Method and apparatus for reducing solvent luminescence background emissions

DOEpatents

Affleck, Rhett L.; Ambrose, W. Patrick; Demas, James N.; Goodwin, Peter M.; Johnson, Mitchell E.; Keller, Richard A.; Petty, Jeffrey T.; Schecker, Jay A.; Wu, Ming

1998-01-01

The detectability of luminescent molecules in solution is enhanced by reducing the background luminescence due to impurity species also present in the solution. A light source that illuminates the solution acts to photolyze the impurities so that the impurities do not luminesce in the fluorescence band of the molecule of interest. Molecules of interest may be carried through the photolysis region in the solution or may be introduced into the solution after the photolysis region.

Ground Based Program for the Physical Analysis of Macromolecular Crystal Growth

NASA Technical Reports Server (NTRS)

Malkin, Alexander J.

1998-01-01

During the past year we have focused on application of in situ Atomic Force Microscopy (AFM) for studies of the growth mechanisms and kinetics of crystallization for different macromolecular systems. Mechanisms of macrostep formation and their decay, which are important in understanding of defect formation, were studied on the surfaces of thaumatin, catalase, canavalin and lysozyme crystals. Experiments revealed that step bunching on crystalline surfaces occurred either due to two- or three-dimensional nucleation on the terraces of vicinal slopes or as a result of uneven step generation by complex dislocation sources. No step bunching arising from interaction of individual steps in the course of the experiment was observed. The molecular structure of the growth steps for thaumatin and lipase crystals were deduced. It was further shown that growth step advance occurs by incorporation of single protein molecules. In singular directions growth steps move by one-dimensional nucleation on step edges followed by lateral growth. One-dimensional nuclei have different sizes, less then a single unit cell, varying for different directions of step movement. There is no roughness due to thermal fluctuations, and each protein molecule which incorporated into the step remained. Growth kinetics for catalase crystals was investigated over wide supersaturation ranges. Strong directional kinetic anisotropy in the tangential step growth rates in different directions was seen. The influence of impurities on growth kinetics and cessation of macromolecular crystals was studied. Thus, for catalase, in addition to pronounced impurity effects on the kinetics of crystallization, we were also able to directly observe adsorption of some impurities. At low supersaturation we repeatedly observed filaments which formed from impurity molecules sedimenting on the surfaces. Similar filaments were observed on the surfaces of thaumatin, canavalin and STMV crystals as well, but the frequency was low compared with catalase crystallization. Cessation of growth of xylanase and lysozyme crystals was also observed and appeared to be a consequence of the formation of dense impurity adsorption layers. Attachment: "An in situ AFM investigation of catalase crystallization", "Atomic force microscopy studies of living cells: visualization of motility, division, aggregation, transformation, and apoptosis", AFM studies on mechanisms of nucleation and growth of macromolecular crystals", and "In situ atomic force microscopy studies of surface morphology, growth kinetics, defect structure and dissolution in macromolecular crystallization".

Persistent Infrared Spectral Hole-Burning for Impurity Vibrational Modes in Solids.

DTIC Science & Technology

1986-09-30

infrared vibrational transitions of impurity molecules in solids. Examples include 1,2- difluoroethane in rare gas matrices, perrhenate ions in alkali...observed consists of infrared vibrational transitions of impurity molecules in solids. Examples include 1,2- difluoroethane in rare gas matrices...solids. Examples include 1,2- difluoroethane in rare gas matrices, perrhenate ions in alkali halide crystals, and most recently, cyanide and nitrite

Multi-orbital non-crossing approximation from maximally localized Wannier functions: the Kondo signature of copper phthalocyanine on Ag(100).

PubMed

Korytár, Richard; Lorente, Nicolás

2011-09-07

We have developed a multi-orbital approach to compute the electronic structure of a quantum impurity using the non-crossing approximation. The calculation starts with a mean-field evaluation of the system's electronic structure using a standard quantum chemistry code; here we use density functional theory (DFT). We transformed the one-electron structure into an impurity Hamiltonian by using maximally localized Wannier functions. Hence, we have developed a method to study the Kondo effect in systems based on an initial one-electron calculation. We have applied our methodology to a copper phthalocyanine molecule chemisorbed on Ag(100), and we have described its spectral function for three different cases where the molecule presents a single spin or two spins with ferro- and anti-ferromagnetic exchange couplings. We find that the use of broken-symmetry mean-field theories such as Kohn-Sham DFT cannot deal with the complexity of the spin of open-shell molecules on metal surfaces and extra modeling is needed. © 2011 IOP Publishing Ltd

Cryogenic molecular separation system for radioactive (11)C ion acceleration.

PubMed

Katagiri, K; Noda, A; Suzuki, K; Nagatsu, K; Boytsov, A Yu; Donets, D E; Donets, E D; Donets, E E; Ramzdorf, A Yu; Nakao, M; Hojo, S; Wakui, T; Noda, K

2015-12-01

A (11)C molecular production/separation system (CMPS) has been developed as part of an isotope separation on line system for simultaneous positron emission tomography imaging and heavy-ion cancer therapy using radioactive (11)C ion beams. In the ISOL system, (11)CH4 molecules will be produced by proton irradiation and separated from residual air impurities and impurities produced during the irradiation. The CMPS includes two cryogenic traps to separate specific molecules selectively from impurities by using vapor pressure differences among the molecular species. To investigate the fundamental performance of the CMPS, we performed separation experiments with non-radioactive (12)CH4 gases, which can simulate the chemical characteristics of (11)CH4 gases. We investigated the separation of CH4 molecules from impurities, which will be present as residual gases and are expected to be difficult to separate because the vapor pressure of air molecules is close to that of CH4. We determined the collection/separation efficiencies of the CMPS for various amounts of air impurities and found desirable operating conditions for the CMPS to be used as a molecular separation device in our ISOL system.

The Effects of Impurities on Protein Crystal Growth and Nucleation: A Preliminary Study

NASA Technical Reports Server (NTRS)

Schall, Constance A.

1998-01-01

Kubota and Mullin (1995) devised a simple model to account for the effects of impurities on crystal growth of small inorganic and organic molecules in aqueous solutions. Experimentally, the relative step velocity and crystal growth of these molecules asymptotically approach zero or non-zero values with increasing concentrations of impurities. Alternatively, the step velocity and crystal growth can linearly approach zero as the impurity concentration increases. The Kubota-Mullin model assumes that the impurity exhibits Langmuirian adsorption onto the crystal surface. Decreases in step velocities and subsequent growth rates are related to the fractional coverage (theta) of the crystal surface by adsorbed impurities; theta = Kx / (I +Kx), x = mole fraction of impurity in solution. In the presence of impurities, the relative step velocity, V/Vo, and the relative growth rate of a crystal face, G/Go, are proposed to conform to the following equations: V/Vo approx. = G/Go = 1 - (alpha)(theta). The adsorption of impurity is assumed to be rapid and in quasi-equilibrium with the crystal surface sites available. When the value of alpha, an effectiveness factor, is one the growth will asymptotically approach zero with increasing concentrations of impurity. At values less than one, growth approaches a non-zero value asymptotically. When alpha is much greater than one, there will be a linear relationship between impurity concentration and growth rates. Kubota and Mullin expect alpha to decrease with increasing supersaturation and shrinking size of a two dimensional nucleus. It is expected that impurity effects on protein crystal growth will exhibit behavior similar to that of impurities in small molecule growth. A number of proteins were added to purified chicken egg white lysozyme, the effect on crystal nucleation and growth assessed.

Single-Molecule Optical Spectroscopy and Imaging: From Early Steps to Recent Advances

NASA Astrophysics Data System (ADS)

Moerner, William E.

The initial steps toward optical detection and spectroscopy of single molecules arose out of the study of spectral hole-burning in inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989. In the early 1990s, many fascinating physical effects were observed for individual molecules such as spectral diffusion, optical switching, vibrational spectra, and magnetic resonance of a single molecular spin. Since the mid-1990s when experiments moved to room temperature, a wide variety of biophysical effects may be explored, and a number of physical phenomena from the low temperature studies have analogs at high temperature. Recent advances worldwide cover a huge range, from in vitro studies of enzymes, proteins, and oligonucleotides, to observations in real time of a single protein performing a specific function inside a living cell. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation of individual fluorophores leads naturally to localization beyond the optical diffraction limit. Combining this with active optical control of the number of emitting molecules leads to superresolution imaging, a new frontier for optical microscopy beyond the optical diffraction limit and for chemical design of photoswitchable fluorescent labels. Finally, to study one molecule in aqueous solution without surface perturbations, a new electrokinetic trap is described (the ABEL trap) which can trap single small biomolecules without the need for large dielectric beads.

Optical Spectra and Kinetics of Single Impurity Molecules in a Polymer: Spectral Diffusion and Persistent Spectral Hole-Burning

DTIC Science & Technology

1991-11-07

new area of opticAl sp,,ctroscopy of solids where truly unique single environments and quantum effects can be studied in detail. In the pentacene in p...observed. Until very recentlx, the reports of SMI) have concentrated on the crystalline system of pentacene in p-terphenyl. Owing to the complex physical...excessive PSIIB, pentacene in benzoi, acid, is described briefly. The advantages of the perylene in PF_. system become evident immediately when

Magnetic field effect on pentacene-doped sexithiophene diodes

NASA Astrophysics Data System (ADS)

Pham, Song-Toan; Fayolle, Marine; Ohto, Tatsuhiko; Tada, Hirokazu

2017-11-01

We studied the effect of impurities on the magnetoresistance of sexithiophene-based diodes using impedance spectroscopy. The impurities were introduced by doping pentacene molecules into a sexithiophene film through a co-evaporation process. The pentacene molecules act as charge-scattering centers, which trigger the negative magnetoresistance of the device. This makes it possible to tune the value of magnetoresistance from positive to negative by increasing the applied voltage. The beneficial properties induced by impurities suggest a potential route to integrate additional functions into organic devices.

Solutal Convection Around Growing Protein Crystal and Diffusional Purification in Space

NASA Technical Reports Server (NTRS)

Lee, Chun P.; Chernov, Alexander A.

