low cross-polarization. The novel design geometry can be scaled with minor modifications up to about four times higher or down to about half the current design frequencies for any application requiring a dual-polarized, wide-bandwidth steerable antenna array. EcoSAR is an airborne interferometric P-band synthetic aperture radar (SAR) research application for studying two- and three-dimensional fine-scale measurements of terrestrial ecosystem structure and biomass, which will ultimately aid in the broader study of the carbon cycle and climate change. The two 2×8 element Pband antenna arrays required by the system will be separated by a baseline of about 25 m, allowing for interferometry measurements. The wide 100-to- 200-MHz bandwidth dual-polarized beams employed will allow the determination of the amount of biomass and even tree height on the ground. To reduce the size of the patches along the boresight dimension in order to fit them into the available space, two techniques were employed. One technique is to add slots along the edges of each patch where the main electric currents are expected to flow, and the other technique is to bend the central part of the patch away from the ground plane. The latter also facilitates higher mechanical rigidity. The high port isolation of more than 40 dB was achieved by employing a highly symmetrical feed mechanism for each

Sources and sinks of methane beneath polar ice

NASA Astrophysics Data System (ADS)

Priscu, J. C.; Adams, H. E.; Hand, K. P.; Dore, J. E.; Matheus-Carnevali, P.; Michaud, A. B.; Murray, A. E.; Skidmore, M. L.; Vick-Majors, T.

2014-12-01

Several icy moons of the outer solar system carry subsurface oceans containing many times the volume of liquid water on Earth and may provide the greatest volume of habitable space in our solar system. Functional sub-ice polar ecosystems on Earth provide compelling models for the habitability of extraterrestrial sub-ice oceans. A key feature of sub-ice environments is that most of them receive little to no solar energy. Consequently, organisms inhabiting these environments must rely on chemical energy to assimilate either carbon dioxide or organic molecules to support their metabolism. Methane can be utilized by certain bacteria as both a carbon and energy source. Isotopic data show that methane in Earth's polar lakes is derived from both biogenic and thermogenic sources. Thermogenic sources of methane in the thermokarst lakes of the north slope of Alaska yield supersaturated water columns during winter ice cover that support active populations of methanotrophs during the polar night. Methane in the permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica varies widely in concentration and is produced either by contemporary methanogenesis or is a relic from subglacial flow. Rate measurements revealed that microbial methane oxidation occurs beneath the ice in both the arctic and Antarctic lakes. The first samples collected from an Antarctic subglacial environment beneath 800 m of ice (Subglacial Lake Whillans) revealed an active microbial ecosystem that has been isolated from the atmosphere for many thousands of years. The sediments of Lake Whillans contained high levels of methane with an isotopic signature that indicates it was produced via methanogenesis. The source of this methane appears to be from the decomposition of organic carbon deposited when this region of Antarctica was covered by the sea. Collectively, data from these sub-ice environments show that methane transformations play a key role in microbial community metabolism. The discovery of

Circularly polarized harmonic generation by intense bicircular laser pulses: electron recollision dynamics and frequency dependent helicity

NASA Astrophysics Data System (ADS)

Bandrauk, André D.; Mauger, François; Yuan, Kai-Jun

2016-12-01

Numerical solutions of time-dependent Schrödinger equations for one and two electron cyclic molecules {{{H}}}nq+ exposed to intense bichromatic circularly polarized laser pulses of frequencies {ω }1 and {ω }2, such that {ω }1/{ω }2={n}1/{n}2 (integer) produce circularly polarized high order harmonics with a cut-off recollision maximum energy at and greater than the linear polarization law (in atomic units) {N}m{ω }1={I}p+3.17{U}p, where I p is the ionization potential and {U}p={(2{E}0)}2/4{ω }2 is the ponderomotive energy defined by the field E 0 (intensity I={{cE}}02/8π ) from each pulse and mean frequency ω =({ω }1+{ω }2)/2 . An electron recollision model in a rotating frame at rotating frequency {{Δ }}ω =({ω }1-{ω }2)/2 predicts this simple result as a result of recollision dynamics in a combination of bichromatic circularly polarized pulses. The harmonic helicities and their intensities are shown to depend on compatible symmetries of the net pulse electric fields with that of the molecules.

Developments in Coherent Perfect Polarization Rotation

NASA Astrophysics Data System (ADS)

Crescimanno, Michael; Andrews, James; Zhou, Chaunhong; Baker, Michael

2015-05-01

Coherent Perfect Polarization Rotation (CPR) is a useful technique akin to Coherent Perfect Absorption (CPA, also known as the anti-laser) but that results in very high efficiency optical mode conversion. We describe the analysis of recent experimental data from our CPR testbed, the use of CPR in miniaturizing optical isolators and CPR phenomena in non-linear optics. Work supported by the N.S.F. under Grant No. ECCS-1360725.

Ab Initio Cluster Calculations for the Adsorption of Small Molecules on Oxide Surfaces - from Single Molecules to Monolayers

NASA Astrophysics Data System (ADS)

Pykavy, M.; Staemmler, V.; Rittner, F.

2000-04-01

Quantum chemical ab initio cluster calculations were performed for the adsorption of small molecules on metal oxide surfaces. Two systems were studied in detail: The adsorption of N2 on the (110) surface plane of TiO2 (rutile) and the adsorption of CO on the polar (0001) surface of Cr2O3. In both cases a full five-dimensional potential for the interaction of a single molecule with the respective surface was calculated. For N2/TiO2 (110) the minimum was found for the end-on adsorption of N2 atop a coordinately unsaturated surface Ti atom, with an adsorption energy of (35 ± 5) kJ/mol. In the case of CO/Cr2O3 (0001) the CO molecule is adsorbed strongly tilted (almost side-on) along a line connecting two Cr3+ ions at the surface; the calculated adsorption energy is 22 kJ/mol. In conjunction with empirical pair potentials for the N2/N2 and CO/CO interaction in the gas phase, Monte Carlo simulations were carried out to determine adsorption isotherms and the geometric structure of adsorbed monolayers.

The characteristics of polyimide photoalignment layer with chalcone derivatives produced by linear polarized UV light

NASA Astrophysics Data System (ADS)

Jung, Kyoung Hoon; Hyun, Soon-Young; Song, Dong-Mee; Shin, Dong-Myung

2003-01-01

The photoalignment of liquid crystal (LC) molecules located onto polyimide films with chalcone derivatives using linearly polarized UV (LPUV) light is investigated. The LPUV light irradiation generated dimerization products of the chalcones followed by isomerization of the chalcone derivatives. The alignment directions of LC molecules were either homeotropic or planar with respect to plane of polyimide film, depending upon the alkyl chain length attached on the chalcones.

Synthesis of biphenyl derivative and its application as dichroic materials in poly (vinyl alcohol) polarizing films

NASA Astrophysics Data System (ADS)

Shahab, Siyamak; Almodarresiyeh, Hora A.; Filippovich, Ljudmila; Kumar, Rakesh; Darroudi, Mahdieh; Hajikolaee, Fatemeh Haji

2016-03-01

In the present work, first time on the basis of polyvinyl alcohol (PVA) and new designed structure (Potassium 2,2‧-([1,1‧-biphenyl]-4,4‧-diylbis(azanediyl))diacetate) (I) thermostable polarizing film was created. The structure (I) was first modeled and then synthesized and obtained polarizing film absorbing at λmax = 300 nm used for electronic applications. Polarizing efficiency (PE) of polarizing film is 96% at stretching degree (Rs) 4.0. On the basis of PVA, Potassium 2,2‧-([1,1‧-biphenyl]-4,4‧-diylbis(azanediyl))diacetate (I), Sodium 2-hydroxy-5-((2-methoxy-4-((4-sulfonatophenyl)diazenyl)phenyl)diazenyl)benzoate (II) and commercial dye (Congo Red) thermostable polarizing film for wide spectral range of spectrum (λmax = 288-561 nm) was developed. During the work it was established that oriented PVA-films is phenomenon of anisotropy of thermal conductivity (λ||/λ⊥). It is very important for creation of thermostable polarizing films. Thermal conductivity in a direction of orientation (λ||) is higher than in a direction perpendicular orientations (λ⊥). The optimization of the molecule (1) was carried out by Density Functional Theory (DFT) using B3LYP/6-311 + G* method. Electronic absorption spectrum of the molecule (I) in dimethylformamide (DMF) solution was calculated using TDB3LYP/6-311 + G* level. The nature of absorption bands in the UV spectral region was interpreted.

Ozone decrease outside Arctic polar vortex due to polar vortex processing in 1997

NASA Astrophysics Data System (ADS)

Akiyoshi, H.; Sugata, S.; Yoshiki, M.; Sugita, T.

2006-11-01

We examine the effect of polar vortex processing on ozone concentrations outside the 1997 Arctic polar vortex. The Arctic vortex in this year was well isolated, cold, and circumpolar, and it broke up unusually late. However, time threshold diagnostics (TTD) analysis using a middle vortex boundary defined by the first derivative of the equivalent latitude gradient of potential vorticity and calculations using the nudging chemical transport model (CTM) of the Center for Climate System Research/National Institute for Environmental Studies (CCSR/NIES) show that there were intermittently several relatively large transport events from the vortex to the outside region in the lower stratosphere, with timescales and spatial scales that can be resolved at T42 CTM horizontal resolution (2.8° by 2.8° grid). These intermittent outflow events of polar air are also identified in TTD analysis using an outer vortex boundary defined by the second derivative of potential vorticity and a boundary defined by the N2O concentration. These intermittent events had a significant effect on the ozone concentration outside the vortex near the boundary in this year. A CTM calculation with a polar chemical ozone tracer shows that the effect on the ozone concentration outside the polar vortex near the vortex boundary in the equivalent latitude band of 55°-65°N and 450 K is 0.3 ppmv (15-20% of the ozone concentration at this height) and that on the total ozone is 12-15 Dobson units (1 DU = 0.001 atm cm) (3-4% of the total ozone) by the end of April just before the final vortex breakup. The effect in the equivalent latitude band of 30°-60°N is much smaller, with a reduction of 2 DU at the end of March and 4 DU by the end of April (less than 1% of the total ozone). The effect is about the half if we use the inner boundary or a boundary of 73°N equivalent latitude for the polar tracer calculations. The CTM calculations also show that these polar vortex processing effects might be masked at

Molecular frame photoemission by a comb of elliptical high-order harmonics: a sensitive probe of both photodynamics and harmonic complete polarization state.

PubMed

Veyrinas, K; Gruson, V; Weber, S J; Barreau, L; Ruchon, T; Hergott, J-F; Houver, J-C; Lucchese, R R; Salières, P; Dowek, D

2016-12-16

Due to the intimate anisotropic interaction between an XUV light field and a molecule resulting in photoionization (PI), molecular frame photoelectron angular distributions (MFPADs) are most sensitive probes of both electronic/nuclear dynamics and the polarization state of the ionizing light field. Consequently, they encode the complex dipole matrix elements describing the dynamics of the PI transition, as well as the three normalized Stokes parameters s 1 , s 2 , s 3 characterizing the complete polarization state of the light, operating as molecular polarimetry. The remarkable development of advanced light sources delivering attosecond XUV pulses opens the perspective to visualize the primary steps of photochemical dynamics in time-resolved studies, at the natural attosecond to few femtosecond time-scales of electron dynamics and fast nuclear motion. It is thus timely to investigate the feasibility of measurement of MFPADs when PI is induced e.g., by an attosecond pulse train (APT) corresponding to a comb of discrete high-order harmonics. In the work presented here, we report MFPAD studies based on coincident electron-ion 3D momentum imaging in the context of ultrafast molecular dynamics investigated at the PLFA facility (CEA-SLIC), with two perspectives: (i) using APTs generated in atoms/molecules as a source for MFPAD-resolved PI studies, and (ii) taking advantage of molecular polarimetry to perform a complete polarization analysis of the harmonic emission of molecules, a major challenge of high harmonic spectroscopy. Recent results illustrating both aspects are reported for APTs generated in unaligned SF 6 molecules by an elliptically polarized infrared driving field. The observed fingerprints of the elliptically polarized harmonics include the first direct determination of the complete s 1 , s 2 , s 3 Stokes vector, equivalent to (ψ, ε, P), the orientation and the signed ellipticity of the polarization ellipse, and the degree of polarization P. They are

Increased Ocean Heat Convergence Into the High Latitudes With CO 2 Doubling Enhances Polar-Amplified Warming: OCEAN HEAT AND POLAR WARMING

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

Singh, H. A.; Rasch, P. J.; Rose, B. E. J.

We isolate the role of the ocean in polar climate change by directly evaluating how changes in ocean dynamics with quasi-equilibrium CO2-doubling impact high-latitude climate. With CO2-doubling, the ocean heat flux convergence (OHFC) shifts poleward in winter in both hemispheres. Imposing this pattern of perturbed OHFC in a global climate model results in a poleward shift in ocean-to-atmosphere turbulent heat fluxes (both sensible and latent) and sea ice retreat; the high-latitudes warm while the midlatitudes cool, thereby amplifying polar warming. Furthermore, midlatitude cooling is propagated to the polar mid-troposphere on isentropic surfaces, augmenting the (positive) lapse rate feedback at highmore » latitudes. These results highlight the key role played by the partitioning of meridional energy transport changes between the atmosphere and ocean in high-latitude climate change.« less

Neurologically Potent Molecules from Crataegus oxyacantha; Isolation, Anticholinesterase Inhibition, and Molecular Docking

PubMed Central

Ali, Mumtaz; Muhammad, Sultan; Shah, Muhammad R.; Khan, Ajmal; Rashid, Umer; Farooq, Umar; Ullah, Farhat; Sadiq, Abdul; Ayaz, Muhammad; Ali, Majid; Ahmad, Manzoor; Latif, Abdul

2017-01-01

Crataegus oxyacantha is an important herbal supplement and famous for its antioxidant potential. The antioxidant in combination with anticholinesterase activity can be considered as an important target in the management of Alzheimer’s disease. The compounds isolated from C. oxyacantha were evaluated for cholinesterases inhibitory activity using Ellman’s assay with Galantamine as standard drug. Total of nine (1–9) compounds were isolated. Compounds 1 and 2 were isolated for the first time from natural source. Important natural products like β-Sitosterol-3-O-β-D-Glucopyranoside (3), lupeol (4), β-sitosterol (5), betulin (6), betulinic acid (7), oleanolic acid (8), and chrysin (9) have also been isolated from C. oxyacantha. Overall, all the compounds exhibited an overwhelming acetylcholinesterase (AChE) inhibition potential in the range 5.22–44.47 μM. The compound 3 was prominent AChE inhibitor with IC50 value of 5.22 μM. Likewise, all the compounds were also potent in butyrylcholinesterase (BChE) inhibitions with IC50s of up to 0.55–15.36 μM. All the compounds, except 3, were selective toward BChE. Mechanism of the inhibition of both the enzymes were further studied by docking procedures using Genetic Optimization for Ligand Docking suit v5.4.1. Furthermore, computational blood brain barrier prediction of the isolated compounds suggest that these are BBB+. PMID:28638340

Dynamic fluctuations in single-molecule biophysics experiments. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

NASA Astrophysics Data System (ADS)

Krapf, Diego

2015-06-01

Single-molecule biophysics includes the study of isolated molecules and that of individual molecules within living cells. In both cases, dynamic fluctuations at the nanoscale play a critical role. Colomb and Sarkar emphasize how different noise sources affect the analysis of single molecule data [1]. Fluctuations in biomolecular systems arise from two very different mechanisms. On one hand thermal fluctuations are a predominant feature in the behavior of individual molecules. On the other hand, non-Gaussian fluctuations can arise from inter- and intramolecular interactions [2], spatial heterogeneities [3], non-Poisson external perturbations [4] and complex non-linear dynamics in general [5,6].

[Polarization of neutrophils from patients with asthma, chronic obstructive pulmonary disease and asthma-chronic obstructive pulmonary disease overlap syndrome].

PubMed

Deng, Fan; Dong, Hangming; Zou, Mengchen; Zhao, Haijin; Cai, Chunqing; Cai, Shaoxi

2014-12-30

To explore the polarization of migration dynamics of neutrophils isolated from patients with asthma, chronic obstructive pulmonary disease (COPD) and asthma-COPD overlap syndrome (ACOS) compared with healthy smoking and non-smoking controls. Recruited volunteers were classified as healthy controls, healthy smokers, asthma, COPD and ACOS at Nanfang Hospital from April 2013 to June 2014 according to the Global Strategy for the Diagnosis, Management and Prevention of COPD 2011, Global Strategy for Asthma Management and Prevention 2011 and Consensus on Overlap Phenotype COPD-asthma in COPD 2012. Neutrophils were freshly isolated from whole blood with density gradient technique. The proportion of polarized cells with gradient concentration of formyl-Met-Leu-Phe (fMLP) in Zigmond chamber and vital component of Store Operated Calcium Entry (SOCE) (stromal interaction molecule (STIM) 1, 2 and Orai1) in neutrophils was detected by Western blot. Asthma, COPD and ACOS neutrophils demonstrated a higher spontaneous polarization rate versus healthy controls and healthy smokers ((25.05 ± 4.06)%, (16.20 ± 4.46)%, (29.43 ± 5.53)% vs (7.27 ± 0.99)%, (7.06 ± 3.12)%, all P < 0.01), asthma and ACOS neutrophils showed a higher directed polarization rate ((14.62 ± 2.26)%, (8.00 ± 1.75)%, all P < 0.05), but COPD had a relatively lower rate of directional polarization rate than healthy controls and healthy smokers ((2.45 ± 0.54)% vs (5.12 ± 1.28)%, (5.24 ± 1.34)%, all P < 0.01). The vital component of SOCE in neutrophils from asthma, COPD and ACOS were all up-regulated versus healthy controls and healthy smokers (STIM1: 1.63 ± 0.14, 0.88 ± 0.41, 1.29 ± 0.22 vs 0.26 ± 0.14, 0.38 ± 0.12; STIM2: 0.52 ± 0.19, 0.22 ± 0.13, 0.24 ± 0.10 vs 0.05 ± 0.03, 0.10 ± 0.06; Orai1: 0.56 ± 0.04, 0.39 ± 0.05, 0.48 ± 0.05 vs 0.13 ± 0.04, 0.13 ± 0.03) (all P < 0.01). Asthma, COPD and ACOS neutrophils are intrinsically different than counterparts from healthy control subjects and

[Antibacterial activity of rare Streptomyces species against clinical resistant bacteria].

PubMed

Boughachiche, Faiza; Reghioua, Sihem; Zerizer, Habiba; Boulahrouf, Abderrahmane

2012-01-01

In the search for new antibiotics from Steptomyces, investigating extremes habitats enhances the probability of isolating novel producers. In this context, the antibacterial activity of four Streptomyces strains isolated from Ezzmoul saltpans was studied. Two of them showed antibacterial activity against antibiotic's resistant bacteria (Bacillus cereus: β-lactamines and sulfamides resistant, Streptococcus faecalis: penicillin, tetracycline and cotrimoxazole resistant, and Staphylococcus aureus Mu 50: vancomycine resistant). The most active Streptomyces strain produces one type of polar bioactive molecules that resists to temperature variation and light exposition. Its activity appears in the first culture day and reaches its maximal value in the fourth day. The second strain presents themoresistant activity that reaches its maximal value in the first culture day. It produces two types of bioactive molecules, one is polar and the second is non polar (according to thin layer chromatography technique results).

Plasmon-shaped polarization gating for high-order-harmonic generation

NASA Astrophysics Data System (ADS)

Wang, Feng; He, Lixin; Chen, Jiawei; Wang, Baoning; Zhu, Xiaosong; Lan, Pengfei; Lu, Peixiang

2017-12-01

We present a plasmon-shaped polarization gating for high-order-harmonic generation by using a linearly polarized laser field to illuminate two orthogonal bow-tie nanostructures. The results show that when these two bow-tie nanostructures have nonidentical geometrical sizes, the transverse and longitudinal components of the incident laser field will experience different phase responses, thus leading to a time-dependent ellipticity of laser field. For the polarizing angle of incident laser field in the range from 45∘ to 60∘, the dominant harmonic emission is gated within the few optical cycles where the laser ellipticity is below 0.3. Then sub-50-as isolated attosecond pulses (IAPs) can be generated. Such a plasmon-shaped polarization gating is robust for IAP generation against the variations of the carrier-envelope phases of the laser pulse. Moreover, by changing the geometrical size of one of the bow-tie nanostructures, the electron dynamics can be effectively controlled and the more efficient supercontinuum as well as IAP can be generated.

Doubling transmission capacity in optical wireless system by antenna horizontal- and vertical-polarization multiplexing.

PubMed

Li, Xinying; Yu, Jianjun; Zhang, Junwen; Dong, Ze; Chi, Nan

2013-06-15

We experimentally demonstrate 2×56 Gb/s two-channel polarization-division-multiplexing quadrature-phase-shift-keying signal delivery over 80 km single-mode fiber-28 and 2 m Q-band (33-50 GHz) wireless link, adopting antenna horizontal- (H-) and vertical-polarization (V-polarization) multiplexing. At the wireless receiver, classic constant-modulus-algorithm equalization based on digital signal processing can realize polarization demultiplexing and remove the crosstalk at the same antenna polarization. By adopting antenna polarization multiplexing, the signal baud rate and performance requirements for optical and wireless devices can be reduced but at the cost of double antennas and devices, while wireless transmission capacity can also be increased but at the cost of stricter requirements for V-polarization. The isolation is only about 19 dB when V-polarization deviation approaches 10°, which will affect high-speed (>50 Gb/s) wireless delivery.

Ab initio calculation of hyperfine splitting constants of molecules

NASA Astrophysics Data System (ADS)

Ohta, K.; Nakatsuji, H.; Hirao, K.; Yonezawa, T.

1980-08-01

Hyperfine splitting (hfs) constants of molecules, methyl, ethyl, vinyl, allyl, cyclopropyl, formyl, O3-, NH2, NO2, and NF2 radicals have been calculated by the pseudo-orbital (PO) theory, the unrestricted HF (UHF), projected UHF (PUHF) and single excitation (SE) CI theories. The pseudo-orbital (PO) theory is based on the symmetry-adapted-cluster (SAC) expansion proposed previously. Several contractions of the Gaussian basis sets of double-zeta accuracy have been examined. The UHF results were consistently too large to compare with experiments and the PUHF results were too small. For molecules studied here, the PO theory and SECI theory gave relatively close results. They were in fair agreement with experiments. The first-order spin-polarization self-consistency effect, which was shown to be important for atoms, is relatively small for the molecules. The present result also shows an importance of eliminating orbital-transformation dependence from conventional first-order perturbation calculations. The present calculations have explained well several important variations in the experimental hfs constants.

Indirect observation of unobservable interstellar molecules

NASA Technical Reports Server (NTRS)

Herbst, E.; Green, S.; Thaddeus, P.; Klemperer, W.

1977-01-01

It is suggested that the abundances of neutral non-polar interstellar molecules unobservable by radio astronomy can be systematically determined by radio observation of the protonated ions. As an example, observed N2H(+) column densities are analyzed to infer molecular nitrogen abundances in dense interstellar clouds. The chemistries and expected densities of the protonated ions of O2, C2, CO2, C2H2 and CH4 are then discussed. Microwave transition frequencies fo HCO2(+) and C2H3(+) are estimated, and a preliminary astronomical search for HCO2(+) is described.