2004-01-01

At least some protein crystals were found to preferentially trap microheterogeneous impurities. The latter are, for example, dimmer molecules of the crystallizing proteines (e.g. ferritin, lysozyme), or the regular molecules on which surfaces small molecules or ions are adsorbed (e.g. acetilated lysozyme) and modi@ molecular charge. Impurities may induce lattice defects and deteriorate structural resolution. Distribution of impurities between mother solution and gorwing crystal is defined by two interrelated distribution coefficients: kappa = rho(sup c, sub 2) and K = (rho(sup c, sub 2)/rho(sup c, sub 1)/rho(sub 2)/rho(sub 1). Here, rho(sub 2), rho(sub 1) and rho(sup c, sub 2) are densities of impurity (2) and regular protein (1) in solution at the growing interface and within the crystal ("c"). For the microheterogeneous impurities studied, K approx. = 2 - 4, so that kappa approx. - 10(exp 2) - 10(exp 3), since K = kappa (rho(sub 1)/rho(sup c, sub 1) and protein solubility ratio rho(sub 1)/rho(sub=p c, sub 2) much less than 1. Therefore, a crystal growing in absence of convection purifies mother solution around itself, grows cleaner and, probably, more perfect. If convection is present, the solution flow permanently brings new impurities to the crystal. This work theoretically addressed two subjects: 1) onset of convection, 2) distribution of impurities.

Impurity bound states in mesoscopic topological superconducting loops

NASA Astrophysics Data System (ADS)

Jin, Yan-Yan; Zha, Guo-Qiao; Zhou, Shi-Ping

2018-06-01

We study numerically the effect induced by magnetic impurities in topological s-wave superconducting loops with spin-orbit interaction based on spin-generalized Bogoliubov-de Gennes equations. In the case of a single magnetic impurity, it is found that the midgap bound states can cross the Fermi level at an appropriate impurity strength and the circulating spin current jumps at the crossing point. The evolution of the zero-energy mode can be effectively tuned by the located site of a single magnetic impurity. For the effect of many magnetic impurities, two independent midway or edge impurities cannot lead to the overlap of zero modes. The multiple zero-energy modes can be effectively realized by embedding a single Josephson junction with impurity scattering into the system, and the spin current displays oscillatory feature with increasing the layer thickness.

Screening of charged impurities as a possible mechanism for conductance change in graphene gas sensing

NASA Astrophysics Data System (ADS)

Liang, Sang-Zi; Chen, Gugang; Harutyunyan, Avetik R.; Sofo, Jorge O.

2014-09-01

In carbon nanotube and graphene gas sensing, the measured conductance change after the sensor is exposed to target molecules has been traditionally attributed to carrier density change due to charge transfer between the sample and the adsorbed molecule. However, this explanation has many problems when it is applied to graphene: The increased amount of Coulomb impurities should lead to decrease in carrier mobility which was not observed in many experiments, carrier density is controlled by the gate voltage in the experimental setup, and there are inconsistencies in the energetics of the charge transfer. In this paper we explore an alternative mechanism. Charged functional groups and dipolar molecules on the surface of graphene may counteract the effect of charged impurities on the substrate. Because scattering of electrons with these charged impurities has been shown to be the limiting factor in graphene conductivity, this leads to significant changes in the transport behavior. A model for the conductivity is established using the random phase approximation dielectric function of graphene and the first-order Born approximation for scattering. The model predicts optimal magnitudes for the charge and dipole moment which maximally screen a given charged impurity. The dipole screening is shown to be generally weaker than the charge screening although the former becomes more effective with higher gate voltage away from the charge neutrality point. The model also predicts that with increasing amount of adsorbates, the charge impurities eventually become saturated and additional adsorption always lead to decreasing conductivity.

The threshold sensitivity of the molecular condensation nuclei detector

NASA Astrophysics Data System (ADS)

Kuptsov, Vladimir D.; Katelevsky, Vadim Y.; Valyukhov, Vladimir P.

2015-05-01

Molecular condensation nuclei (MCN) method is used in production engineering and process monitoring and relates to optical metrology methods of measuring the concentrations of various contaminants in the environment. Ultra high sensitivity of MCN method to a class of substances is determined by measuring the optical scattering aerosol particles, at the centers of which are located the detectable impurities molecules. This article investigates the influence of MCN manifestations coefficient (ratio of the concentration of aerosol particles to the concentration of molecules detectable impurities) on the sensitivity of the MCN detector. The MCN method is based on the application of various physicochemical processes to the flow of a gas containing impurities. As a result of these processes aerosol particle that are about 106 times larger than the original molecule of the impurity are produced. The ability of the aerosol particle to scatter incident light also increases ~1014 ÷1016 times compared with the original molecule and the aerosol particle with the molecule of the impurity in the center is easily detected by light scattering inside a photometer. By measuring of the light scattering intensity is determined concentration of chemical impurities in the air. An application nephelometric optical metrology scheme of light scattering by aerosol particles ensures stable operation of reliable and flexible measuring systems. Light scattering by aerosol particles is calculated on the basis of the Mie's theory as aerosol particle sizes comparable to the wavelength of the optical radiation. The experimental results are shown for detectable impurities of metal carbonyls. Gas analyzers based on the MCN method find application in industries with the possibility of highly toxic emissions into the atmosphere (carbonyl technology of metal coatings and products, destruction of chemical weapons, etc.), during storage and transportation of toxic substances, as well as in the inspection of large-scale objects. There are some perspective areas of use MCN detector: prevention of illegal use of dangerous substances, revealing of their origin and leakage paths by means of marking with special non-radioactive chemical compounds; investigation of large-scale atmospheric circulation with the help of marking substances; nondestructive inspection for highly efficient filters with indicating agent concentration and for the inspection of the devices of high level tightness (heat-exchangers of fast nuclear reactors).

Paramagnetic Attraction of Impurity-Helium Solids

NASA Technical Reports Server (NTRS)

Bernard, E. P.; Boltnev, R. E.; Khmelenko, V. V.; Lee, D. M.

2003-01-01

Impurity-helium solids are formed when a mixture of impurity and helium gases enters a volume of superfluid helium. Typical choices of impurity gas are hydrogen deuteride, deuterium, nitrogen, neon and argon, or a mixture of these. These solids consist of individual impurity atoms and molecules as well as clusters of impurity atoms and molecules covered with layers of solidified helium. The clusters have an imperfect crystalline structure and diameters ranging up to 90 angstroms, depending somewhat on the choice of impurity. Immediately following formation the clusters aggregate into loosely connected porous solids that are submerged in and completely permeated by the liquid helium. Im-He solids are extremely effective at stabilizing high concentrations of free radicals, which can be introduced by applying a high power RF dis- charge to the impurity gas mixture just before it strikes the super fluid helium. Average concentrations of 10(exp 19) nitrogen atoms/cc and 5 x 10(exp 18) deuterium atoms/cc can be achieved this way. It shows a typical sample formed from a mixture of atomic and molecular hydrogen and deuterium. It shows typical sample formed from atomic and molecular nitrogen. Much of the stability of Im-He solids is attributed to their very large surface area to volume ratio and their permeation by super fluid helium. Heat resulting from a chance meeting and recombination of free radicals is quickly dissipated by the super fluid helium instead of thermally promoting the diffusion of other nearby free radicals.

Chromatographic resolution of closely related species in pharmaceutical chemistry: dehalogenation impurities and mixtures of halogen isomers.

PubMed

Regalado, Erik L; Zhuang, Ping; Chen, Yadan; Makarov, Alexey A; Schafer, Wes A; McGachy, Neil; Welch, Christopher J

2014-01-07

In recent years, the use of halogen-containing molecules has proliferated in the pharmaceutical industry, where the incorporation of halogens, especially fluorine, has become vitally important for blocking metabolism and enhancing the biological activity of pharmaceuticals. The chromatographic separation of halogen-containing pharmaceuticals from associated isomers or dehalogenation impurities can sometimes be quite difficult. In an attempt to identify the best current tools available for addressing this important problem, a survey of the suitability of four chromatographic method development platforms (ultra high-performance liquid chromatography (UHPLC), core shell HPLC, achiral supercritical fluid chromatography (SFC) and chiral SFC) for separating closely related mixtures of halogen-containing pharmaceuticals and their dehalogenated isosteres is described. Of the 132 column and mobile phase combinations examined for each mixture, a small subset of conditions were found to afford the best overall performance, with a single UHPLC method (2.1 × 50 mm, 1.9 μm Hypersil Gold PFP, acetonitrile/methanol based aqueous eluents containing either phosphoric or perchloric acid with 150 mM sodium perchlorate) affording excellent separation for all samples. Similarly, a survey of several families of closely related halogen-containing small molecules representing the diversity of impurities that can sometimes be found in purchased starting materials for synthesis revealed chiral SFC (Chiralcel OJ-3 and Chiralpak IB, isopropanol or ethanol with 25 mM isobutylamine/carbon dioxide) as well as the UHPLC (2.1 × 50 mm, 1.8 μm ZORBAX RRHD Eclipse Plus C18 and the Gold PFP, acetonitrile/methanol based aqueous eluents containing phosphoric acid) as preferred methods.

Sub-molecular modulation of a 4f driven Kondo resonance by surface-induced asymmetry

NASA Astrophysics Data System (ADS)

Warner, Ben; El Hallak, Fadi; Atodiresei, Nicolae; Seibt, Philipp; Prüser, Henning; Caciuc, Vasile; Waters, Michael; Fisher, Andrew J.; Blügel, Stefan; van Slageren, Joris; Hirjibehedin, Cyrus F.

2016-09-01

Coupling between a magnetic impurity and an external bath can give rise to many-body quantum phenomena, including Kondo and Hund's impurity states in metals, and Yu-Shiba-Rusinov states in superconductors. While advances have been made in probing the magnetic properties of d-shell impurities on surfaces, the confinement of f orbitals makes them difficult to access directly. Here we show that a 4f driven Kondo resonance can be modulated spatially by asymmetric coupling between a metallic surface and a molecule containing a 4f-like moment. Strong hybridization of dysprosium double-decker phthalocyanine with Cu(001) induces Kondo screening of the central magnetic moment. Misalignment between the symmetry axes of the molecule and the surface induces asymmetry in the molecule's electronic structure, spatially mediating electronic access to the magnetic moment through the Kondo resonance. This work demonstrates the important role that molecular ligands have in mediating electronic and magnetic coupling and in accessing many-body quantum states.

Acetylated Lysozyme as Impurity in Lysozyme Crystals: Constant Distribution Coefficient

NASA Technical Reports Server (NTRS)

Thomas, B. R.; Chernov, A. A.