In vitro characterization of multivalent adhesion molecule 7-based inhibition of multidrug-resistant bacteria isolated from wounded military personnel

PubMed Central

Krachler, Anne Marie; Mende, Katrin; Murray, Clinton; Orth, Kim

2012-01-01

Treatment of wounded military personnel at military medical centers is often complicated by colonization and infection of wounds with pathogenic bacteria. These include nosocomially transmitted, often multidrug-resistant pathogens such as Acinetobacter baumannii-calcoaceticus complex, Pseudomonas aeruginosa and extended spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae. We analyzed the efficacy of multivalent adhesion molecule (MAM) 7-based anti-adhesion treatment of host cells against aforementioned pathogens in a tissue culture infection model. Herein, we observed that a correlation between two important hallmarks of virulence, attachment and cytotoxicity, could serve as a useful predictor for the success of MAM7-based inhibition against bacterial infections. Initially, we characterized 20 patient isolates (five from each pathogen mentioned above) in terms of genotypic diversity, antimicrobial susceptibility and important hallmarks of pathogenicity (biofilm formation, attachment to and cytotoxicity toward cultured host cells). All isolates displayed a high degree of genotypic diversity, which was also reflected by large strain-to-strain variability in terms of biofilm formation, attachment and cytotoxicity within each group of pathogen. Using non-pathogenic bacteria expressing MAM7 or latex beads coated with recombinant MAM7 for anti-adhesion treatment, we showed a decrease in cytotoxicity, indicating that MAM7 has potential as a prophylactic agent to attenuate infection by multidrug-resistant bacterial pathogens. PMID:22722243

Polarization Dependence Suppression of Optical Fiber Grating Sensor in a π-Shifted Sagnac Loop Interferometer

PubMed Central

Son, Jaebum; Lee, Min-Kyoung; Jeong, Myung Yung; Kim, Chang-Seok

2010-01-01

In the sensing applications of optical fiber grating, it is necessary to reduce the transmission-type polarization dependence to isolate the sensing parameter. It is experimentally shown that the polarization-dependent spectrum of acousto-optic long-period fiber grating sensors can be suppressed in the transmission port of a π-shifted Sagnac loop interferometer. General expressions for the transmittance and reflectance are derived for transmission-type, reflection-type, and partially reflecting/transmitting-type polarization-dependent optical devices. The compensation of polarization dependence through the counter propagation in the Sagnac loop interferometer is quantitatively measured for a commercial in-line polarizer and an acousto-optic long-period fiber grating sensor. PMID:22399884

Asymmetric chemical reactions by polarized quantum beams

NASA Astrophysics Data System (ADS)

Takahashi, Jun-Ichi; Kobayashi, Kensei

One of the most attractive hypothesis for the origin of homochirality in terrestrial bio-organic compounds (L-amino acid and D-sugar dominant) is nominated as "Cosmic Scenario"; a chiral impulse from asymmetric excitation sources in space triggered asymmetric reactions on the surfaces of such space materials as meteorites or interstellar dusts prior to the existence of terrestrial life. 1) Effective asymmetric excitation sources in space are proposed as polarized quantum beams, such as circularly polarized light and spin polarized electrons. Circularly polarized light is emitted as synchrotron radiation from tightly captured electrons by intense magnetic field around neutron stars. In this case, either left-or right-handed polarized light can be observed depending on the direction of observation. On the other hand, spin polarized electrons is emitted as beta-ray in beta decay from radioactive nuclei or neutron fireballs in supernova explosion. 2) The spin of beta-ray electrons is longitudinally polarized due to parity non-conservation in the weak interaction. The helicity (the the projection of the spin onto the direction of kinetic momentum) of beta-ray electrons is universally negative (left-handed). For the purpose of verifying the asymmetric structure emergence in bio-organic compounds by polarized quantum beams, we are now carrying out laboratory simulations using circularly polarized light from synchrotron radiation facility or spin polarized electron beam from beta-ray radiation source. 3,4) The target samples are solid film or aqueous solution of racemic amino acids. 1) K.Kobayashi, K.Kaneko, J.Takahashi, Y.Takano, in Astrobiology: from simple molecules to primitive life; Ed. V.Basiuk; American Scientific Publisher: Valencia, 2008. 2) G.A.Gusev, T.Saito, V.A.Tsarev, A.V.Uryson, Origins Life Evol. Biosphere. 37, 259 (2007). 3) J.Takahashi, H.Shinojima, M.Seyama, Y.Ueno, T.Kaneko, K.Kobayashi, H.Mita, M.Adachi, M.Hosaka, M.Katoh, Int. J. Mol. Sci. 10, 3044

Fine structure and optical properties of biological polarizers in crustaceans and cephalopods

NASA Astrophysics Data System (ADS)

Chiou, Tsyr-Huei; Caldwell, Roy L.; Hanlon, Roger T.; Cronin, Thomas W.

2008-04-01

The lighting of the underwater environment is constantly changing due to attenuation by water, scattering by suspended particles, as well as the refraction and reflection caused by the surface waves. These factors pose a great challenge for marine animals which communicate through visual signals, especially those based on color. To escape this problem, certain cephalopod mollusks and stomatopod crustaceans utilize the polarization properties of light. While the mechanisms behind the polarization vision of these two animal groups are similar, several distinctive types of polarizers (i.e. the structure producing the signal) have been found in these animals. To gain a better knowledge of how these polarizers function, we studied the relationships between fine structures and optical properties of four types of polarizers found in cephalopods and stomatopods. Although all the polarizers share a somewhat similar spectral range, around 450- 550 nm, the reflectance properties of the signals and the mechanisms used to produce them have dramatic differences. In cephalopods, stack-plates polarizers produce the polarization patterns found on the arms and around their eyes. In stomatopods, we have found one type of beam-splitting polarizer based on photonic structures and two absorptive polarizer types based on dichroic molecules. These stomatopod polarizers may be found on various appendages, and on the cuticle covering dorsal or lateral sides of the animal. Since the efficiencies of all these polarizer types are somewhat sensitive to the change of illumination and viewing angle, how these animals compensate with different behaviors or fine structural features of the polarizer also varies.

Tentative identification of polar and mid-polar compounds in extracts from wine lees by liquid chromatography-tandem mass spectrometry in high-resolution mode.

PubMed

Delgado de la Torre, M P; Priego-Capote, F; Luque de Castro, M D

2015-06-01

Sustainable agriculture has a pending goal in the revalorization of agrofood residues. Wine lees are an abundant residue in the oenological industry. This residue, so far, has been used to obtain tartaric acid or pigments but not for being qualitatively characterized as a source of polar and mid-polar compounds such as flavonoids, phenols and essential amino acids. Lees extracts from 11 Spanish wineries have been analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in high resolution mode. The high-resolution power of LC-MS/MS has led to the tentative identification of the most representative compounds present in wine lees, comprising primary amino acids, anthocyans, flavanols, flavonols, flavones and non-flavonoid phenolic compounds, among others. Attending to the profile and content of polar and mid-polar compounds in wine lees, this study underlines the potential of wine lees as an exploitable source to isolate interesting compounds. Copyright © 2015 John Wiley & Sons, Ltd.

Defining RNA-Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA.

PubMed

Velagapudi, Sai Pradeep; Luo, Yiling; Tran, Tuan; Haniff, Hafeez S; Nakai, Yoshio; Fallahi, Mohammad; Martinez, Gustavo J; Childs-Disney, Jessica L; Disney, Matthew D

2017-03-22

RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif-small molecule interactions identified via selection. Named High Throughput Structure-Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif-small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule-RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs.

Chiral Sensitivity in Electron-Molecule Interactions

NASA Astrophysics Data System (ADS)

Dreiling, Joan

2015-09-01

All molecular forms of life possess a chiral asymmetry, with amino acids and sugars found respectively in L- and D-enantiomers only. The primordial origin of this enantiomeric excess is unknown. One possible explanation is given by the Vester- Ulbricht hypothesis, which suggests that left-handed electrons present in beta-radiation, produced by parity-violating weak decays, interacted with biological precursors and preferentially destroyed one of the two enantiomers. Experimental tests of this idea have thus far yielded inconclusive results. We show direct evidence for chirally-dependent bond breaking through a dissociative electron attachment (DEA) reaction when spin-polarized electrons are incident on gas-phase chiral molecules. This provides unambiguous evidence for a well-defined, chirally-sensitive destructive molecular process and, as such, circumstantial evidence for the Vester-Ulbricht hypothesis. I will also present the results of our systematic study of the DEA asymmetry for different chiral halocamphor molecules. Three halocamphor molecules were investigated: 3-bromocamphor (C10H15BrO), 3-iodocamphor(C10H15IO), and 10-iodocamphor. The DEA asymmetries collected for bromocamphor and iodocamphor are qualitatively different, suggesting that the atomic number of the heaviest atom in the molecule plays a crucial role in the asymmetric interactions. The DEA asymmetry data for 3- and 10-iodocamphor have the same qualitative behavior, but the 10-iodocamphor asymmetry is about twice as large at the lowest energies investigated, so the location of the heavy atom in the camphor molecule also affects the asymmetries. This work was performed at the University of Nebraska-Lincoln. This project is funded by NSF Grant PHY-1206067.

Progress in Computational Electron-Molecule Collisions

NASA Astrophysics Data System (ADS)

Rescigno, Tn

1997-10-01

The past few years have witnessed tremendous progress in the development of sophisticated ab initio methods for treating collisions of slow electrons with isolated small molecules. Researchers in this area have benefited greatly from advances in computer technology; indeed, the advent of parallel computers has made it possible to carry out calculations at a level of sophistication inconceivable a decade ago. But bigger and faster computers are only part of the picture. Even with today's computers, the practical need to study electron collisions with the kinds of complex molecules and fragments encountered in real-world plasma processing environments is taxing present methods beyond their current capabilities. Since extrapolation of existing methods to handle increasingly larger targets will ultimately fail as it would require computational resources beyond any imagined, continued progress must also be linked to new theoretical developments. Some of the techniques recently introduced to address these problems will be discussed and illustrated with examples of electron-molecule collision calculations we have carried out on some fairly complex target gases encountered in processing plasmas. Electron-molecule scattering continues to pose many formidable theoretical and computational challenges. I will touch on some of the outstanding open questions.

Quantum Behavior of Water Molecules Confined to Nanocavities in Gemstones.

PubMed

Gorshunov, Boris P; Zhukova, Elena S; Torgashev, Victor I; Lebedev, Vladimir V; Shakurov, Gil'man S; Kremer, Reinhard K; Pestrjakov, Efim V; Thomas, Victor G; Fursenko, Dimitry A; Dressel, Martin

2013-06-20

When water is confined to nanocavities, its quantum mechanical behavior can be revealed by terahertz spectroscopy. We place H2O molecules in the nanopores of a beryl crystal lattice and observe a rich and highly anisotropic set of absorption lines in the terahertz spectral range. Two bands can be identified, which originate from translational and librational motions of the water molecule isolated within the cage; they correspond to the analogous broad bands in liquid water and ice. In the present case of well-defined and highly symmetric nanocavities, the observed fine structure can be explained by macroscopic tunneling of the H2O molecules within a six-fold potential caused by the interaction of the molecule with the cavity walls.

Isolating isomers of perfluorocarboxylates in polar bears (Ursus maritimus) from two geographical locations.

PubMed

De Silva, Amila O; Mabury, Scott A

2004-12-15

The source of involatile, anthropogenic perfluorocarboxylate anions (PFCAs) in biota from remote regions is of heightened interest due to the persistence, toxicity, and bioaccumulation of these materials. Large-scale production of fluorinated compounds is carried out primarily by one of two methods: electrochemical fluorination (ECF) and telomerization. Products of the two processes may be distinguished based on constitutional isomer pattern as ECF products are characteristically comprised of a variety of constitutional isomers. The objective of this research was to develop a method for identifying the constitutional isomer profile of PFCAs in environmental samples and to apply the method to polar bear livers from two different locations. Resolution of constitutional isomers of derivatized PFCAs (8-13 carbons) was accomplished via GC-MS. Seven isomers of an authentic ECF perfluorooctanoate (PFOA) standard were separated. The linear isomer comprised 78% of this standard. Isomer profiles of PFCAs in liver samples of 15 polar bears (Ursus maritimus) from the Canadian Arctic and eastern Greenland were determined by GC-MS. The PFOA isomer pattern in Greenland polar bear samples showed a variety of branched isomers while only the linear PFOA isomer was determined in Canadian samples. Samples of both locations had primarily (>99%) linear isomers of perfluorononanoate and perfluorotridecanoate. Branched isomers of perfluorodecanoate, perfluoroundecanoate, and perfluorododecanoate were determined in the polar bear samples. Unlike the PFOA isomer signature, only a single branched isomer peak on the chromatograms was observed for these longer chain PFCAs. The presence of branched isomers suggests some contribution from ECF sources. However, in comparison to the amount of branched isomers in the ECF PFOA standard, such minor percentages of branched PFCAs may suggest additional input from an exclusively linear isomer source.

Polarization of Hazes and Aurorae on Jupiter

NASA Astrophysics Data System (ADS)

Yanamandra-Fisher, Padma A.; McLean, Will; PACA_Jupiter

2017-10-01

Our solar system planets show a large variety of atmospheric polarization properties, from the thick, highly polarizing haze on Titan and the poles of Jupiter, Rayleigh scattering by molecules on Uranus and Neptune, to clouds in the equatorial region of Jupiter or on Venus. Changes in the clouds/thermal filed can be brought about by endogenic dynamical processes such merger of vortices; global, planetary scale upheavals, and external factors such as celestial collisions (such as D/Shoemaker-Levy 9 impact with Jupiter in 1994, etc.). Although the range of phase angles available from Earth for outer planets is restricted to a narrow range, limb polarization measurements provide constraints on the polarimetric properties. For example, at the equator, much of the observed reflected radiation is due to the presence of clouds and therefore, low polarization. Polar asymmetry exists between the two poles, while the planetary disk is unpolarized. Jupiter is known to exhibit a strong polar limb polarization and a low equatorial limb polarization due to the presence of haze particles and Rayleigh scattering at the poles. In contrast, at the equator, the concentration of particulates in the high atmosphere might change, changing the polarimetric signature and aurorae at both poles. The polarimetric maps, in conjunction with thermal maps and albedo maps, can provide constraints on modeling efforts to understand the nature of the aerosols/hazes in Jovian atmosphere. With Jupiter experiencing morphological changes at many latitudes, we have initiated a polarimetric observing campaign of Jupiter, in conjunction with The PACA Project. With NASA/Juno mission in a 53-day orbit around Jupiter, and recent outbreaks in the atmosphere, changes in the polarimetric signature will provide insight to the changes occurring in the atmosphere. Some of our observations are acquired by a team of professional/amateur planetary imagers astronomers based in the U.K., Australia and Europe. France

Singularities of interference of three waves with different polarization states.