2000-01-01

Hen egg white lysozyme (HEWL) was acetylated to modify molecular charge keeping the molecular size and weight nearly constant. Two derivatives, A and B, more and less acetylated, respectively, were obtained, separated, purified and added to the solution from which crystals of tetragonal HEWL crystals were grown. Amounts of the A or B impurities added were 0.76, 0.38 and 0.1 milligram per millimeter while HEWL concentration were 20, 30 and 40 milligram per milliliter. The crystals grown in 18 experiments for each impurity were dissolved and quantities of A or B additives in these crystals were analyzed by cation exchange high performance liquid chromatography. All the data for each set of 18 samples with the different impurity and regular HEWL concentrations is well described by one distribution coefficient K = 2.15 plus or minus 0.13 for A and K = 3.42 plus or minus 0.25 for B. The observed independence of the distribution coefficient on both the impurity concentration and supersaturation is explained by the dilution model described in this paper. It shows that impurity adsorption and incorporation rate is proportional to the impurity concentration and that the growth rate is proportional to the crystallizing protein in solution. With the kinetic coefficient for crystallization, beta = 5.10(exp -7) centimeters per second, the frequency at which an impurity molecule near the growing interface irreversibly joins a molecular site on the crystal was found to be 3 1 per second, much higher than the average frequency for crystal molecules. For best quality protein crystals it is better to have low microheterogeneous protein impurity concentration and high supers aturation.

Adsorption site analysis of impurity embedded single-walled carbon nanotube bundles

USGS Publications Warehouse

Agnihotri, S.; Mota, J.P.B.; Rostam-Abadi, M.; Rood, M.J.

2006-01-01

Bundle morphology and adsorptive contributions from nanotubes and impurities are studied both experimentally and by simulation using a computer-aided methodology, which employs a small physisorbed probe molecule to explore the porosity of nanotube samples. Grand canonical Monte Carlo simulation of nitrogen adsorption on localized sites of a bundle is carried out to predict adsorption in its accessible internal pore volume and on its external surface as a function of tube diameter. External adsorption is split into the contributions from the clean surface of the outermost nanotubes of the bundle and from the surface of the impurities. The site-specific isotherms are then combined into a global isotherm for a given sample using knowledge of its tube-diameter distribution obtained by Raman spectroscopy. The structural parameters of the sample, such as the fraction of open-ended nanotubes and the contributions from impurities and nanotube bundles to total external surface area, are determined by fitting the experimental nitrogen adsorption data to the simulated isotherm. The degree of closure between experimental and calculated adsorption isotherms for samples manufactured by two different methods, to provide different nanotube morphology and contamination level, further strengthens the validity and resulting interpretations based on the proposed approach. The average number of nanotubes per bundle and average bundle size, within a sample, are also quantified. The proposed method allows for extrapolation of adsorption properties to conditions where the purification process is 100% effective at removing all impurities and opening access to all intrabundle adsorption sites. ?? 2006 Elsevier Ltd. All rights reserved.

Influence of impurities on the high temperature conductivity of SrTiO3

NASA Astrophysics Data System (ADS)

Bowes, Preston C.; Baker, Jonathon N.; Harris, Joshua S.; Behrhorst, Brian D.; Irving, Douglas L.

2018-01-01

In studies of high temperature electrical conductivity (HiTEC) of dielectrics, the impurity in the highest concentration is assumed to form a single defect that controls HiTEC. However, carrier concentrations are typically at or below the level of background impurities, and all impurities may complex with native defects. Canonical defect models ignore complex formation and lump defects from multiple impurities into a single effective defect to reduce the number of associated reactions. To evaluate the importance of background impurities and defect complexes on HiTEC, a grand canonical defect model was developed with input from density functional theory calculations using hybrid exchange correlation functionals. The influence of common background impurities and first nearest neighbor complexes with oxygen vacancies (vO) was studied for three doping cases: nominally undoped, donor doped, and acceptor doped SrTiO3. In each case, conductivity depended on the ensemble of impurity defects simulated with the extent of the dependence governed by the character of the dominant impurity and its tendency to complex with vO. Agreement between simulated and measured conductivity profiles as a function of temperature and oxygen partial pressure improved significantly when background impurities were included in the nominally undoped case. Effects of the impurities simulated were reduced in the Nb and Al doped cases as both elements did not form complexes and were present in concentrations well exceeding all other active impurities. The influence of individual impurities on HiTEC in SrTiO3 was isolated and discussed and motivates further experiments on singly doped SrTiO3.

Simulating Asymmetric Top Impurities in Superfluid Clusters: A para-Water Dopant in para-Hydrogen.

PubMed

Zeng, Tao; Li, Hui; Roy, Pierre-Nicholas

2013-01-03

We present the first simulation study of bosonic clusters doped with an asymmetric top molecule. The path-integral Monte Carlo method with the latest methodological advance in treating rigid-body rotation [Noya, E. G.; Vega, C.; McBride, C. J. Chem. Phys.2011, 134, 054117] is employed to study a para-water impurity in para-hydrogen clusters with up to 20 para-hydrogen molecules. The growth pattern of the doped clusters is similar in nature to that of pure clusters. The para-water molecule appears to rotate freely in the cluster. The presence of para-water substantially quenches the superfluid response of para-hydrogen with respect to the space-fixed frame.

Specific Heat of Octahydro - 1,3,5,7 - Tetranitro - 1,3,5,7 - Tetrazocine (HMX).

DTIC Science & Technology

1983-01-01

impurities probably consist of molecules of similar atomic weights as those present in the HMX molecule. Usually the major impurity in HMX is RDX (5...crystal and powdered blend HMX . Data beyond the normal transformation temperature (i.e. 0*6 transition ) were obtained from 472 to 486*K. Also, due to the...Cady, H.H.; Smith, L.C., "Studies on the Polymorphs of HMX ," Los Alamos Scientific Laboratory, Los Alamos, N.M., LAMS-2652, May 1962. (6) Brill, T.B

Magnetic field effects on the local electronic structure near a single impurity in Graphene

NASA Astrophysics Data System (ADS)

Yang, Ling; Zhu, Jian-Xin; Tsai, Shan-Wen

2011-03-01

Impurities in graphene can have a significant effect on the local electronic structure of graphene when the Fermi level is near the Dirac point. We study the problem of an isolated impurity in a single layer graphene in the presence of a perpendicular magnetic field. We use a linearization approximation for the energy dispersion and employ a T-matrix formalism to calculate the Green's function. We investigate the effect of an external magnetic field on the Friedel oscillations and impurity-induced resonant states. Different types of impurities, such as vacancies, substitutional impurities, and adatoms, are also considered. LY and SWT acknowledge financial support from NSF(DMR-0847801)and from the UC Lab Fees Research Program.

Numerical renormalization group method for entanglement negativity at finite temperature

NASA Astrophysics Data System (ADS)

Shim, Jeongmin; Sim, H.-S.; Lee, Seung-Sup B.

2018-04-01

We develop a numerical method to compute the negativity, an entanglement measure for mixed states, between the impurity and the bath in quantum impurity systems at finite temperature. We construct a thermal density matrix by using the numerical renormalization group (NRG), and evaluate the negativity by implementing the NRG approximation that reduces computational cost exponentially. We apply the method to the single-impurity Kondo model and the single-impurity Anderson model. In the Kondo model, the negativity exhibits a power-law scaling at temperature much lower than the Kondo temperature and a sudden death at high temperature. In the Anderson model, the charge fluctuation of the impurity contributes to the negativity even at zero temperature when the on-site Coulomb repulsion of the impurity is finite, while at low temperature the negativity between the impurity spin and the bath exhibits the same power-law scaling behavior as in the Kondo model.

Stereoselective synthesis from a process research perspective.

PubMed

Hillier, Michael C; Reider, Paul J

2002-03-01

The process chemists' primary responsibility is to develop efficient and reproducible syntheses of pharmaceutically active compounds. This task is complicated when dealing with chiral molecules that often must be made as single isomers according to regulatory guidelines. The presence of any isomeric impurity in the final product, even in small amounts, is usually not acceptable. This requirement necessitates an exquisite understanding of the methods employed in the construction of chiral drugs. However, the chemistry available for this purpose is sometimes limited and often requires a significant amount of effort and creativity to be made both functional and consistent.

Polaronic and dressed molecular states in orbital Feshbach resonances

NASA Astrophysics Data System (ADS)

Xu, Junjun; Qi, Ran

2018-04-01

We consider the impurity problem in an orbital Feshbach resonance (OFR), with a single excited clock state | e ↑⟩ atom immersed in a Fermi sea of electronic ground state | g ↓⟩. We calculate the polaron effective mass and quasi-particle residue, as well as the polaron to molecule transition. By including one particle-hole excitation in the molecular state, we find significant correction to the transition point. This transition point moves toward the BCS side for increasing particle densities, which suggests that the corresponding many-body physics is similar to a narrow resonance.

Organic light-emitting devices using spin-dependent processes

DOEpatents

Vardeny, Z. Valy; Wohlgenannt, Markus

2010-03-23

The maximum luminous efficiency of organic light-emitting materials is increased through spin-dependent processing. The technique is applicable to all electro-luminescent processes in which light is produced by singlet exciton decay, and all devices which use such effects, including LEDs, super-radiant devices, amplified stimulated emission devices, lasers, other optical microcavity devices, electrically pumped optical amplifiers, and phosphorescence (Ph) based light emitting devices. In preferred embodiments, the emissive material is doped with an impurity, or otherwise modified, to increase the spin-lattice relaxation rate (i.e., decrease the spin-lattice time), and hence raise the efficiency of the device. The material may be a polymer, oligomer, small molecule, single crystal, molecular crystal, or fullerene. The impurity is preferably a magnetic or paramagnetic substance. The invention is applicable to IR, UV, and other electromagnetic radiation generation and is thus not limited to the visible region of the spectrum. The methods of the invention may also be combined with other techniques used to improve device performance.

Studies of Atomic Free Radicals Stored in a Cryogenic Environment

NASA Technical Reports Server (NTRS)

Lee, David M.; Hubbard, Dorthy (Technical Monitor); Alexander, Glen (Technical Monitor)

2003-01-01

Impurity-Helium Solids are porous gel-like solids consisting of impurity atoms and molecules surrounded by thin layers of solid helium. They provide an ideal medium for matrix isolation of free radicals to prevent recombination and store chemical energy. In this work electron spin resonance, nuclear magnetic resonance, X-ray diffraction, and ultrasound techniques have all been employed to study the properties of these substances. Detailed studies via electron spin resonance of exchange tunneling chemical reactions involving hydrogen and deuterium molecular and atomic impurities in these solids have been performed and compared with theory. Concentrations of hydrogen approaching the quantum solid criterion have been produced. Structured studies involving X ray diffraction, ultrasound, and electron spin resonance have shown that the impurities in impurity helium solids are predominantly contained in impurity clusters, with each cluster being surrounded by thin layers of solid helium.

Method and apparatus for measuring purity of noble gases

DOEpatents

Austin, Robert

2008-04-01

A device for detecting impurities in a noble gas includes a detection chamber and a source of pulsed ultraviolet light. The pulse of the ultraviolet light is transferred into the detection chamber and onto a photocathode, thereby emitting a cloud of free electrons into the noble gas within the detection chamber. The cloud of electrons is attracted to the opposite end of the detection chamber by a high positive voltage potential at that end and focused onto a sensing anode. If there are impurities in the noble gas, some or all of the electrons within the cloud will bond with the impurity molecules and not reach the sensing anode. Therefore, measuring a lower signal at the sensing anode indicates a higher level of impurities while sensing a higher signal indicates fewer impurities. Impurities in the range of one part per billion can be measured by this device.

Continuous-time quantum Monte Carlo impurity solvers

NASA Astrophysics Data System (ADS)

Gull, Emanuel; Werner, Philipp; Fuchs, Sebastian; Surer, Brigitte; Pruschke, Thomas; Troyer, Matthias

2011-04-01

Continuous-time quantum Monte Carlo impurity solvers are algorithms that sample the partition function of an impurity model using diagrammatic Monte Carlo techniques. The present paper describes codes that implement the interaction expansion algorithm originally developed by Rubtsov, Savkin, and Lichtenstein, as well as the hybridization expansion method developed by Werner, Millis, Troyer, et al. These impurity solvers are part of the ALPS-DMFT application package and are accompanied by an implementation of dynamical mean-field self-consistency equations for (single orbital single site) dynamical mean-field problems with arbitrary densities of states. Program summaryProgram title: dmft Catalogue identifier: AEIL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: ALPS LIBRARY LICENSE version 1.1 No. of lines in distributed program, including test data, etc.: 899 806 No. of bytes in distributed program, including test data, etc.: 32 153 916 Distribution format: tar.gz Programming language: C++ Operating system: The ALPS libraries have been tested on the following platforms and compilers: Linux with GNU Compiler Collection (g++ version 3.1 and higher), and Intel C++ Compiler (icc version 7.0 and higher) MacOS X with GNU Compiler (g++ Apple-version 3.1, 3.3 and 4.0) IBM AIX with Visual Age C++ (xlC version 6.0) and GNU (g++ version 3.1 and higher) compilers Compaq Tru64 UNIX with Compq C++ Compiler (cxx) SGI IRIX with MIPSpro C++ Compiler (CC) HP-UX with HP C++ Compiler (aCC) Windows with Cygwin or coLinux platforms and GNU Compiler Collection (g++ version 3.1 and higher) RAM: 10 MB-1 GB Classification: 7.3 External routines: ALPS [1], BLAS/LAPACK, HDF5 Nature of problem: (See [2].) Quantum impurity models describe an atom or molecule embedded in a host material with which it can exchange electrons. They are basic to nanoscience as representations of quantum dots and molecular conductors and play an increasingly important role in the theory of "correlated electron" materials as auxiliary problems whose solution gives the "dynamical mean field" approximation to the self-energy and local correlation functions. Solution method: Quantum impurity models require a method of solution which provides access to both high and low energy scales and is effective for wide classes of physically realistic models. The continuous-time quantum Monte Carlo algorithms for which we present implementations here meet this challenge. Continuous-time quantum impurity methods are based on partition function expansions of quantum impurity models that are stochastically sampled to all orders using diagrammatic quantum Monte Carlo techniques. For a review of quantum impurity models and their applications and of continuous-time quantum Monte Carlo methods for impurity models we refer the reader to [2]. Additional comments: Use of dmft requires citation of this paper. Use of any ALPS program requires citation of the ALPS [1] paper. Running time: 60 s-8 h per iteration.

Mobile spin impurity in an optical lattice

NASA Astrophysics Data System (ADS)

Duncan, C. W.; Bellotti, F. F.; Öhberg, P.; Zinner, N. T.; Valiente, M.

2017-07-01

We investigate the Fermi polaron problem in a spin-1/2 Fermi gas in an optical lattice for the limit of both strong repulsive contact interactions and one dimension. In this limit, a polaronic-like behaviour is not expected, and the physics is that of a magnon or impurity. While the charge degrees of freedom of the system are frozen, the resulting tight-binding Hamiltonian for the impurity’s spin exhibits an intriguing structure that strongly depends on the filling factor of the lattice potential. This filling dependency also transfers to the nature of the interactions for the case of two magnons and the important spin balanced case. At low filling, and up until near unit filling, the single impurity Hamiltonian faithfully reproduces a single-band, quasi-homogeneous tight-binding problem. As the filling is increased and the second band of the single particle spectrum of the periodic potential is progressively filled, the impurity Hamiltonian, at low energies, describes a single particle trapped in a multi-well potential. Interestingly, once the first two bands are fully filled, the impurity Hamiltonian is a near-perfect realisation of the Su-Schrieffer-Heeger model. Our studies, which go well beyond the single-band approximation, that is, the Hubbard model, pave the way for the realisation of interacting one-dimensional models of condensed matter physics.

Culture of impure human islet fractions in the presence of alpha-1 antitrypsin prevents insulin cleavage and improves islet recovery.

PubMed

Loganathan, G; Dawra, R K; Pugazhenthi, S; Wiseman, A C; Sanders, M A; Saluja, A K; Sutherland, D E R; Hering, B J; Balamurugan, A N

2010-01-01

Exocrine tissue is commonly cotransplanted with islets in autografting and allotransplantation of impure preparations. Proteases and insulin are released by acinar cells and islets, respectively, during pretransplantation culture and also systemically after transplantation. We hypothesized that released proteases could cleave insulin molecules and that addition of alpha-1 antitrypsin (A1AT) to impure islet cultures would block this cleavage, improving islet recovery and function. Trypsin, chymotrypsin, and elastase (TCE) activity and insulin levels were measured in culture supernates of pure (n = 5) and impure (n = 5) islet fractions, which were isolated from deceased donors. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was used to detect insulin after incubation with proteases. We assessed the effects of A1AT supplementation (0.5 mg/mL; n = 4] on TCE activity, insulin levels, culture recovery, and islet quality. The ultrastructure of islets exposed to TCE versus control medium was examined using electron microscopy (EM). Protease (TCE) activity in culture supernatants was indirectly proportional to the percentage purity of islets: pure, impure, or highly impure. Increasingly lower levels of insulin were detected in culture supernatants when higher protease activity levels were present. Insulin levels measured from supernatants of impure and highly impure islet preparations were 61 +/- 23.7% and 34 +/- 33% of that in pure preparations, respectively. Incubation with commercially available proteases (TCE) or exocrine acinar cell supernatant cleaved insulin molecules as assessed using SDS-PAGE. Addition of A1AT to impure islet preparations reduced protease activity and restored normal insulin levels as detected using enzyme-linked immunosorbent assay (ELISA) and SDS-PAGE of culture supernates. A1AT improved insulin levels to 98% +/- 1.3% in impure and 78% +/- 34.2% in highly impure fractions compared with pure islet fractions. A1AT supplementation improved postculture recovery of islets in impure preparations compared with nontreated controls (72% +/- 9% vs 47% +/- 15%). Islet viability as measured using membrane integrity assays was similar in both the control (98% +/- 2%) and the A1AT-treated groups (99% +/- 1%). EM results revealed a reduction or absence of secretory granules after exposure to proteases (TCE). Culture of impure human islet fractions in the presence of A1AT prevented insulin cleavage and improved islet recovery. A1AT supplementation of islet culture media, therefore, may increase the proportion of human islet products that meet release criteria for transplantation. Copyright 2010 Elsevier Inc. All rights reserved.

Force and Conductance Spectroscopy of Single Molecule Junctions

NASA Astrophysics Data System (ADS)

Frei, Michael

Investigation of mechanical properties of single molecule junctions is crucial to develop an understanding and enable control of single molecular junctions. This work presents an experimental and analytical approach that enables the statistical evaluation of force and simultaneous conductance data of metallic atomic point contacts and molecular junctions. A conductive atomic force microscope based break junction technique is developed to form single molecular junctions and collect conductance and force data simultaneously. Improvements of the optical components have been achieved through the use of a super-luminescent diode, enabling tremendous increases in force resolution. An experimental procedure to collect data for various molecular junctions has been developed and includes deposition, calibration, and analysis methods. For the statistical analysis of force, novel approaches based on two dimensional histograms and a direct force identification method are presented. The two dimensional method allows for an unbiased evaluation of force events that are identified using corresponding conductance signatures. This is not always possible however, and in these situations, the force based identification of junction rearrangement events is an attractive alternative method. This combined experimental and analytical approach is then applied to three studies: First, the impact of molecular backbones to the mechanical behavior of single molecule junctions is investigated and it is found that junctions formed with identical linkers but different backbone structure result in junctions with varying breaking forces. All molecules used show a clear molecular signature and force data can be evaluated using the 2D method. Second, the effects of the linker group used to attach molecules to gold electrodes are investigated. A study of four alkane molecules with different linkers finds a drastic difference in the evolution of donor-acceptor and covalently bonded molecules respectively. In fact, the covalent bond is found to significantly distort the metal electrode rearrangement such that junction rearrangement events can no longer be identified with a clean and well defined conductance signature. For this case, the force based identification process is used. Third, results for break junction measurements with different metals are presented. It is found that silver and palladium junctions rupture with forces different from those of gold contacts. In the case of silver experiments in ambient conditions, we can also identify oxygen impurities in the silver contact formation process, leading to force and conductance measurements of silver-oxygen structures. For the future, this work provides an experimental and analytical foundation that will enable insights into single molecule systems not previously accessible.

Impurity coupled to an artificial magnetic field in a Fermi gas in a ring trap

NASA Astrophysics Data System (ADS)

Ünal, F. Nur; Hetényi, B.; Oktel, M. Ã.-.

2015-05-01

The dynamics of a single impurity interacting with a many-particle background is one of the central problems of condensed-matter physics. Recent progress in ultracold-atom experiments makes it possible to control this dynamics by coupling an artificial gauge field specifically to the impurity. In this paper, we consider a narrow toroidal trap in which a Fermi gas is interacting with a single atom. We show that an external magnetic field coupled to the impurity is a versatile tool to probe the impurity dynamics. Using a Bethe ansatz, we calculate the eigenstates and corresponding energies exactly as a function of the flux through the trap. Adiabatic change of flux connects the ground state to excited states due to flux quantization. For repulsive interactions, the impurity disturbs the Fermi sea by dragging the fermions whose momentum matches the flux. This drag transfers momentum from the impurity to the background and increases the effective mass. The effective mass saturates to the total mass of the system for infinitely repulsive interactions. For attractive interactions, the drag again increases the effective mass which quickly saturates to twice the mass of a single particle as a dimer of the impurity and one fermion is formed. For excited states with momentum comparable to number of particles, effective mass shows a resonant behavior. We argue that standard tools in cold-atom experiments can be used to test these predictions.