PubMed

Kurzynowski, Piotr; Woźniak, Władysław A; Zdunek, Marzena; Borwińska, Monika

2012-11-19

We presented the interference setup which can produce interesting two-dimensional patterns in polarization state of the resulting light wave emerging from the setup. The main element of our setup is the Wollaston prism which gives two plane, linearly polarized waves (eigenwaves of both Wollaston's wedges) with linearly changed phase difference between them (along the x-axis). The third wave coming from the second arm of proposed polarization interferometer is linearly or circularly polarized with linearly changed phase difference along the y-axis. The interference of three plane waves with different polarization states (LLL - linear-linear-linear or LLC - linear-linear-circular) and variable change difference produce two-dimensional light polarization and phase distributions with some characteristic points and lines which can be claimed to constitute singularities of different types. The aim of this article is to find all kind of these phase and polarization singularities as well as their classification. We postulated in our theoretical simulations and verified in our experiments different kinds of polarization singularities, depending on which polarization parameter was considered (the azimuth and ellipticity angles or the diagonal and phase angles). We also observed the phase singularities as well as the isolated zero intensity points which resulted from the polarization singularities when the proper analyzer was used at the end of the setup. The classification of all these singularities as well as their relationships were analyzed and described.

Large low-field magnetoresistance in Fe3O4/molecule nanoparticles at room temperature

NASA Astrophysics Data System (ADS)

Yue, F. J.; Wang, S.; Lin, L.; Zhang, F. M.; Li, C. H.; Zuo, J. L.; Du, Y. W.; Wu, D.

2011-01-01

Acetic acid molecule-coated Fe3O4 nanoparticles, 450-650 nm in size, have been synthesized using a chemical solvothermal reduction method. Fourier transform infrared spectroscopy measurements confirm one monolayer acetic acid molecules chemically bond to the Fe3O4 nanoparticles. The low-field magnetoresistance (LFMR) of more than -10% at room temperature and -23% at 140 K is achieved with saturation field of less than 2 kOe. In comparison, the resistivity of cold-pressed bare Fe3O4 nanoparticles is six orders of magnitudes smaller than that of Fe3O4/molecule nanoparticles, and the LFMR ratio is one order of magnitude smaller. Our results indicate that the large LFMR in Fe3O4/molecule nanoparticles is associated with spin-polarized electrons tunnelling through molecules instead of direct nanoparticle contacts. These results suggest that magnetic oxide-molecule hybrid materials are an alternative type of materials to develop spin-based devices by a simple low-cost approach.

Small Molecule Injection into Single-Cell C. elegans Embryos via Carbon-Reinforced Nanopipettes

PubMed Central

Morton, Diane G.; Fellman, Shanna M.; Chung, SueYeon; Soltani, Mohammad; Kevek, Joshua W.; McEuen, Paul M.; Kemphues, Kenneth J.; Wang, Michelle D.

2013-01-01

The introduction of chemical inhibitors into living cells at specific times in development is a useful method for investigating the roles of specific proteins or cytoskeletal components in developmental processes. Some embryos, such as those of Caenorhabditis elegans, however, possess a tough eggshell that makes introducing drugs and other molecules into embryonic cells challenging. We have developed a procedure using carbon-reinforced nanopipettes (CRNPs) to deliver molecules into C. elegans embryos with high temporal control. The use of CRNPs allows for cellular manipulation to occur just subsequent to meiosis II with minimal damage to the embryo. We have used our technique to replicate classical experiments using latrunculin A to inhibit microfilaments and assess its effects on early polarity establishment. Our injections of latrunculin A confirm the necessity of microfilaments in establishing anterior-posterior polarity at this early stage, even when microtubules remain intact. Further, we find that latrunculin A treatment does not prevent association of PAR-2 or PAR-6 with the cell cortex. Our experiments demonstrate the application of carbon-reinforced nanopipettes to the study of one temporally-confined developmental event. The use of CRNPs to introduce molecules into the embryo should be applicable to investigations at later developmental stages as well as other cells with tough outer coverings. PMID:24086620

Small molecule injection into single-cell C. elegans embryos via carbon-reinforced nanopipettes.

PubMed

Brennan, Lucy D; Roland, Thibault; Morton, Diane G; Fellman, Shanna M; Chung, SueYeon; Soltani, Mohammad; Kevek, Joshua W; McEuen, Paul M; Kemphues, Kenneth J; Wang, Michelle D

2013-01-01

The introduction of chemical inhibitors into living cells at specific times in development is a useful method for investigating the roles of specific proteins or cytoskeletal components in developmental processes. Some embryos, such as those of Caenorhabditis elegans, however, possess a tough eggshell that makes introducing drugs and other molecules into embryonic cells challenging. We have developed a procedure using carbon-reinforced nanopipettes (CRNPs) to deliver molecules into C. elegans embryos with high temporal control. The use of CRNPs allows for cellular manipulation to occur just subsequent to meiosis II with minimal damage to the embryo. We have used our technique to replicate classical experiments using latrunculin A to inhibit microfilaments and assess its effects on early polarity establishment. Our injections of latrunculin A confirm the necessity of microfilaments in establishing anterior-posterior polarity at this early stage, even when microtubules remain intact. Further, we find that latrunculin A treatment does not prevent association of PAR-2 or PAR-6 with the cell cortex. Our experiments demonstrate the application of carbon-reinforced nanopipettes to the study of one temporally-confined developmental event. The use of CRNPs to introduce molecules into the embryo should be applicable to investigations at later developmental stages as well as other cells with tough outer coverings.

Computational laser intensity stabilisation for organic molecule concentration estimation in low-resource settings

NASA Astrophysics Data System (ADS)

Haider, Shahid A.; Kazemzadeh, Farnoud; Wong, Alexander

2017-03-01

An ideal laser is a useful tool for the analysis of biological systems. In particular, the polarization property of lasers can allow for the concentration of important organic molecules in the human body, such as proteins, amino acids, lipids, and carbohydrates, to be estimated. However, lasers do not always work as intended and there can be effects such as mode hopping and thermal drift that can cause time-varying intensity fluctuations. The causes of these effects can be from the surrounding environment, where either an unstable current source is used or the temperature of the surrounding environment is not temporally stable. This intensity fluctuation can cause bias and error in typical organic molecule concentration estimation techniques. In a low-resource setting where cost must be limited and where environmental factors, like unregulated power supplies and temperature, cannot be controlled, the hardware required to correct for these intensity fluctuations can be prohibitive. We propose a method for computational laser intensity stabilisation that uses Bayesian state estimation to correct for the time-varying intensity fluctuations from electrical and thermal instabilities without the use of additional hardware. This method will allow for consistent intensities across all polarization measurements for accurate estimates of organic molecule concentrations.

Spin transport properties of n-polyacene molecules (n = 1–15) connected to Ni surface electrodes: Theoretical analysis

PubMed Central

Caliskan, S.; Laref, A.

2014-01-01

Using non-equilibrium Green function formalism in conjunction with density functional theory, we explore the spin-polarized transport characteristics of several planar n-acene molecules suspended between two semi-infinite Ni electrodes via the thiol group. We examine the spin-dependence transport on Ni-n-acenes-Ni junctions, while the number of fused benzene rings varies between 1 and 15. Intriguingly, the induced magnetic moments of small acene molecules are higher than that of longer acene rings. The augmentation of fused benzene rings affects both the magnetic and transport features, such as the transmission function and conductance owing to their coupling to the Ni surface contacts via the anchoring group. The interplay between the spin-polarized transport properties, structural configuration and molecular electronic is a fortiori essential in these attractive molecular devices. Thus, this can conduct to the engineering of the electron spin transport in atomistic and molecular junctions. These prominent molecules convincingly infer that the molecular spin valves can conduct to thriving molecular devices. PMID:25482076

Thermooptics of magnetoactive media: Faraday isolators for high average power lasers

NASA Astrophysics Data System (ADS)

Khazanov, E. A.

2016-09-01

The Faraday isolator, one of the key high-power laser elements, provides optical isolation between a master oscillator and a power amplifier or between a laser and its target, for example, a gravitational wave detector interferometer. However, the absorbed radiation inevitably heats the magnetoactive medium and leads to thermally induced polarization and phase distortions in the laser beam. This self-action process limits the use of Faraday isolators in high average power lasers. A unique property of magnetoactive medium thermooptics is that parasitic thermal effects arise on the background of circular birefringence rather than in an isotropic medium. Also, even insignificant polarization distortions of the radiation result in a worse isolation ratio, which is the key characteristic of the Faraday isolator. All possible laser beam distortions are analyzed for their deteriorating effect on the Faraday isolator parameters. The mechanisms responsible for and key physical parameters associated with different kinds of distortions are identified and discussed. Methods for compensating and suppressing parasitic thermal effects are described in detail, the published experimental data are systematized, and avenues for further research are discussed based on the results achieved.

CTS attenuation and cross polarization measurements at 11.7 GHz

NASA Technical Reports Server (NTRS)

Vogel, W. J.

1980-01-01

The long-term attenuation, cross-polarization, and rain-rate data monitored in Austin, Texas from the circularly polarized 11.7 GHz satellite beacon transmitter aboard the Communications Technology Satellite are analyzed. Data events are significantly more likely during April-September, than during October-March, except for ice deplorization which predominates during the winter months. A time of day dependence of the events is also noted. The 10 dB fade level is exceeded for .03% during the thunderstorm months. Isolation with the same probability is 23 dB.

Improved alternating gradient transport and focusing of neutral molecules

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

Kalnins, Juris; Lambertson, Glen; Gould, Harvey

2001-12-02

Polar molecules, in strong-field seeking states, can be transported and focused by an alternating sequence of electric field gradients that focus in one transverse direction while defocusing in the other. We show by calculation and numerical simulation, how one may greatly improve the alternating gradient transport and focusing of molecules. We use a new optimized multipole lens design, a FODO lattice beam transport line, and lenses to match the beam transport line to the beam source and the final focus. We derive analytic expressions for the potentials, fields, and gradients that may be used to design these lenses. We describemore » a simple lens optimization procedure and derive the equations of motion for tracking molecules through a beam transport line. As an example, we model a straight beamline that transports a 560 m/s jet-source beam of methyl fluoride molecules 15 m from its source and focuses it to 2 mm diameter. We calculate the beam transport line acceptance and transmission, for a beam with velocity spread, and estimate the transmitted intensity for specified source conditions. Possible applications are discussed.« less

A multi purpose source chamber at the PLEIADES beamline at SOLEIL for spectroscopic studies of isolated species: cold molecules, clusters, and nanoparticles.

PubMed

Lindblad, Andreas; Söderström, Johan; Nicolas, Christophe; Robert, Emmanuel; Miron, Catalin

2013-11-01

This paper describes the philosophy and design goals regarding the construction of a versatile sample environment: a source capable of producing beams of atoms, molecules, clusters, and nanoparticles in view of studying their interaction with short wavelength (vacuum ultraviolet and x-ray) synchrotron radiation. In the design, specific care has been taken of (a) the use standard components, (b) ensuring modularity, i.e., that swiftly switching between different experimental configurations was possible. To demonstrate the efficiency of the design, proof-of-principle experiments have been conducted by recording x-ray absorption and photoelectron spectra from isolated nanoparticles (SiO2) and free mixed clusters (Ar/Xe). The results from those experiments are showcased and briefly discussed.

Broadband polarized emission from P(NDI2OD-T2) polymer.

PubMed

Ulrich, Steve; Sutch, Tabitha; Szulczewski, Greg; Schweizer, Matthias; Barbosa, Newton; Araujo, Paulo

2018-05-18

We investigate the P(NDI2OD-T2) photophysical properties via absorbance and fluorescence spectroscopy, in association with the experimental approach baptized Stokes Spectroscopy, which provides valuable material information through the acquisition and analysis of the fluorescence polarization degree. By changing solvents and using different samples such as solutions, thick, and thin films, it is possible to control the polarization degree spectrum associated to the fluorescence emitted by the polymer's isolated chains and aggregates. We show that the polarization degree could become a powerful tool to obtain information related to the samples morphology, which is connected to their microscopic structure. Moreover, the polarization degree spectra suggest that depolarization effects linked to energy and charge transfer mechanisms are likely taking place. Our findings indicate that P(NDI2OD-T2) polymers are excellent candidates for the advancement of organic technologies that rely on the emission and detection of polarized lights. © 2018 IOP Publishing Ltd.