Protein crystal growth; Proceedings of the First International Conference, Stanford University, CA, August 14-16, 1985

NASA Technical Reports Server (NTRS)

Feigelson, R. S. (Editor)

1986-01-01

Papers are presented on mechanisms of nucleation and growth of protein crystals, the role of purification in the crystallization of proteins and nucleic acids, and the effect of chemical impurities in polyethylene glycol on macromolecular crystallization. Also considered are growth kinetics of tetragonal lysozyme crystals, thermodynamic and kinetic considerations for crystal growth of complex molecules from solution, protein single-crystal growth under microgravity, and growth of organic crystals in a microgravity environment. Papers are also presented on preliminary investigations of protein crystal growth using the Space Shuttle, convective diffusion in protein crystal growth, and the growth and characterization of membrane protein crystals.

Mixed valent metals

NASA Astrophysics Data System (ADS)

Riseborough, P. S.; Lawrence, J. M.

2016-08-01

We review the theory of mixed-valent metals and make comparison with experiments. A single-impurity description of the mixed-valent state is discussed alongside the description of the nearly-integer valent or Kondo limit. The degeneracy N of the f-shell plays an important role in the description of the low-temperature Fermi-liquid state. In particular, for large N, there is a rapid cross-over between the mixed-valent and the Kondo limit when the number of f electrons is changed. We discuss the limitations on the application of the single-impurity description to concentrated compounds such as those caused by the saturation of the Kondo effect and those due to the presence of magnetic interactions between the impurities. This discussion is followed by a description of a periodic lattice of mixed-valent ions, including the role of the degeneracy N. The article concludes with a comparison of theory and experiment. Topics covered include the single-impurity Anderson model, Luttinger’s theorem, the Friedel sum rule, the Schrieffer-Wolff transformation, the single-impurity Kondo model, Kondo screening, the Wilson ratio, local Fermi-liquids, Fermi-liquid sum rules, the Noziéres exhaustion principle, Doniach’s diagram, the Anderson lattice model, the Slave-Boson method, etc.

Mixed valent metals

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

Riseborough, P. S.; Lawrence, Jon M.

Here, we review the theory of mixed-valent metals and make comparison with experiments. A single-impurity description of the mixed-valent state is discussed alongside the description of the nearly-integer valent or Kondo limit. The degeneracy N of the f-shell plays an important role in the description of the low-temperature Fermi-liquid state. In particular, for large N, there is a rapid cross-over between the mixed-valent and the Kondo limit when the number of f electrons is changed. We discuss the limitations on the application of the single-impurity description to concentrated compounds such as those caused by the saturation of the Kondo effectmore » and those due to the presence of magnetic interactions between the impurities. This discussion is followed by a description of a periodic lattice of mixed-valent ions, including the role of the degeneracy N. The article concludes with a comparison of theory and experiment. Topics covered include the single-impurity Anderson model, Luttinger's theorem, the Friedel sum rule, the Schrieffer–Wolff transformation, the single-impurity Kondo model, Kondo screening, the Wilson ratio, local Fermi-liquids, Fermi-liquid sum rules, the Nozieres exhaustion principle, Doniach's diagram, the Anderson lattice model, the Slave-Boson method, etc.« less

Mixed valent metals

DOE PAGES

Riseborough, P. S.; Lawrence, Jon M.

2016-07-04

Here, we review the theory of mixed-valent metals and make comparison with experiments. A single-impurity description of the mixed-valent state is discussed alongside the description of the nearly-integer valent or Kondo limit. The degeneracy N of the f-shell plays an important role in the description of the low-temperature Fermi-liquid state. In particular, for large N, there is a rapid cross-over between the mixed-valent and the Kondo limit when the number of f electrons is changed. We discuss the limitations on the application of the single-impurity description to concentrated compounds such as those caused by the saturation of the Kondo effectmore » and those due to the presence of magnetic interactions between the impurities. This discussion is followed by a description of a periodic lattice of mixed-valent ions, including the role of the degeneracy N. The article concludes with a comparison of theory and experiment. Topics covered include the single-impurity Anderson model, Luttinger's theorem, the Friedel sum rule, the Schrieffer–Wolff transformation, the single-impurity Kondo model, Kondo screening, the Wilson ratio, local Fermi-liquids, Fermi-liquid sum rules, the Nozieres exhaustion principle, Doniach's diagram, the Anderson lattice model, the Slave-Boson method, etc.« less

Monte Carlo method for magnetic impurities in metals

NASA Technical Reports Server (NTRS)

Hirsch, J. E.; Fye, R. M.

1986-01-01

The paper discusses a Monte Carlo algorithm to study properties of dilute magnetic alloys; the method can treat a small number of magnetic impurities interacting wiith the conduction electrons in a metal. Results for the susceptibility of a single Anderson impurity in the symmetric case show the expected universal behavior at low temperatures. Some results for two Anderson impurities are also discussed.

Scattering of waves by impurities in precompressed granular chains.

PubMed

Martínez, Alejandro J; Yasuda, Hiromi; Kim, Eunho; Kevrekidis, P G; Porter, Mason A; Yang, Jinkyu

2016-05-01

We study scattering of waves by impurities in strongly precompressed granular chains. We explore the linear scattering of plane waves and identify a closed-form expression for the reflection and transmission coefficients for the scattering of the waves from both a single impurity and a double impurity. For single-impurity chains, we show that, within the transmission band of the host granular chain, high-frequency waves are strongly attenuated (such that the transmission coefficient vanishes as the wavenumber k→±π), whereas low-frequency waves are well-transmitted through the impurity. For double-impurity chains, we identify a resonance-enabling full transmission at a particular frequency-in a manner that is analogous to the Ramsauer-Townsend (RT) resonance from quantum physics. We also demonstrate that one can tune the frequency of the RT resonance to any value in the pass band of the host chain. We corroborate our theoretical predictions both numerically and experimentally, and we directly observe almost complete transmission for frequencies close to the RT resonance frequency. Finally, we show how this RT resonance can lead to the existence of reflectionless modes in granular chains (including disordered ones) with multiple double impurities.

Impurity transport in enhanced confinement regimes in RFX-mod Reversed Field Pinch

NASA Astrophysics Data System (ADS)

Carraro, Lorella; Menmuir, Sheena; Fassina, Alessandro

2010-11-01

The results of impurity transport studies in RFX-mod enhanced confinement quasi-single helicity (QSH) and single helical axis (SHAx) regimes are presented and discussed. The impurity diffusion coefficient and pinch velocity are obtained through comparing experimental emission pattern (line emission and SXR time evolutions, SXR profiles) with the results of a 1-D impurity transport code. Previous analysis [S. Menmuir et al. to be published in Plasma Phys. Contr. Fus.] of impurity transport in RFX-mod standard discharges showed that the impurity pinch velocity, always directed outwards, features a barrier with high values around r/a = 0.8, where the diffusion coefficient decreases by one order of magnitude. In the QSH regime, the transition region in D and v is more internal and the barrier in velocity is wider and stronger. New results have been obtained in experiments with Ni laser blow-off (LBO) injection in high current discharges (Ip>1.5 MA) with long lasting QSH, to better characterize the Ni behavior inside the helical magnetic topology.

A real-time extension of density matrix embedding theory for non-equilibrium electron dynamics

NASA Astrophysics Data System (ADS)

Kretchmer, Joshua S.; Chan, Garnet Kin-Lic

2018-02-01

We introduce real-time density matrix embedding theory (DMET), a dynamical quantum embedding theory for computing non-equilibrium electron dynamics in strongly correlated systems. As in the previously developed static DMET, real-time DMET partitions the system into an impurity corresponding to the region of interest coupled to the surrounding environment, which is efficiently represented by a quantum bath of the same size as the impurity. In this work, we focus on a simplified single-impurity time-dependent formulation as a first step toward a multi-impurity theory. The equations of motion of the coupled impurity and bath embedding problem are derived using the time-dependent variational principle. The accuracy of real-time DMET is compared to that of time-dependent complete active space self-consistent field (TD-CASSCF) theory and time-dependent Hartree-Fock (TDHF) theory for a variety of quantum quenches in the single impurity Anderson model (SIAM), in which the Hamiltonian is suddenly changed (quenched) to induce a non-equilibrium state. Real-time DMET shows a marked improvement over the mean-field TDHF, converging to the exact answer even in the non-trivial Kondo regime of the SIAM. However, as expected from analogous behavior in static DMET, the constrained structure of the real-time DMET wavefunction leads to a slower convergence with respect to active space size, in the single-impurity formulation, relative to TD-CASSCF. Our initial results suggest that real-time DMET provides a promising framework to simulate non-equilibrium electron dynamics in which strong electron correlation plays an important role, and lays the groundwork for future multi-impurity formulations.

A real-time extension of density matrix embedding theory for non-equilibrium electron dynamics.

PubMed

Kretchmer, Joshua S; Chan, Garnet Kin-Lic

2018-02-07

We introduce real-time density matrix embedding theory (DMET), a dynamical quantum embedding theory for computing non-equilibrium electron dynamics in strongly correlated systems. As in the previously developed static DMET, real-time DMET partitions the system into an impurity corresponding to the region of interest coupled to the surrounding environment, which is efficiently represented by a quantum bath of the same size as the impurity. In this work, we focus on a simplified single-impurity time-dependent formulation as a first step toward a multi-impurity theory. The equations of motion of the coupled impurity and bath embedding problem are derived using the time-dependent variational principle. The accuracy of real-time DMET is compared to that of time-dependent complete active space self-consistent field (TD-CASSCF) theory and time-dependent Hartree-Fock (TDHF) theory for a variety of quantum quenches in the single impurity Anderson model (SIAM), in which the Hamiltonian is suddenly changed (quenched) to induce a non-equilibrium state. Real-time DMET shows a marked improvement over the mean-field TDHF, converging to the exact answer even in the non-trivial Kondo regime of the SIAM. However, as expected from analogous behavior in static DMET, the constrained structure of the real-time DMET wavefunction leads to a slower convergence with respect to active space size, in the single-impurity formulation, relative to TD-CASSCF. Our initial results suggest that real-time DMET provides a promising framework to simulate non-equilibrium electron dynamics in which strong electron correlation plays an important role, and lays the groundwork for future multi-impurity formulations.

Growth Defects in Biomacromolecular Crystals

NASA Technical Reports Server (NTRS)

2003-01-01

NASA's ground based program confirmed close similarity between protein and small molecules crystal growth, but also revealed essential differences. No understanding exists as to why and when crystals grown in space are, in approx. 20 percent of cases, of higher quality. More rationale is needed in flight experiments. Ferritin crystals grown in space are 2.5 times cleaner than their terrestrial counterparts. This may occur because of the existence of a zone depleted with respect to impurities around a crystal growing in stagnant solution. This zone should appear since the distribution coefficient for homologous impurities exceeds unity. This impurity depletion zone hypothesis requires verification and development. Thorough purification from homologous impurities brought about resolution improvement from 2.6 to 1.8 angstroms for ferritin and from 2.6 to 2.0 angstroms for canavalin.