Broadband polarized emission from P(NDI2OD-T2) polymer

NASA Astrophysics Data System (ADS)

Ulrich, Steven V.; Sutch, Tabitha; Szulczewski, Greg; Schweizer, Matthias; Barbosa Neto, Newton M.; Araujo, Paulo T.

2018-07-01

We investigate the P(NDI2OD-T2) photophysical properties via absorbance and fluorescence spectroscopy, in association with the experimental approach baptized Stokes Spectroscopy, which provides valuable material information through the acquisition and analysis of the fluorescence polarization degree. By changing solvents and using different samples such as solutions, thick, and thin films, it is possible to control the polarization degree spectrum associated to the fluorescence emitted by the polymer’s isolated chains and aggregates. We show that the polarization degree could become a powerful tool to obtain information related to the samples morphology, which is connected to their microscopic structure. Moreover, the polarization degree spectra suggest that depolarization effects linked to energy and charge transfer mechanisms are likely taking place. Our findings indicate that P(NDI2OD-T2) polymers are excellent candidates for the advancement of organic technologies that rely on the emission and detection of polarized lights.

Single molecule optical measurements of orientation and rotations of biological macromolecules

PubMed Central

Shroder, Deborah Y; Lippert, Lisa G; Goldman, Yale E

2016-01-01

The subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measuring their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, we review the relevant types of probes and labeling techniques, and we highlight the advantages and disadvantages of these technologies for addressing specific inquiries. PMID:28192292

Single molecule optical measurements of orientation and rotations of biological macromolecules.

PubMed

Shroder, Deborah Y; Lippert, Lisa G; Goldman, Yale E

2016-11-22

Subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measurement of their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, review the relevant types of probes and labeling techniques, and highlight the advantages and disadvantages of these technologies for addressing specific inquiries.

Nonreciprocal optical isolation via graphene based photonic crystals

NASA Astrophysics Data System (ADS)

Roshan Entezar, S.; Karimi Habil, M.

2018-03-01

The transmission properties of a one-dimensional photonic crystal containing graphene mono-layers are studied using the transfer matrix method. It is shown that the structure can be used as a polarization-selective nonreciprocal device which discriminates between the two circularly polarized waves with different handedness impinging in the same direction. This structure may be utilized in designing optical isolators for the circularly polarized waves due to the gyrotropic behavior of the graphene mono-layers under the perpendicularly applied external magnetic field. Moreover, the effect of an external magnetic field and the chemical potential of the graphene mono-layers on the band gap of the structure are investigated.

Thin Crystal Film Polarizer for Display Application

NASA Astrophysics Data System (ADS)

Paukshto, Michael

2003-03-01

Optiva Inc. has pioneered the development of nano-thin crystalline film (TCF) optical coatings for use in information displays and other applications. TCF is a material based on water-based dichroic dye solutions. Disk-like dye molecules aggregate in a ``plane-to-plane" manner; this self-assembly results in formation of highly anisometric rod-like stacks. These stacks have an aspect ratio of approximately 200:1. At a certain threshold of dye concentration, a nematic ordering of the rod-like stacks appears. Such a system acquires polarizing properties according to the following mechanism. Flow-induced alignment is known to occur in the lyotropic systems in a shear flow. In our case, the material undergoes shear alignment while being coated onto a glass or plastic substrate. In the coated thin film, the long molecular stacks are oriented in the flow direction parallel to the flow direction and substrate plane. The planes of the dye molecules are perpendicular to the substrate plane with the optical transition oscillators lying in the molecule plane. After the coating, as the thin film dries, crystallization occurs due to water evaporation. In a dry film, the molecular planes maintain their orthogonal orientation with respect to the substrate surface. TCF is known to possess properties of an E-mode polarizer. TCF technology has now migrated out of the R stage into manufacturing and is currently being incorporated into new display products. This presentation will provide an overview of TCF technology. The first part of the presentation will describe material structure, optical properties and characterization, material processing and associated coating equipment. This will be followed by a presentation on optical modeling and simulation of display performance with TCF components. Comparisons of display performance will be made for exemplar configurations of a variety of LCDs, including TN, STN and AMLCD designs in both transmissive and reflective modes.

Do centrioles generate a polar ejection force?

PubMed

Wells, Jonathan

2005-01-01

A microtubule-dependent polar ejection force that pushes chromosomes away from spindle poles during prometaphase is observed in animal cells but not in the cells of higher plants. Elongating microtubules and kinesin-like motor molecules have been proposed as possible causes, but neither accounts for all the data. In the hypothesis proposed here a polar ejection force is generated by centrioles, which are found in animals but not in higher plants. Centrioles consist of nine microtubule triplets arranged like the blades of a tiny turbine. Instead of viewing centrioles through the spectacles of molecular reductionism and neo-Darwinism, this hypothesis assumes that they are holistically designed to be turbines. Orthogonally oriented centriolar turbines could generate oscillations in spindle microtubules that resemble the motion produced by a laboratory vortexer. The result would be a microtubule-mediated ejection force tending to move chromosomes away from the spindle axis and the poles. A rise in intracellular calcium at the onset of anaphase could regulate the polar ejection force by shutting down the centriolar turbines, but defective regulation could result in an excessive force that contributes to the chromosomal instability characteristic of most cancer cells.

Atomic-scale inversion of spin polarization at an organic-antiferromagnetic interface

NASA Astrophysics Data System (ADS)

Caffrey, Nuala M.; Ferriani, Paolo; Marocchi, Simone; Heinze, Stefan

2013-10-01

Using first-principles calculations, we show that the magnetic properties of a two-dimensional antiferromagnetic transition-metal surface are modified on the atomic scale by the adsorption of small organic molecules. We consider benzene (C6H6), cyclooctatetraene (C8H8), and a small transition-metal-benzene complex (BzV) adsorbed on a single atomic layer of Mn deposited on the W(110) surface—a surface which exhibits a nearly antiferromagnetic alignment of the magnetic moments in adjacent Mn rows. Due to the spin dependent hybridization of the molecular pz orbitals with the d states of the Mn monolayer, there is a significant reduction of the magnetic moments in the Mn film. Furthermore, the spin polarization at this organic-antiferromagnetic interface is found to be modulated on the atomic scale, both enhanced and inverted, as a result of the molecular adsorption. We show that this effect can be resolved by spin-polarized scanning tunneling microscopy (SP-STM). Our simulated SP-STM images display a spatially dependent spin resolved vacuum charge density above an adsorbed molecule—i.e., different regions above the molecule sustain different signs of spin polarization. While states with s and p symmetry dominate the vacuum charge density in the vicinity of the Fermi energy for the clean magnetic surface, we demonstrate that after a molecule is adsorbed those d states, which are normally suppressed due to their symmetry, can play a crucial role in the vacuum due to their interaction with the molecular orbitals. We also model the effect of small deviations from perfect antiferromagnetic ordering, induced by the slight canting of magnetic moments due to the spin spiral ground state of Mn/W(110).

The sign of the polarizability anisotropy of polar molecules is obtained from the terahertz Kerr effect

NASA Astrophysics Data System (ADS)

Kampfrath, Tobias; Wolf, Martin; Sajadi, Mohsen

2018-01-01

The terahertz Kerr effect (TKE) of polar molecular vapors is reported. The birefringence signal of fluoroform appears with opposite polarity compared to acetonitrile and water. This behavior is a hallmark of the opposite sign of a new molecular polarizability anisotropy ΔαTKE =αzz - (αxx +αyy) / 2 , with αzz being the polarizability along the permanent dipole moment. As the excitation of the rotational states orients the permanent dipoles along the terahertz electric field, the orientation is translated into an optical birefringence proportional to ΔαTKE . Thus, the sign of ΔαTKE is imprinted onto the TKE signal, providing novel insights into the polarizability tensor of water.

Angular motion of a PAH molecule in interstellar environment

NASA Technical Reports Server (NTRS)

Rouan, D.; Leger, Alain; Omont, A.; Giard, Martin

1989-01-01

Polycyclic aromatic hydrocarbon (PAH) molecules have recently been proposed as an important and hitherto undetected component of the Interstellar Medium (ISM). The theory was based on an explanation of the Unidentified IR Emission Bands by Leger et al. It has already led to a verified prediction on extended galactic and extragalactic emissions measured by IRAS, or by a recent balloon borne experiment. The physics that rules the motion of such molecules in the ISM was studied, taking into account their coupling with the ambient gas, the radiation field (absorption and emission) and the static magnetic field. This is important for many implications of the PAH theory such as the radio emission by these molecules or the expected polarization of their IR emission. A reflection nebulae is considered where the situation is rather well known. Every day life of a mean PAH molecule in such a region is as follows: every 3 hrs a UV photon is absorbed heating the molecule to a thousand degs; the temperature decay due to cooling by IR emission follows then within a few seconds. A collision with a molecule of gas occurs typically once a week, while an H atom is ejected or captured at the same rate. A typical cooling cycle after a heat impulse is given. The PAH molecules studied as representative of the family has typically 50 atoms, a radius of 4.5 A, is circular and has a molecular mass of M = 300; its permanent dipole moment is 3 Debye.

Influence of cell shape, inhomogeneities and diffusion barriers in cell polarization models

NASA Astrophysics Data System (ADS)

Giese, Wolfgang; Eigel, Martin; Westerheide, Sebastian; Engwer, Christian; Klipp, Edda

2015-12-01

In silico experiments bear the potential for further understanding of biological transport processes by allowing a systematic modification of any spatial property and providing immediate simulation results. Cell polarization and spatial reorganization of membrane proteins are fundamental for cell division, chemotaxis and morphogenesis. We chose the yeast Saccharomyces cerevisiae as an exemplary model system which entails the shuttling of small Rho GTPases such as Cdc42 and Rho, between an active membrane-bound form and an inactive cytosolic form. We used partial differential equations to describe the membrane-cytosol shuttling of proteins. In this study, a consistent extension of a class of 1D reaction-diffusion systems into higher space dimensions is suggested. The membrane is modeled as a thin layer to allow for lateral diffusion and the cytosol is modeled as an enclosed volume. Two well-known polarization mechanisms were considered. One shows the classical Turing-instability patterns, the other exhibits wave-pinning dynamics. For both models, we investigated how cell shape and diffusion barriers like septin structures or bud scars influence the formation of signaling molecule clusters and subsequent polarization. An extensive set of in silico experiments with different modeling hypotheses illustrated the dependence of cell polarization models on local membrane curvature, cell size and inhomogeneities on the membrane and in the cytosol. In particular, the results of our computer simulations suggested that for both mechanisms, local diffusion barriers on the membrane facilitate Rho GTPase aggregation, while diffusion barriers in the cytosol and cell protrusions limit spontaneous molecule aggregations of active Rho GTPase locally.

Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling.

PubMed

Liu, Hui; Dong, Peng; Ioannou, Maria S; Li, Li; Shea, Jamien; Pasolli, H Amalia; Grimm, Jonathan B; Rivlin, Patricia K; Lavis, Luke D; Koyama, Minoru; Liu, Zhe

2018-01-09

Our ability to unambiguously image and track individual molecules in live cells is limited by packing of multiple copies of labeled molecules within the resolution limit. Here we devise a universal genetic strategy to precisely control copy number of fluorescently labeled molecules in a cell. This system has a dynamic range of ∼10,000-fold, enabling sparse labeling of proteins expressed at different abundance levels. Combined with photostable labels, this system extends the duration of automated single-molecule tracking by two orders of magnitude. We demonstrate long-term imaging of synaptic vesicle dynamics in cultured neurons as well as in intact zebrafish. We found axon initial segment utilizes a "waterfall" mechanism gating synaptic vesicle transport polarity by promoting anterograde transport processivity. Long-time observation also reveals that transcription factor hops between clustered binding sites in spatially restricted subnuclear regions, suggesting that topological structures in the nucleus shape local gene activities by a sequestering mechanism. This strategy thus greatly expands the spatiotemporal length scales of live-cell single-molecule measurements, enabling new experiments to quantitatively understand complex control of molecular dynamics in vivo.