Accurate evaporation rates of pure and doped water clusters in vacuum: A statistico-dynamical approach

NASA Astrophysics Data System (ADS)

Calvo, F.; Douady, J.; Spiegelman, F.

2010-01-01

Unimolecular evaporation of selected pure (H2O)n and heterogeneous (H2O)n-1X+ water clusters containing a single hydronium or ammonium impurity is investigated in the framework of phase space theory (PST) in its orbiting transition state version. Using the many-body polarizable Kozack-Jordan potential and its extensions for X+=H3O+ and NH4+, the thermal evaporation of clusters containing 21 and 50 molecules is simulated at several total energies. Numerous molecular dynamics (MD) trajectories at high internal energies provide estimates of the decay rate constant, as well as the kinetic energy and angular momentum released upon dissociation. Additional Monte Carlo simulations are carried out to determine the anharmonic densities of vibrational states, which combined with suitable forms for the rotational densities of states provide expressions for the energy-resolved differential rates. Successful comparison between the MD results and the independent predictions of PST for the distributions of kinetic energy and angular momentum released shows that the latter statistical approach is quantitative. Using MD data as a reference, the absolute evaporation rates are calculated from PST over broad energy and temperature ranges. Based on these results, the presence of an ionic impurity is generally found to decrease the rate, however the effect is much more significant in the 21-molecule clusters. Our calculations also suggest that due to backbendings in the microcanonical densities of states the variations of the evaporation rates may not be strictly increasing with energy or temperature.

Impurity screening behavior of the high-field side scrape-off layer in near-double-null configurations: prospect for mitigating plasma-material interactions on RF actuators and first-wall components

NASA Astrophysics Data System (ADS)

LaBombard, B.; Kuang, A. Q.; Brunner, D.; Faust, I.; Mumgaard, R.; Reinke, M. L.; Terry, J. L.; Howard, N.; Hughes, J. W.; Chilenski, M.; Lin, Y.; Marmar, E.; Rice, J. E.; Rodriguez-Fernandez, P.; Wallace, G.; Whyte, D. G.; Wolfe, S.; Wukitch, S.

2017-07-01

The impurity screening response of the high-field side (HFS) scrape-off layer (SOL) to localized nitrogen injection is investigated on Alcator C-Mod for magnetic equilibria spanning lower-single-null, double-null and upper-single-null configurations under otherwise identical plasma conditions. L-mode, EDA H-mode and I-mode discharges are investigated. HFS impurity screening is found to depend on magnetic flux balance and the direction of B  ×  \

Single layer multi-color luminescent display and method of making

NASA Technical Reports Server (NTRS)

Robertson, James B. (Inventor)

1992-01-01

The invention is a multi-color luminescent display comprising an insulator substrate and a single layer of host material, which may be a phosphor deposited thereon that hosts one or more different impurities, therein forming a pattern of selected and distinctly colored phosphors such as blue, green, and red phosphors in a single layer of host material. Transparent electrical conductor means may be provided for subjecting selected portions of the pattern of colored phosphors to an electric field, thereby forming a multi-color, single layer electroluminescent display. A method of forming a multi-color luminescent display includes the steps of depositing on an insulator substrate a single layer of host material, which itself may be a phosphor, with the properties to host varying quantities of different impurities and introducing one or more of said different impurities into selected areas of the said single layer of host material by thermal diffusion or ion implantation to form a pattern of phosphors of different colors in the said single layer of host material.

Energetics of Single Substitutional Impurities in NiTi

NASA Technical Reports Server (NTRS)

Good, Brian S.; Noebe, Ronald

2003-01-01

Shape-memory alloys are of considerable current interest, with applications ranging from stents to Mars rover components. In this work, we present results on the energetics of single substitutional impurities in B2 NiTi. Specifically, energies of Pd, Pt, Zr and Hf impurities at both Ni and Ti sites are computed. All energies are computed using the CASTEP ab initio code, and, for comparison, using the quantum approximate energy method of Bozzolo, Ferrante and Smith. Atomistic relaxation in the vicinity of the impurities is investigated via quantum approximate Monte Carlo simulation, and in cases where the relaxation is found to be important, the resulting relaxations are applied to the ab initio calculations. We compare our results with available experimental work.

Effect of a Nitrogen Impurity on the Fundamental Raman Band of Diamond Single Crystals

NASA Astrophysics Data System (ADS)

Gusakov, G. A.; Samtsov, M. P.; Voropay, E. S.

2018-05-01

The effect of nitrogen defects in natural and synthetic diamond single crystals on the position and half-width of the fundamental Raman band was investigated. Samples containing the main types of nitrogen lattice defects at impurity contents of 1-1500 ppm were studied. The parameters of the Stokes and anti-Stokes components in Raman spectra of crystals situated in a cell with distilled water to minimize the influence of heating by the exciting laser radiation were analyzed to determine the effect of a nitrogen impurity in the diamond crystal lattice. It was shown that an increase of impurity atoms in the crystals in the studied concentration range resulted in broadening of the Raman band from 1.61 to 2.85 cm-1 and shifting of the maximum to lower frequency from 1332.65 to 1332.3 cm-1. The observed effect was directly proportional to the impurity concentration and depended on the form of the impurity incorporated into the diamond lattice. It was found that the changes in the position and half-width of the fundamental Raman band for diamond were consistent with the magnitude of crystal lattice distortions due to the presence of impurity defects and obeyed the Gruneisen law.

Behavior of some singly ionized, heavy-ion impurities during compression in a theta-pinch plasma

NASA Technical Reports Server (NTRS)

Jalufka, N. W.

1975-01-01

The introduction of a small percentage of an impurity gas containing a desired element into a theta-pinch plasma is a standard procedure used to investigate the spectra and atomic processes of the element. This procedure assumes that the mixing ratio of impurity-to-fill gases remains constant during the collapse and heating phase. Spectroscopic investigations of the constant-mixing-ratio assumption for a 2% neon and argon impurity verifies the assumption only for the neon impurity. However, for the 2% argon impurity, only 20 to 25% of the argon is in the high-temperature compressed plasma. It is concluded that the constant-mixing-ratio assumption is not applicable to the argon impurity.

Argon metastable dynamics and lifetimes in a direct current microdischarge

NASA Astrophysics Data System (ADS)

Stefanović, Ilija; Kuschel, Thomas; Schröter, Sandra; Böke, Marc

2014-09-01

In this paper we study the properties of a pulsed dc microdischarge with the continuous flow of argon. Argon metastable lifetimes are measured by tunable diode laser absorption spectroscopy (TDLAS) and are compared with calculated values which yield information about excitation and de-excitation processes. By increasing the gas flow-rate about 5 times from 10 to 50 sccm, the Arm lifetime increases from 1 to 5 μs due to the reduction of metastable quenching with gas impurities. Optical emission spectroscopy reveals nitrogen and water molecules as the main gas impurities. The estimated N2 density [N2] = 0.1% is too low to explain the measured metastable lifetimes. Water impurity was found to be the main de-excitation source of argon metastable atoms due to high quenching coefficients. The water impurity level of [H2O] = 0.15% to 1% is sufficient to bring calculated metastable lifetimes in line with experiments. The maximum value of water content in the discharge compared to the argon atoms is estimated to approximately 6%, due to the large surface to volume ratio of the microdischarge. The current pulse releases the water molecules from the electrode surface and they are either re-adsorbed in the time between 0.4 ms for [H2O] = 1% and 2.6 ms for [H2O] = 0.15% or pumped out of the discharge with the speed equal to the gas flow-rate. Depending on its partial pressure, the water impurity re-adsorption time is of the order of magnitude or less then the argon gas residence time.

Oscillations and accelerations of ice crystal growth rates in microgravity in presence of antifreeze glycoprotein impurity in supercooled water.

PubMed

Furukawa, Yoshinori; Nagashima, Ken; Nakatsubo, Shun-Ichi; Yoshizaki, Izumi; Tamaru, Haruka; Shimaoka, Taro; Sone, Takehiko; Yokoyama, Etsuro; Zepeda, Salvador; Terasawa, Takanori; Asakawa, Harutoshi; Murata, Ken-Ichiro; Sazaki, Gen

2017-03-06

The free growth of ice crystals in supercooled bulk water containing an impurity of glycoprotein, a bio-macromolecule that functions as 'antifreeze' in living organisms in a subzero environment, was observed under microgravity conditions on the International Space Station. We observed the acceleration and oscillation of the normal growth rates as a result of the interfacial adsorption of these protein molecules, which is a newly discovered impurity effect for crystal growth. As the convection caused by gravity may mitigate or modify this effect, secure observations of this effect were first made possible by continuous measurements of normal growth rates under long-term microgravity condition realized only in the spacecraft. Our findings will lead to a better understanding of a novel kinetic process for growth oscillation in relation to growth promotion due to the adsorption of protein molecules and will shed light on the role that crystal growth kinetics has in the onset of the mysterious antifreeze effect in living organisms, namely, how this protein may prevent fish freezing.

Oscillations and accelerations of ice crystal growth rates in microgravity in presence of antifreeze glycoprotein impurity in supercooled water

PubMed Central

Furukawa, Yoshinori; Nagashima, Ken; Nakatsubo, Shun-ichi; Yoshizaki, Izumi; Tamaru, Haruka; Shimaoka, Taro; Sone, Takehiko; Yokoyama, Etsuro; Zepeda, Salvador; Terasawa, Takanori; Asakawa, Harutoshi; Murata, Ken-ichiro; Sazaki, Gen

2017-01-01

The free growth of ice crystals in supercooled bulk water containing an impurity of glycoprotein, a bio-macromolecule that functions as ‘antifreeze’ in living organisms in a subzero environment, was observed under microgravity conditions on the International Space Station. We observed the acceleration and oscillation of the normal growth rates as a result of the interfacial adsorption of these protein molecules, which is a newly discovered impurity effect for crystal growth. As the convection caused by gravity may mitigate or modify this effect, secure observations of this effect were first made possible by continuous measurements of normal growth rates under long-term microgravity condition realized only in the spacecraft. Our findings will lead to a better understanding of a novel kinetic process for growth oscillation in relation to growth promotion due to the adsorption of protein molecules and will shed light on the role that crystal growth kinetics has in the onset of the mysterious antifreeze effect in living organisms, namely, how this protein may prevent fish freezing. PMID:28262787

Antiguided fiber ribbon laser

DOEpatents

Wilcox, Russel B [El Cerrito, CA; Page, Ralph H [Castro Valley, CA; Beach, Raymond J [Livermore, CA; Feit, Michael D [Livermore, CA; Payne, Stephen A [Castro Valley, CA

2003-05-27

The invention is a ribbon of an optical material with a plurality of cores that run along its length. The plurality of cores includes lasing impurity doped cores in an alternating spaced arrangement with index-modifying impurity doped cores. The ribbon comprises an index of refraction that is substantially equal to or greater than the indices of refraction of said array of lasing impurity doped cores. Index-increasing impurity doped cores promote antiguiding and leaky modes which provide more robust single "supermode" operation.