Manipulating spins of magnetic molecules: Hysteretic behavior with respect to bias voltage

NASA Astrophysics Data System (ADS)

Płomińska, Anna; Misiorny, Maciej; Weymann, Ireneusz

2018-02-01

Formation of a magnetic hysteresis loop with respect to a bias voltage is investigated theoretically in a spin-valve device based on a single magnetic molecule. We consider a device consisting of two ferromagnetic electrodes bridged by a carbon nanotube, acting as a quantum dot, to which a spin-anisotropic molecule is exchange-coupled. Such a coupling allows for transfer of angular momentum between the molecule and a spin current flowing through the dot, and thus, for switching orientation of the molecular spin. We demonstrate that this current-induced switching process exhibits a hysteretic behavior with respect to a bias voltage applied to the device. The analysis is carried out with the use of the real-time diagrammatic technique in the lowest-order expansion of the tunnel coupling of the dot to electrodes. The influence of both the intrinsic properties of the spin-valve device (the spin polarization of electrodes and the coupling strength of the molecule to the dot) and those of the molecule itself (magnetic anisotropy and spin relaxation) on the size of the magnetic hysteresis loop is discussed.

Exploring Cosmic X-ray Source Polarization

NASA Technical Reports Server (NTRS)

Swank, Jean Hebb; Jahodal, K.; Kallman, T. R.; Kaaret, P.

2008-01-01

Cosmic X-ray sources are expected to be polarized, either because of their asymmetry and the role of scattering in their emission or the role of magnetic fields. Polarization at other wavelengths has been useful. X-ray polarization will provide a new handle on black hole parameters, in particular the spin, on accretion flows and outflows, on neutron star spin orientations and emission mechanisms, on the quantum mechanical effects of super-strong magnetic fields of magnetars, and on the structure of supernovae shocks. The proposed Gravity and Extreme Magnetism SMEX (GEMS) will use high efficiency polarimeters behind thin foil mirrors. The statistical sensitivity and control of systematics will allow measurement of polarization fractions as small as 1% from many galactic and extragalactic sources. Targets which should be polarized at the level that GEMS can easily measure include stellar black holes, Seyfert galaxies and quasars, blazars, rotation-powered and accretion-powered pulsars, magnetars, shell supernova remnants and pulsar wind nebulae. The polarimeters are Time Projection Chambers that allow reconstruction of images of photoelectron tracks for 2-10 keV Xrays. They can be deep without sacrificing modulation. These polarimeters do not image the sky, but the telescope point spread function and detector collimation allow structure to be resolved at the 10 arcmin level. Rotation of the spacecraft is not needed for the signal measurement in the Time Projection Chambers, but provides for measurement and correction of systematic errors. It also allows a small Bragg reflection soft X-ray experiment to be included that can be used for isolated neutron stars and blazars.

DUO: Spectra of diatomic molecules

NASA Astrophysics Data System (ADS)

Yurchenko, Sergei N.; Lodi, Lorenzo; Tennyson, Jonathan; Stolyarov, Andrey V.

2016-05-01

Duo computes rotational, rovibrational and rovibronic spectra of diatomic molecules. The software, written in Fortran 2003, solves the Schrödinger equation for the motion of the nuclei for the simple case of uncoupled, isolated electronic states and also for the general case of an arbitrary number and type of couplings between electronic states. Possible couplings include spin-orbit, angular momenta, spin-rotational and spin-spin. Introducing the relevant couplings using so-called Born-Oppenheimer breakdown curves can correct non-adiabatic effects.

Dynamic Nuclear Polarization and the Paradox of Quantum Thermalization.

PubMed

De Luca, Andrea; Rosso, Alberto

2015-08-21

Dynamic nuclear polarization (DNP) is to date the most effective technique to increase the nuclear polarization opening disruptive perspectives for medical applications. In a DNP setting, the interacting spin system is quasi-isolated and brought out of equilibrium by microwave irradiation. Here we show that the resulting stationary state strongly depends on the ergodicity properties of the spin many-body eigenstates. In particular, the dipolar interactions compete with the disorder induced by local magnetic fields resulting in two distinct dynamical phases: while for weak interaction, only a small enhancement of polarization is observed, for strong interactions the spins collectively equilibrate to an extremely low effective temperature that boosts DNP efficiency. We argue that these two phases are intimately related to the problem of thermalization in closed quantum systems where a many-body localization transition can occur varying the strength of the interactions.

Expression of Opacity Proteins Interferes with the Transmigration of Neisseria gonorrhoeae across Polarized Epithelial Cells.

PubMed

Stein, Daniel C; LeVan, Adriana; Hardy, Britney; Wang, Liang-Chun; Zimmerman, Lindsey; Song, Wenxia

2015-01-01

Neisseria gonorrhoeae (GC) establishes infection at the mucosal surface of the human genital tract, most of which is lined with polarized epithelial cells. GC can cause localized as well as disseminated infections, leading to various complications. GC constantly change their surface structures via phase and antigenic variation, which has been implicated as a means for GC to establish infection at various anatomic locations of male and female genital tracks. However, the exact contribution of each surface molecule to bacterial infectivity remains elusive due to their phase variation. Using a GC derivative that is genetically devoid of all opa genes (MS11∆Opa), this study shows that Opa expression interferes with GC transmigration across polarized human epithelial cells. MS11∆Opa transmigrates across polarized epithelial cells much faster and to a greater extent than MS11Opa+, while adhering at a similar level as MS11Opa+. When MS11Opa+, able to phase vary Opa expression, was inoculated, only those bacteria that turn off Opa expression transmigrate across the polarized epithelial monolayer. Similar to bacteria alone or co-cultured with non-polarized epithelial cells, MS11∆Opa fails to form large microcolonies at the apical surface of polarized epithelial cells. Apical inoculation of MS11Opa+, but not MS11∆Opa, induces the recruitment of the Opa host-cell receptor carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) to the apical junction and the vicinity of bacterial adherent sites. Our results suggest that Opa expression limits gonococcal ability to invade into subepithelial tissues by forming tight interactions with neighboring bacteria and by inducing CEACAM redistribution to cell junctions.

Cortical Polarity of the RING Protein PAR-2 Is Maintained by Exchange Rate Kinetics at the Cortical-Cytoplasmic Boundary.

PubMed

Arata, Yukinobu; Hiroshima, Michio; Pack, Chan-Gi; Ramanujam, Ravikrishna; Motegi, Fumio; Nakazato, Kenichi; Shindo, Yuki; Wiseman, Paul W; Sawa, Hitoshi; Kobayashi, Tetsuya J; Brandão, Hugo B; Shibata, Tatsuo; Sako, Yasushi

2016-08-23

Cell polarity arises through the spatial segregation of polarity regulators. PAR proteins are polarity regulators that localize asymmetrically to two opposing cortical domains. However, it is unclear how the spatially segregated PAR proteins interact to maintain their mutually exclusive partitioning. Here, single-molecule detection analysis in Caenorhabditis elegans embryos reveals that cortical PAR-2 diffuses only short distances, and, as a result, most PAR-2 molecules associate and dissociate from the cortex without crossing into the opposing domain. Our results show that cortical PAR-2 asymmetry is maintained by the local exchange reactions that occur at the cortical-cytoplasmic boundary. Additionally, we demonstrate that local exchange reactions are sufficient to maintain cortical asymmetry in a parameter-free mathematical model. These findings suggest that anterior and posterior PAR proteins primarily interact through the cytoplasmic pool and not via cortical diffusion. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Flux and polarization signals of spatially inhomogeneous gaseous exoplanets

NASA Astrophysics Data System (ADS)

Karalidi, T.; Stam, D. M.; Guirado, D.

2013-07-01

Aims: We present numerically calculated, disk-integrated, spectropolarimetric signals of starlight that is reflected by vertically and horizontally inhomogeneous gaseous exoplanets. We include various spatial features that are present on Solar System's gaseous planets: belts and zones, cyclonic spots, and polar hazes, to test whether such features leave traces in the disk-integrated fux and polarization signals. Methods: Broadband flux and polarization signals of starlight that is reflected by gaseous exoplanets are calculated using an efficient, adding-doubling radiative transfer code, that fully includes single and multiple scattering and polarization. The planetary model atmospheres are vertically inhomogeneous and can be horizontally inhomogeneous, and contain gas molecules and/or cloud and/or aerosol particles. Results: The broadband flux and polarization signals are sensitive to cloud top pressures, although in the presence of local pressure differences, such as in belts and clouds, the flux and polarization phase functions have similar shapes as those of horizontally homogeneous planets. Fitting flux phase functions of a planet with belts and zones using a horizontally homogeneous planet could theoretically yield cloud top pressures that differ by a few hundred mbar from those derived from fitting polarization phase functions. In practice, however, observational errors and uncertainties in cloud properties would make such a fit unreliable. A cyclonic spot like Jupiter's Great Red Spot, covering a few percent of the disk, located in equatorial regions, and rotating in and out of the observer's view yields a temporal variation of a few percent in the broadband flux and a few percent in the degree of polarization. Polar hazes leave strong traces in the polarization of reflected starlight in spatially resolved observations, especially seen at phase angles near 90°. Integrated across the planetary disk, polar hazes that cover only part of the planetary disk

An ensemble and single-molecule fluorescence microscopy investigation of phase-separated monolayer films stained with Nile Red.

PubMed

Lu, Yin; Porterfield, Robyn; Thunder, Terri; Paige, Matthew F

2011-01-01

Phase-separated Langmuir-Blodgett monolayer films prepared from mixtures of arachidic acid (C19H39COOH) and perfluorotetradecanoic acid (C13F27COOH) were stained via spin-casting with the polarity sensitive phenoxazine dye Nile Red, and characterized using a combination of ensemble and single-molecule fluorescence microscopy measurements. Ensemble fluorescence microscopy and spectromicroscopy showed that Nile Red preferentially associated with the hydrogenated domains of the phase-separated films, and was strongly fluorescent in these areas of the film. These measurements, in conjunction with single-molecule fluorescence imaging experiments, also indicated that a small sub-population of dye molecules localizes on the perfluorinated regions of the sample, but that this sub-population is spectroscopically indistinguishable from that associated with the hydrogenated domains. The relative importance of selective dye adsorption and local polarity sensitivity of Nile Red for staining applications in phase-separated LB films as well as in cellular environments is discussed in context of the experimental results. Copyright © 2010 Elsevier B.V. All rights reserved.

Building one molecule from a reservoir of two atoms

NASA Astrophysics Data System (ADS)

Liu, L. R.; Hood, J. D.; Yu, Y.; Zhang, J. T.; Hutzler, N. R.; Rosenband, T.; Ni, K.-K.

2018-05-01

Chemical reactions typically proceed via stochastic encounters between reactants. Going beyond this paradigm, we combined exactly two atoms in a single, controlled reaction. The experimental apparatus traps two individual laser-cooled atoms [one sodium (Na) and one cesium (Cs)] in separate optical tweezers and then merges them into one optical dipole trap. Subsequently, photoassociation forms an excited-state NaCs molecule. The discovery of previously unseen resonances near the molecular dissociation threshold and measurement of collision rates are enabled by the tightly trapped ultracold sample of atoms. As laser-cooling and trapping capabilities are extended to more elements, the technique will enable the study of more diverse, and eventually more complex, molecules in an isolated environment, as well as synthesis of designer molecules for qubits.

Parasitic helminths: a pharmacopeia of anti-inflammatory molecules.

PubMed

Johnston, M J G; MacDonald, J A; McKay, D M

2009-02-01

Infection with parasitic helminths takes a heavy toll on the health and well-being of humans and their domestic livestock, concomitantly resulting in major economic losses. Analyses have consistently revealed bioactive molecules in extracts of helminths or in their excretory/secretory products that modulate the immune response of the host. It is our view that parasitic helminths are an untapped source of immunomodulatory substances that, in pure form, could become new drugs (or models for drug design) to treat disease. Here, we illustrate the range of immunomodulatory molecules in selected parasitic trematodes, cestodes and nematodes, their impact on the immune cells in the host and how the host may recognize these molecules. There are many examples of the partial characterization of helminth-derived immunomodulatory molecules, but these have not yet translated into new drugs, reflecting the difficulty of isolating and fully characterizing proteins, glycoproteins and lipid-based molecules from small amounts of parasite material. However, this should not deter the investigator, since analytical techniques are now being used to accrue considerable structural information on parasite-derived molecules, even when only minute quantities of tissue are available. With the introduction of methodologies to purify and structurally-characterize molecules from small amounts of tissue and the application of high throughput immunological assays, one would predict that an assessment of parasitic helminths will yield a variety of novel drug candidates in the coming years.

Defining RNA–Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA

PubMed Central

2017-01-01

RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif–small molecule interactions identified via selection. Named High Throughput Structure–Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif–small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule–RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs. PMID:28386598

Dielectric response of molecules in empirical tight-binding theory

NASA Astrophysics Data System (ADS)

Boykin, Timothy B.; Vogl, P.