Impurity-limited resistance and phase interference of localized impurities under quasi-one dimensional nano-structures

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

Sano, Nobuyuki, E-mail: sano@esys.tsukuba.ac.jp

2015-12-28

The impurity-limited resistance and the effect of the phase interference among localized multiple impurities in the quasi-one dimensional (quasi-1D) nanowire structures are systematically investigated under the framework of the scattering theory. We derive theoretical expressions of the impurity-limited resistance in the nanowire under the linear response regime from the Landauer formula and from the Boltzmann transport equation (BTE) with the relaxation time approximation. We show that the formula from the BTE exactly coincides with that from the Landauer approach with the weak-scattering limit when the energy spectrum of the in-coming electrons from the reservoirs is narrow and, thus, point outmore » a possibility that the distinction of the impurity-limited resistances derived from the Landauer formula and that of the BTE could be made clear. The derived formulas are applied to the quasi-1D nanowires doped with multiple localized impurities with short-range scattering potential and the validity of various approximations on the resistance are discussed. It is shown that impurity scattering becomes so strong under the nanowire structures that the weak-scattering limit breaks down in most cases. Thus, both phase interference and phase randomization simultaneously play a crucial role in determining the impurity-limited resistance even under the fully coherent framework. When the impurity separation along the wire axis direction is small, the constructive phase interference dominates and the resistance is much greater than the average resistance. As the separation becomes larger, however, it approaches the series resistance of the single-impurity resistance due to the phase randomization. Furthermore, under the uniform configuration of impurities, the space-average resistance of multiple impurities at room temperature is very close to the series resistance of the single-impurity resistance, and thus, each impurity could be regarded as an independent scattering center. The physical origin of this “self-averaging” under the fully coherent environments is attributed to the broadness of the energy spectrum of the in-coming electrons from the reservoirs.« less

Investigation of emission properties of doped aromatic derivative organic semiconductor crystals

NASA Astrophysics Data System (ADS)

Stanculescu, A.; Mihut, L.; Stanculescu, F.; Alexandru, H.

2008-04-01

Fluorescence measurements have been made on pure and doped bulk, mechanically polished wafers of crystalline m-DNB and benzil obtained by cutting ingots grown by the Bridgman-Stockbarger method modified for organic compounds crystallization. By comparison with pure matrices, we have investigated the effect of an inorganic dopant (iodine, silver, sodium) and of an organic dopant (m-DNB, naphthalene) on the emission characteristics (position and shape) of these molecular crystals. A slight shift of the emission peaks through high energy and an intense emission peak situated around 2.35 eV correlated with the local trapping level attributed to structural defects, which are involved in radiative processes, have been evidenced in iodine-doped m-DNB. The emission peak of m-DNB-doped benzil situated in the high-energy range (2.97 eV) is associated with direct emission activity of m-DNB, suggesting that this is an active impurity in benzil molecular matrix. We have not observed in benzil any evidence of indirect action of the impurity molecules (atoms) associated with the traps represented by the structural defects that generate changes in the energy levels of the neighbouring molecules and are correlated with different growth conditions. We have not remarked any involvement of the studied inorganic metallic impurities and of some organic impurities, such as naphthalene, in the radiative recombination processes in benzil matrix.

Single-site properties of U impurities doped in La2Zn17 (abstract)

NASA Astrophysics Data System (ADS)

Suzuki, H.; Anzai, K.; Takagi, S.

1997-04-01

Thermodynamic and transport properties of heavy Fermion (HF) U compounds show similar behavior to HF Ce compounds. Although most of the magnetic properties of HF Ce compounds can be qualitatively understood on the basis of the impurity Kondo model, no such consensus for HF U compounds has been reached. In addition to this, the single-site properties of U impurities are not understood so well, in contrast to the case of Ce impurities. Recent works for dilute U systems reported new features as are not seen in dilute Ce systems. We have investigated a dilute-U2Zn17 system of (La1-zUz)2Zn17 in order to reveal the single U ion site properties of this system by preparing single crystals. The impurity contributions to various physical quantities such as ρimp(T), χimp(T), and Cimp(T) can be scaled by the U concentration between z=0.025 and 0.05, and the system is considered as in the dilute limit still for z=0.05. The electrical resistivity shows the typical impurity-Kondo upturn at low temperatures. The electronic specific-heat coefficient is strongly enhanced (γimp≈1.5 J/K2 mole U) and about 4 times as large as that for dense U2Zn17. Suppressions of the Kondo effect by the magnetic field are seen in γimp(H) and magnetoresistance. The relatively large anisotropy in χimp(T) indicates an existence of the crystal field. These features of this system will be explained in terms of the Kondo effect in the presence of the crystal field.

DETECTING LOW-LEVEL SYNTHESIS IMPURITIES IN MODIFIED PHOSPHOROTHIOATE OLIGONUCLEOTIDES USING LIQUID CHROMATOGRAPHY – HIGH RESOLUTION MASS SPECTROMETRY

PubMed Central

Nikcevic, Irena; Wyrzykiewicz, Tadeusz K.; Limbach, Patrick A.

2010-01-01

Summary An LC-MS method based on the use of high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS) for profiling oligonucleotides synthesis impurities is described. Oligonucleotide phosphorothioatediesters (phosphorothioate oligonucleotides), in which one of the non-bridging oxygen atoms at each phosphorus center is replaced by a sulfur atom, are now one of the most popular oligonucleotide modifications due to their ease of chemical synthesis and advantageous pharmacokinetic properties. Despite significant progress in the solid-phase oligomerization chemistry used in the manufacturing of these oligonucleotides, multiple classes of low-level impurities always accompany synthetic oligonucleotides. Liquid chromatography-mass spectrometry has emerged as a powerful technique for the identification of these synthesis impurities. However, impurity profiling, where the entire complement of low-level synthetic impurities is identified in a single analysis, is more challenging. Here we present an LC-MS method based the use of high resolution-mass spectrometry, specifically Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS or FTMS). The optimal LC-FTMS conditions, including the stationary phase and mobile phases for the separation and identification of phosphorothioate oligonucleotides, were found. The characteristics of FTMS enable charge state determination from single m/z values of low-level impurities. Charge state information then enables more accurate modeling of the detected isotopic distribution for identification of the chemical composition of the detected impurity. Using this approach, a number of phosphorothioate impurities can be detected by LC-FTMS including failure sequences carrying 3′-terminal phosphate monoester and 3′-terminal phosphorothioate monoester, incomplete backbone sulfurization and desulfurization products, high molecular weight impurities, and chloral, isobutyryl, and N3 (2-cyanoethyl) adducts of the full length product. When compared with low resolution LC-MS, ~60% more impurities can be identified when charge state and isotopic distribution information is available and used for impurity profiling. PMID:21811394

Quantum interference on electron scattering in graphene by carbon impurities in underlying h -BN

NASA Astrophysics Data System (ADS)

Kaneko, Tomoaki; Koshino, Mikito; Saito, Riichiro

2017-03-01

Electronic structures and transport properties of graphene on h -BN with carbon impurities are investigated by first-principles calculation and the tight-binding model. We show that the coupling between the impurity level and the graphene's Dirac cone sensitively depends on the impurity position, and in particular, it nearly vanishes when the impurity is located right below the center of the six membered ring of graphene. The Bloch phase factor at the Brillouin zone edge plays a decisive role in the cancellation of the hopping integrals. The impurity position dependence on the electronic structures of graphene on h -BN is investigated by the first-principles calculation, and its qualitative feature is well explained by a tight-binding model with graphene and a single impurity site. We also propose a simple one-dimensional chain-impurity model to analytically describe the role of the quantum interference in the position-dependent coupling.

Effects of impurities on crystal growth in fructose crystallization

NASA Astrophysics Data System (ADS)

Chu, Y. D.; Shiau, L. D.; Berglund, K. A.

1989-10-01

The influence of impurities on the crystallization of anhydrous fructose from aqueous solution was studied. The growth kinetics of fructose crystals in the fructose-water-glucose and fructose-water-difructose dianhydrides systems were investigated using photomicroscopic contact nucleation techniques. Glucose is the major impurity likely to be present in fructose syrup formed during corn wet milling, while several difructose dianhydrides are formed in situ under crystallization conditions and have been proposed as a cause in the decrease of overall yields. Both sets of impurities were found to cause inhibition of crystal growth, but the mechanisms responsible in each case are different. It was found that the presence of glucose increases the solubility of fructose in water and thus lowers the supersaturation of the solution. This is probably the main effect responsible for the decrease of crystal growth. Since the molecular structures of difructose dianhydrides are similar to that of fructose, they are probably "tailor-made" impurities. The decrease of crystal growth is probably caused by the incorporation of these impurities into or adsorption to the crystal surface which would accept fructose molecules in the orientation that existed in the difructose dianhydride.

Enhancement in production of recombinant two-chain Insulin Glargine by over-expression of Kex2 protease in Pichia pastoris.

PubMed

Sreenivas, Suma; Krishnaiah, Sateesh M; Govindappa, Nagaraja; Basavaraju, Yogesh; Kanojia, Komal; Mallikarjun, Niveditha; Natarajan, Jayaprakash; Chatterjee, Amarnath; Sastry, Kedarnath N

2015-01-01

Glargine is an analog of Insulin currently being produced by recombinant DNA technology using two different hosts namely Escherichia coli and Pichia pastoris. Production from E. coli involves the steps of extraction of inclusion bodies by cell lysis, refolding, proteolytic cleavage and purification. In P. pastoris, a single-chain precursor with appropriate disulfide bonding is secreted to the medium. Downstream processing currently involves use of trypsin which converts the precursor into two-chain final product. The use of trypsin in the process generates additional impurities due to presence of Lys and Arg residues in the Glargine molecule. In this study, we describe an alternate approach involving over-expression of endogenous Kex2 proprotein convertase, taking advantage of dibasic amino acid sequence (Arg-Arg) at the end of B-chain of Glargine. KEX2 gene over-expression in Pichia was accomplished by using promoters of varying strengths to ensure production of greater levels of fully functional two-chain Glargine product, confirmed by HPLC and mass analysis. In conclusion, this new production process involving Kex2 protease over-expression improves the downstream process efficiency, reduces the levels of impurities generated and decreases the use of raw materials.