2002-01-01

In this paper we generalize our previous approach to electromagnetic interactions within empirical tight-binding theory to encompass molecular solids and isolated molecules. In order to guarantee physically meaningful results, we rederive the expressions for relevant observables using commutation relations appropriate to the finite tight-binding Hilbert space. In carrying out this generalization, we examine in detail the consequences of various prescriptions for the position and momentum operators in tight binding. We show that attempting to fit parameters of the momentum matrix directly generally results in a momentum operator which is incompatible with the underlying tight-binding model, while adding extra position parameters results in numerous difficulties, including the loss of gauge invariance. We have applied our scheme, which we term the Peierls-coupling tight-binding method, to the optical dielectric function of the molecular solid PPP, showing that this approach successfully predicts its known optical properties even in the limit of isolated molecules.

Synaptic Polarity Depends on Phosphatidylinositol Signaling Regulated by myo-Inositol Monophosphatase in Caenorhabditis elegans

PubMed Central

Kimata, Tsubasa; Tanizawa, Yoshinori; Can, Yoko; Ikeda, Shingo; Kuhara, Atsushi; Mori, Ikue

2012-01-01

Although neurons are highly polarized, how neuronal polarity is generated remains poorly understood. An evolutionarily conserved inositol-producing enzyme myo-inositol monophosphatase (IMPase) is essential for polarized localization of synaptic molecules in Caenorhabditis elegans and can be inhibited by lithium, a drug for bipolar disorder. The synaptic defect of IMPase mutants causes defects in sensory behaviors including thermotaxis. Here we show that the abnormalities of IMPase mutants can be suppressed by mutations in two enzymes, phospholipase Cβ or synaptojanin, which presumably reduce the level of membrane phosphatidylinositol 4,5-bisphosphate (PIP2). We also found that mutations in phospholipase Cβ conferred resistance to lithium treatment. Our results suggest that reduction of PIP2 on plasma membrane is a major cause of abnormal synaptic polarity in IMPase mutants and provide the first in vivo evidence that lithium impairs neuronal PIP2 synthesis through inhibition of IMPase. We propose that the PIP2 signaling regulated by IMPase plays a novel and fundamental role in the synaptic polarity. PMID:22446320

Comment on "Cosmic-ray-driven reaction and greenhouse effect of halogenated molecules: Culprits for atmospheric ozone depletion and global climate change"

NASA Astrophysics Data System (ADS)

Müller, Rolf; Grooß, Jens-Uwe

2014-04-01

Lu's "cosmic-ray-driven electron-induced reaction (CRE) theory" is based on the assumption that the CRE reaction of halogenated molecules (e.g., chlorofluorocarbons (CFCs), HCl, ClONO2) adsorbed or trapped in polar stratospheric clouds in the winter polar stratosphere is the key step in forming photoactive halogen species that are the cause of the springtime ozone hole. This theory has been extended to a warming theory of halogenated molecules for climate change. In this comment, we discuss the chemical and physical foundations of these theories and the conclusions derived from the theories. First, it is unclear whether the loss rates of halogenated molecules induced by dissociative electron attachment (DEA) observed in the laboratory can also be interpreted as atmospheric loss rates, but even if this were the case, the impact of DEA-induced reactions on polar chlorine activation and ozone loss in the stratosphere is limited. Second, we falsify several conclusions that are reported on the basis of the CRE theory: There is no polar ozone loss in darkness, there is no apparent 11-year periodicity in polar total ozone measurements, the age of air in the polar lower stratosphere is much older than 1-2 years, and the reported detection of a pronounced recovery (by about 20-25%) in Antarctic total ozone measurements by the year 2010 is in error. There are also conclusions about the future development of sea ice and global sea level which are fundamentally flawed because Archimedes' principle is neglected. Many elements of the CRE theory are based solely on correlations between certain datasets which are no substitute for providing physical and chemical mechanisms causing a particular behavior noticeable in observations. In summary, the CRE theory cannot be considered as an independent, alternative mechanism for polar stratospheric ozone loss and the conclusions on recent and future surface temperature and global sea level change do not have a physical basis.

Spin-Dependent Transport through Chiral Molecules Studied by Spin-Dependent Electrochemistry

PubMed Central

2016-01-01

Conspectus Molecular spintronics (spin + electronics), which aims to exploit both the spin degree of freedom and the electron charge in molecular devices, has recently received massive attention. Our recent experiments on molecular spintronics employ chiral molecules which have the unexpected property of acting as spin filters, by way of an effect we call “chiral-induced spin selectivity” (CISS). In this Account, we discuss new types of spin-dependent electrochemistry measurements and their use to probe the spin-dependent charge transport properties of nonmagnetic chiral conductive polymers and biomolecules, such as oligopeptides, L/D cysteine, cytochrome c, bacteriorhodopsin (bR), and oligopeptide-CdSe nanoparticles (NPs) hybrid structures. Spin-dependent electrochemical measurements were carried out by employing ferromagnetic electrodes modified with chiral molecules used as the working electrode. Redox probes were used either in solution or when directly attached to the ferromagnetic electrodes. During the electrochemical measurements, the ferromagnetic electrode was magnetized either with its magnetic moment pointing “UP” or “DOWN” using a permanent magnet (H = 0.5 T), placed underneath the chemically modified ferromagnetic electrodes. The spin polarization of the current was found to be in the range of 5–30%, even in the case of small chiral molecules. Chiral films of the l- and d-cysteine tethered with a redox-active dye, toludin blue O, show spin polarizarion that depends on the chirality. Because the nickel electrodes are susceptible to corrosion, we explored the effect of coating them with a thin gold overlayer. The effect of the gold layer on the spin polarization of the electrons ejected from the electrode was investigated. In addition, the role of the structure of the protein on the spin selective transport was also studied as a function of bias voltage and the effect of protein denaturation was revealed. In addition to �

Cell cycle entry triggers a switch between two modes of Cdc42 activation during yeast polarization

PubMed Central

Witte, Kristen; Strickland, Devin; Glotzer, Michael

2017-01-01

Cell polarization underlies many cellular and organismal functions. The GTPase Cdc42 orchestrates polarization in many contexts. In budding yeast, polarization is associated with a focus of Cdc42•GTP which is thought to self sustain by recruiting a complex containing Cla4, a Cdc42-binding effector, Bem1, a scaffold, and Cdc24, a Cdc42 GEF. Using optogenetics, we probe yeast polarization and find that local recruitment of Cdc24 or Bem1 is sufficient to induce polarization by triggering self-sustaining Cdc42 activity. However, the response to these perturbations depends on the recruited molecule, the cell cycle stage, and existing polarization sites. Before cell cycle entry, recruitment of Cdc24, but not Bem1, induces a metastable pool of Cdc42 that is sustained by positive feedback. Upon Cdk1 activation, recruitment of either Cdc24 or Bem1 creates a stable site of polarization that induces budding and inhibits formation of competing sites. Local perturbations have therefore revealed unexpected features of polarity establishment. DOI: http://dx.doi.org/10.7554/eLife.26722.001 PMID:28682236

Towards attosecond measurement in molecules and at surfaces

NASA Astrophysics Data System (ADS)

Marangos, Jonathan

2015-05-01

1) We will present a number of experimental approaches that are being developed at Imperial College to make attosecond timescale measurements of electronic dynamics in suddenly photoionized molecules and at surfaces. A brief overview will be given of some of the unanswered questions in ultrafast electron and hole dynamics in molecules and solids. These questions include the existence of electronic charge migration in molecules and how this process might couple to nuclear motion even on the few femtosecond timescale. How the timescale of photoemission from a surface may differ from that of an isolated atom, e.g. due to electron transport phenomena associated with the distance from the surface of the emitting atom and the electron dispersion relation, is also an open question. 2) The measurement techniques we are currently developing to answer these questions are HHG spectroscopy, attosecond pump-probe photoelectron/photoion studies, and attosecond pump-probe transient absorption as well as attosecond streaking for measuring surface emission. We will present recent advances in generating two synchronized isolated attosecond pulses at different colours for pump-probe measurements (at 20 eV and 90 eV respectively). Results on generation of isolated attosecond pulses at 300 eV and higher photon energy using a few-cycle 1800 nm OPG source will be presented. The use of these resources for making pump-probe measurements will be discussed. Finally we will present the results of streaking measurement of photoemission wavepackets from two types of surface (WO3 and a evaporated Au film) that show a temporal broadening of ~ 100 as compared to atomic streaks that is consistent with the electron mean free path in these materials. Work supported by ERC and EPSRC.

Extraction, isolation, and aromatase inhibitory evaluation of low-polar ginsenosides from Panax ginseng leaves.

PubMed

Zhang, Yuchi; Zhang, Jianxu; Liu, Chunming; Yu, Min; Li, Sainan

2017-02-03

A hyphenated accelerated solvent extraction (ASE) technique was elaborately coupled with centrifugal partition chromatography (CPC), ultra-high-performance liquid chromatography (UHPLC), and photo-diode array detector (PDA). This approach was applied to obtain low-polar ginsenoside fractions from the leaves of Panax ginseng. The CPC fractions were isolated and analyzed using the hyphenated technique, and followed by testing and evaluation of their aromatase inhibitory effects. Subsequently, the aromatase inhibition rates of the compositions in the CPC fractions were calculated using a multivariable linear regression model. A biphasic ethyl acetate/n-butanol/ethanol/water solvent system with respective volume ratios of 10:2:2:8 was used for the ASE and CPC separation of 200g of leaves of P. ginseng raw material. The (lower) aqueous phase of the abovementioned solvent system was used as the extraction solvent. The ginsenosides were subjected to ASE, and the extraction solution was pumped into the sample loop and then directly into the CPC column. The CPC fractions were collected and monitored by an online UHPLC/PDA system at 5-min intervals. The aromatase inhibitory activities of CPC fractions were analyzed by a fluorescence method, with mathematical calculations indicating that the inhibition rates of ginsenosides Rk 1 , Rg 5 , Rs 5 , 20R-Rg 3 , and Rs 4 exceeded 50.00%; indicating that the aforementioned chemical compounds have potential for further development. The results were validated by comparison with authentic standards, indicating that the method used in this research was accurate and advantageous for matrix analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Crystal structure of a new polar borate Na{sub 2}Ce{sub 2}[BO{sub 2}(OH)][BO{sub 3}]{sub 2} · H{sub 2}O with isolated boron triangles

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

Topnikova, A. P.; Belokoneva, E. L., E-mail: elbel@geol.msu.ru; Dimitrova, O. V.

2016-11-15

Crystals of a new polar borate Na{sub 2}Ce{sub 2}[BO{sub 2}(OH)][BO{sub 3}]{sub 2} · H{sub 2}O were prepared by hydrothermal synthesis. The crystals are orthorhombic, a = 7.2295(7) Å, b = 11.2523(8) Å, c = 5.1285(6) Å, Z = 2, sp. gr. C2mm (Amm2), R = 0.0253. The formula of the compound was derived from the structure determination. The Ce and Na atoms are coordinated by nine and six O atoms, respectively. The Ce position is split, and a small amount of Ce is incorporated into the Na1 site with the isomorphous substitution for Na. The anionic moieties exist as isolatedmore » BO{sub 3} and BO{sub 2}(OH) triangles. The planes of the BO{sub 2}(OH) triangles with mm2 symmetry are parallel to the ab plane. The planes of the BO{sub 3} triangles with m symmetry are perpendicular to the ab plane and are rotated in a diagonal way. The splitting of the Ce positions and the polar arrangement of the BO{sub 2}(OH) triangles, water molecules, and Na atoms are observed along the polar a axis. The new structure is most similar to the new borate NaCa{sub 4}[BO{sub 3}]{sub 3} (sp. gr. Ama2), in which triangles of one type are arranged in a polar fashion along the c axis. Weak nonlinear-optical properties of both polar borates are attributed to the quenching of the second-harmonic generation due to the mutually opposite orientation of two-thirds of B triangles in the unit cell.« less

Measurement of polarization observables in vector meson photoproduction using a transversely-polarized frozen-spin target and polarized photons at CLAS, Jefferson Lab

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

Roy, Priyashree

The study of baryon resonances provides a deeper understanding of the strong interaction because the dynamics and relevant degrees of freedom hidden within them are re ected by the properties of the excited states of baryons. Higher-lying excited states at and above 1.7 GeV/c 2 are generally predicted to have strong couplings to final states involving a heavier meson, e. g. one of the vector mesons, ρ, ω φ, as compared to a lighter pseudoscalar meson, e. g. π and η. Decays to the ππΝ final states via πΔ also become more important through the population of intermediate resonances. We observe that nature invests in mass rather than momentum. The excited states of the nucleon are usually found as broadly overlapping resonances which may decay into a multitude of final states involving mesons and baryons. Polarization observables make it possible to isolate single resonance contributions from other interference terms. The CLAS g9 (FROST) experiment, as part of the N* spectroscopy program at Jefferson Laboratory, accumulated photoproduction data using circularly- & linearly-polarized photons incident on a transversely-polarized butanol target (g9b experiment) in the photon energy range 0:3-2:4 GeV & 0:7-2:1 GeV, respectively. In this work, the analysis of reactions and polarization observables which involve two charged pions, either in the fully exclusive reaction γρ -> ρπ+π- or in the semi-exclusive reaction with a missing neutral pion, γρ -> ρπ +π -(π 0) will be presented. For the reaction ρπ +π -, eight polarization observables (I s, I c, P x, P y,more » $$P^s_{x;y}$$, $$P^c_{x; y}$$) have been extracted. The high statistics data rendered it possible to extract these observables in three dimensions. All of them are first-time measurements. The fairly good agreement of Is, Ic obtained from this analysis with the experimental results from a previous CLAS experiment provides support for the first-time measurements. For the reaction γρ -> �

Radiance, polarization, and ellipticity of the radiation in the earth's atmosphere

NASA Technical Reports Server (NTRS)

Hitzfelder, S. J.; Plass, G. N.; Kattawar, G. W.

1976-01-01

The complete radiation field including polarization is calculated for a model of the real atmosphere by the matrix operator method. The radiance, direction and amount of polarization, and ellipticity are obtained at the top and bottom of the atmosphere for three values of the surface albedo (0; 0.15 0.90) and five solar zenith angles. Scattering and absorption by molecules (including ozone) and by aerosols are taken into account together with the variation of the number density of these substances with height. All results are calculated for both a normal aerosol number and a distribution which is one-third of the normal amount at all heights. The calculated values show general qualitative agreement with the available experimental measurements. The position of the neutral points of the polarization in the principal plane is a sensitive indicator of the characteristics of the aerosol particles in the atmosphere, since it depends on the sign and value of the single scattered polarization for scattering angles around 20 deg and 160 deg for transmitted and reflected photons respectively.

A multi purpose source chamber at the PLEIADES beamline at SOLEIL for spectroscopic studies of isolated species: Cold molecules, clusters, and nanoparticles

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

Lindblad, Andreas; Söderström, Johan; Nicolas, Christophe

2013-11-15

This paper describes the philosophy and design goals regarding the construction of a versatile sample environment: a source capable of producing beams of atoms, molecules, clusters, and nanoparticles in view of studying their interaction with short wavelength (vacuum ultraviolet and x-ray) synchrotron radiation. In the design, specific care has been taken of (a) the use standard components, (b) ensuring modularity, i.e., that swiftly switching between different experimental configurations was possible. To demonstrate the efficiency of the design, proof-of-principle experiments have been conducted by recording x-ray absorption and photoelectron spectra from isolated nanoparticles (SiO{sub 2}) and free mixed clusters (Ar/Xe). Themore » results from those experiments are showcased and briefly discussed.« less

Dramatic enhancement of supercontinuum generation in elliptically-polarized laser filaments

PubMed Central

Rostami, Shermineh; Chini, Michael; Lim, Khan; Palastro, John P.; Durand, Magali; Diels, Jean-Claude; Arissian, Ladan; Baudelet, Matthieu; Richardson, Martin

2016-01-01

Broadband laser sources based on supercontinuum generation in femtosecond laser filamentation have enabled applications from stand-off sensing and spectroscopy to the generation and self-compression of high-energy few-cycle pulses. Filamentation relies on the dynamic balance between self-focusing and plasma defocusing – mediated by the Kerr nonlinearity and multiphoton or tunnel ionization, respectively. The filament properties, including the supercontinuum generation, are therefore highly sensitive to the properties of both the laser source and the propagation medium. Here, we report the anomalous spectral broadening of the supercontinuum for filamentation in molecular gases, which is observed for specific elliptical polarization states of the input laser pulse. The resulting spectrum is accompanied by a modification of the supercontinuum polarization state and a lengthening of the filament plasma column. Our experimental results and accompanying simulations suggest that rotational dynamics of diatomic molecules play an essential role in filamentation-induced supercontinuum generation, which can be controlled with polarization ellipticity. PMID:26847427

On remote sensing of small aerosol particles with polarized light

NASA Astrophysics Data System (ADS)

Sun, W.

2012-12-01

The CALIPSO satellite mission consistently measures volume (including molecule and particulate) light depolarization ratio of ~2% for smoke, compared to ~1% for marine aerosols and ~15% for dust. The observed ~2% smoke depolarization ratio comes primarily from the nonspherical habits of particles in the smoke at certain particle sizes. The depolarization of linearly polarized light by small sphere aggregates and irregular Gaussian-shaped particles is studied, to reveal the physics between the depolarization of linearly polarized light and aerosol shape and size. It is found that randomly oriented nonspherical particles have some common depolarization properties as functions of scattering angle and size parameter. This may be very useful information for active remote sensing of small nonspherical aerosols using polarized light. We also show that the depolarization ratio from the CALIPSO measurements could be used to derive smoke aerosol particle size. The mean particle size of South-African smoke is estimated to be about half of the 532 nm wavelength of the CALIPSO lidar.

Circularly polarized luminescence of syndiotactic polystyrene

NASA Astrophysics Data System (ADS)

Rizzo, Paola; Abbate, Sergio; Longhi, Giovanna; Guerra, Gaetano

2017-11-01

Syndiotactic polystyrene (s-PS) films, when crystallized from the amorphous state by temporary sorption of non-racemic guest molecules (like carvone) not only exhibit unusually high optical activity, both in the UV-Visible and Infrared ranges, but also present circularly polarized luminescence (CPL) with high dissymmetry ratios (g = ΔI/I values in the range 0.02-0.03). Experimental evidences provide support, rather than to the usual molecular circular dichroism, to a supramolecular chiral optical response being extrinsic to the site of photon absorption and emission, possibly associated with a helical morphology of s-PS crystallites.

Demystifying Introductory Chemistry. Part 3: Ionization Energies, Electronegativity, Polar Bonds, and Partial Charges.

ERIC Educational Resources Information Center

Spencer, James; And Others

1996-01-01

Shows how ionization energies provide a convenient method for obtaining electronegativity values that is simpler than the conventional methods. Demonstrates how approximate atomic charges can be calculated for polar molecules and how this method of determining electronegativities may lead to deeper insights than are typically possible for the…

Measuring absolute spin polarization in dissolution-DNP by Spin PolarimetrY Magnetic Resonance (SPY-MR)

NASA Astrophysics Data System (ADS)

Vuichoud, Basile; Milani, Jonas; Chappuis, Quentin; Bornet, Aurélien; Bodenhausen, Geoffrey; Jannin, Sami

2015-11-01

Dynamic nuclear polarization at 1.2 K and 6.7 T allows one to achieve spin temperatures on the order of a few millikelvin, so that the high-temperature approximation (Δ E < kT) is violated for the nuclear Zeeman interaction Δ E = γB0h/(2 π) of most isotopes. Provided that, after rapid dissolution and transfer to an NMR or MRI system, the hyperpolarized molecules contain at least two nuclear spins I and S with a scalar coupling JIS, the polarization of spin I (short for 'investigated') can be determined from the asymmetry AS of the multiplet of spin S (short for 'spy'), provided perturbations due to second-order (strong coupling) effects are properly taken into account. If spin S is suitably discreet and does not affect the relaxation of spin I, this provides an elegant way of measuring spin polarizations 'on the fly' in a broad range of molecules, thus obviating the need for laborious measurements of signal intensities at thermal equilibrium. The method, dubbed Spin PolarimetrY Magnetic Resonance (SPY-MR), is illustrated for various pairs of 13 C spins (I, S) in acetate and pyruvate.

Influence of aerosols, clouds, and sunglint on polarization spectra of Earthshine

NASA Astrophysics Data System (ADS)

Emde, Claudia; Buras-Schnell, Robert; Sterzik, Michael; Bagnulo, Stefano

2017-08-01

Context. Ground-based observations of the Earthshine, I.e., the light scattered by Earth to the Moon, and then reflected back to Earth, simulate space observations of our planet and represent a powerful benchmark for the studies of Earth-like planets. Earthshine spectra are strongly linearly polarized, owing to scattering by molecules and small particles in the atmosphere of the Earth and surface reflection, and may allow us to measure global atmospheric and surface properties of planet Earth. Aims: We aim to interpret already published spectropolarimetric observations of the Earthshine by comparing them with new radiative transfer model simulations including a fully realistic three-dimensional (3D) surface-atmosphere model for planet Earth. Methods: We used the highly advanced Monte Carlo radiative transfer model MYSTIC to simulate polarized radiative transfer in the atmosphere of the Earth without approximations regarding the geometry, taking into account the polarization from surface reflection and multiple scattering by molecules, aerosol particles, cloud droplets, and ice crystals. Results: We have shown that Earth spectropolarimetry is highly sensitive to all these input parameters, and we have presented simulations of a fully realistic Earth atmosphere-surface model including 3D cloud fields and two-dimensional (2D) surface property maps. Our modeling results show that scattering in high ice water clouds and reflection from the ocean surface are crucial to explain the continuum polarization at longer wavelengths as has been reported in Earthshine observations taken at the Very Large Telescope in 2011 (3.8% and 6.6% at 800 nm, depending on which part of Earth was visible from the Moon at the time of the observations). We found that the relatively high degree of polarization of 6.6% can be attributed to light reflected by the ocean surface in the sunglint region. High ice-water clouds reduce the amount of absorption in the O2A band and thus explain the weak O2

Novel papillomavirus isolated from the oral mucosa of a polar bear does not cluster with other papillomaviruses of carnivores.

PubMed

Stevens, Hans; Rector, Annabel; Bertelsen, Mads F; Leifsson, Pall S; Van Ranst, Marc

2008-05-25

Papillomatosis has been documented in several carnivores, and papillomavirus (PV) types have been characterized from lesions in a number of carnivore species: the canine oral PV (COPV), the Felis domesticus PV type 1 (FdPV-1) isolated from a Persian cat, the Procyon lotor PV type 1 (PlPV-1) isolated from a raccoon, the canine PV type 2 (CPV-2) from a dog's foot pad lesion and the canine PV type 3 (CPV-3) associated with a canine epidermodysplasia verruciformis - like disease. A tissue sample was taken from a papillomatous lesion on the oral mucosa of a polar bear (Ursus maritimus). Extracted DNA was used as a template for multiply primed rolling-circle amplification (RCA), and restriction enzyme analysis of the RCA product indicated the presence of papillomaviral DNA. The genome of this PV was cloned and the complete genomic sequence was determined. The Ursus maritimus PV type 1 (UmPV-1) genome counts 7582 basepairs and is smaller than that of other papillomaviruses from carnivore species. UmPV-1 contains the typical noncoding region NCR1, but unlike the carnivore PVs of the Lambda genus, UmPV-1 does not possess a second noncoding region NCR2. Phylogenetic analysis based on a nucleotide sequence alignment of the L1 ORF of UmPV-1 and 51 other PV types indicates that UmPV-1 does not cluster with any of the other carnivore PVs, but branches off near the root of the common branch of the genus Alphapapillomavirus.

Matrix isolation as a tool for studying interstellar chemical reactions

NASA Technical Reports Server (NTRS)

Ball, David W.; Ortman, Bryan J.; Hauge, Robert H.; Margrave, John L.

1989-01-01

Since the identification of the OH radical as an interstellar species, over 50 molecular species were identified as interstellar denizens. While identification of new species appears straightforward, an explanation for their mechanisms of formation is not. Most astronomers concede that large bodies like interstellar dust grains are necessary for adsorption of molecules and their energies of reactions, but many of the mechanistic steps are unknown and speculative. It is proposed that data from matrix isolation experiments involving the reactions of refractory materials (especially C, Si, and Fe atoms and clusters) with small molecules (mainly H2, H2O, CO, CO2) are particularly applicable to explaining mechanistic details of likely interstellar chemical reactions. In many cases, matrix isolation techniques are the sole method of studying such reactions; also in many cases, complexations and bond rearrangements yield molecules never before observed. The study of these reactions thus provides a logical basis for the mechanisms of interstellar reactions. A list of reactions is presented that would simulate interstellar chemical reactions. These reactions were studied using FTIR-matrix isolation techniques.