Impurities in silicon solar cells

NASA Technical Reports Server (NTRS)

Hopkins, R. H.

1985-01-01

Metallic impurities, both singly and in combinations, affect the performance of silicon solar cells. Czochralski silicon web crystals were grown with controlled additions of secondary impurities. The primary electrical dopants were boron and phosphorus. The silicon test ingots were grown under controlled and carefully monitored conditions from high-purity charge and dopant material to minimize unintentional contamination. Following growth, each crystal was characterized by chemical, microstructural, electrical, and solar cell tests to provide a detailed and internally consistent description of the relationships between silicon impurity concentration and solar cell performance. Deep-level spectroscopy measurements were used to measure impurity concentrations at levels below the detectability of other techniques and to study thermally-induced changes in impurity activity. For the majority of contaminants, impurity-induced performance loss is due to a reduction of the base diffusion length. From these observations, a semi-empirical model which predicts cell performance as a function of metal impurity concentration was formulated. The model was then used successfully to predict the behavior of solar cells bearing as many as 11 different impurities.

Impurity-directed transport within a finite disordered lattice

NASA Astrophysics Data System (ADS)

Magnetta, Bradley J.; Ordonez, Gonzalo; Garmon, Savannah

2018-02-01

We consider a finite, disordered 1D quantum lattice with a side-attached impurity. We study theoretically the transport of a single electron from the impurity into the lattice, at zero temperature. The transport is dominated by Anderson localization and, in general, the electron motion has a random character due to the lattice disorder. However, we show that by adjusting the impurity energy the electron can attain quasi-periodic motions, oscillating between the impurity and a small region of the lattice. This region corresponds to the spatial extent of a localized state with an energy matched by that of the impurity. By precisely tuning the impurity energy, the electron can be set to oscillate between the impurity and a region far from the impurity, even distances larger than the Anderson localization length. The electron oscillations result from the interference of hybridized states, which have some resemblance to Pendry's necklace states (Pendry, 1987) [21]. The dependence of the electron motion on the impurity energy gives a potential mechanism for selectively routing an electron towards different regions of a 1D disordered lattice.

Dynamical signatures of bound states in waveguide QED

NASA Astrophysics Data System (ADS)

Sánchez-Burillo, E.; Zueco, D.; Martín-Moreno, L.; García-Ripoll, J. J.

2017-08-01

We study the spontaneous decay of an impurity coupled to a linear array of bosonic cavities forming a single-band photonic waveguide. The average frequency of the emitted photon is different from the frequency for single-photon resonant scattering, which perfectly matches the bare frequency of the excited state of the impurity. We study how the energy of the excited state of the impurity influences the spatial profile of the emitted photon. The farther the energy is from the middle of the photonic band, the farther the wave packet is from the causal limit. In particular, if the energy lies in the middle of the band, the wave packet is localized around the causal limit. Besides, the occupation of the excited state of the impurity presents a rich dynamics: it shows an exponential decay up to intermediate times, this is followed by a power-law tail in the long-time regime, and it finally reaches an oscillatory stationary regime. Finally, we show that this phenomenology is robust under the presence of losses, both in the impurity and in the cavities.

Substitutional impurity in single-layer graphene: The Koster–Slater and Anderson models

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

Davydov, S. Yu., E-mail: sergei-davydov@mail.ru

The Koster–Slater and Anderson models are used to consider substitutional impurities in free-standing single-layer graphene. The density of states of graphene is described using a model (the M model). For the nitrogen and boron impurities, the occupation numbers and the parameter η which defines the fraction of delocalized electrons of the impurity are determined. In this case, experimental data are used for both determination of the model parameters and comparison with the results of theoretical estimations. The general features of the Koster–Slater and Anderson models and the differences between the two models are discussed. Specifically, it is shown that themore » band contributions to the occupation numbers of a nitrogen atom in both models are comparable, whereas the local contributions are substantially different: the local contributions are decisive in the Koster–Slater model and negligible in the Anderson model. The asymptotic behavior of the wave functions of a defect is considered in the Koster–Slater model, and the electron states of impurity dimers are considered in the Anderson model.« less

Impurity mixing and radiation asymmetry in massive gas injection simulations of DIII-D

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

Izzo, V. A.

Simulations of neon massive gas injection into DIII-D are performed with the 3D MHD code NIMROD. The poloidal and toroidal distribution of the impurity source is varied. This report will focus on the effects of the source variation on impurity mixing and radiated power asymmetry. Even toroidally symmetric impurity injection is found to produce asymmetric radiated power due to asymmetric convective heat flux produced by the 1/1 mode. When the gas source is toroidally localized, the phase relationship between the mode and the source location is important, affecting both radiation peaking and impurity mixing. Under certain circumstances, a single, localizedmore » gas jet could produce better radiation symmetry during the disruption thermal quench than evenly distributed impurities.« less

Theoretical study of the dependence of single impurity Anderson model on various parameters within distributional exact diagonalization method

NASA Astrophysics Data System (ADS)

Syaina, L. P.; Majidi, M. A.

2018-04-01

Single impurity Anderson model describes a system consisting of non-interacting conduction electrons coupled with a localized orbital having strongly interacting electrons at a particular site. This model has been proven successful to explain the phenomenon of metal-insulator transition through Anderson localization. Despite the well-understood behaviors of the model, little has been explored theoretically on how the model properties gradually evolve as functions of hybridization parameter, interaction energy, impurity concentration, and temperature. Here, we propose to do a theoretical study on those aspects of a single impurity Anderson model using the distributional exact diagonalization method. We solve the model Hamiltonian by randomly generating sampling distribution of some conducting electron energy levels with various number of occupying electrons. The resulting eigenvalues and eigenstates are then used to define the local single-particle Green function for each sampled electron energy distribution using Lehmann representation. Later, we extract the corresponding self-energy of each distribution, then average over all the distributions and construct the local Green function of the system to calculate the density of states. We repeat this procedure for various values of those controllable parameters, and discuss our results in connection with the criteria of the occurrence of metal-insulator transition in this system.

Energy Trapping, Release, and Transport in Three-Dimensional Energetic Solids and Molecular Crystals: Theory of Defects and Impurities.

DTIC Science & Technology

1984-12-31

and 3. T. Waber, Concerning the Trapping of Positrons in Ionic Solids, in Positron Annihilation , P. G. Coleman, S. C. Sharma and L. M. Diana, Eds., 682...1982). *144. A. B. Kunz and 3. T. Waber, A Theoretical Study of the Binding of Positrons to Gaseous Molecules, in Positron Annihilation . P. G. Coleman, S...variety of other cases which include systems in unusual charge states such as Fe + in SrTiOz or Fe in MgO . Impurity systems in their excited states are

Influence of complex impurity centres on radiation damage in wide-gap metal oxides

NASA Astrophysics Data System (ADS)

Lushchik, A.; Lushchik, Ch.; Popov, A. I.; Schwartz, K.; Shablonin, E.; Vasil'chenko, E.

2016-05-01

Different mechanisms of radiation damage of wide-gap metal oxides as well as a dual influence of impurity ions on the efficiency of radiation damage have been considered on the example of binary ionic MgO and complex ionic-covalent Lu3Al5O12 single crystals. Particular emphasis has been placed on irradiation with ∼2 GeV heavy ions (197Au, 209Bi, 238U, fluence of 1012 ions/cm2) providing extremely high density of electronic excitations within ion tracks. Besides knock-out mechanism for Frenkel pair formation, the additional mechanism through the collapse of mobile discrete breathers at certain lattice places (e.g., complex impurity centres) leads to the creation of complex defects that involve a large number of host atoms. The experimental manifestations of the radiation creation of intrinsic and impurity antisite defects (Lu|Al or Ce|Al - a heavy ion in a wrong cation site) have been detected in LuAG and LuAG:Ce3+ single crystals. Light doping of LuAG causes a small enhancement of radiation resistance, while pair impurity centres (for instance, Ce|Lu-Ce|Al or Cr3+-Cr3+ in MgO) are formed with a rise of impurity concentration. These complex impurity centres as well as radiation-induced intrinsic antisite defects (Lu|Al strongly interacting with Lu in a regular site) tentatively serve as the places for breathers collapse, thus decreasing the material resistance against dense irradiation.

Quasiparticle Properties of a Mobile Impurity in a Bose-Einstein Condensate.

PubMed

Christensen, Rasmus Søgaard; Levinsen, Jesper; Bruun, Georg M

2015-10-16

We develop a systematic perturbation theory for the quasiparticle properties of a single impurity immersed in a Bose-Einstein condensate. Analytical results are derived for the impurity energy, effective mass, and residue to third order in the impurity-boson scattering length. The energy is shown to depend logarithmically on the scattering length to third order, whereas the residue and the effective mass are given by analytical power series. When the boson-boson scattering length equals the boson-impurity scattering length, the energy has the same structure as that of a weakly interacting Bose gas, including terms of the Lee-Huang-Yang and fourth order logarithmic form. Our results, which cannot be obtained within the canonical Fröhlich model of an impurity interacting with phonons, provide valuable benchmarks for many-body theories and for experiments.

Camelid VHH affinity ligands enable separation of closely related biopharmaceuticals

PubMed Central

Pabst, Timothy M.; Wendeler, Michaela; Wang, Xiangyang; Bezemer, Sandra; Hermans, Pim

2016-01-01

Abstract Interest in new and diverse classes of molecules such as recombinant toxins, enzymes, and blood factors continues to grow for use a biotherapeutics. Compared to monoclonal antibodies, these novel drugs typically lack a commercially available affinity chromatography option, which leads to greater process complexity, longer development timelines, and poor platformability. To date, for both monoclonal antibodies and novel molecules, affinity chromatography has been mostly reserved for separation of process‐related impurities such as host cell proteins and DNA. Reports of affinity purification of closely related product variants and modified forms are much rarer. In this work we describe custom affinity chromatography development using camelid VHH antibody fragments as "tunable" immunoaffinity ligands for separation of product‐related impurities. One example demonstrates high selectivity for a recombinant immunotoxin where no binding was observed for an undesired deamidated species. Also discussed is affinity purification of a coagulation factor through specific recognition of the gamma‐carboxylglutamic acid domain. PMID:27677057

Selective laser spectroscopy of molecules and ions in solids: a history, fundamentals and applications

NASA Astrophysics Data System (ADS)

Sapozhnikov, Michael

2018-03-01

A history of the development of selective laser spectroscopy is presented, beginning with a pioneering work by Yu. V. Denisov and V. A. Kizel in 1967, who were the first to demonstrate the possibility of removing the inhomogeneous broadening of luminescence spectra of impurity ions in glasses upon monochromatic resonance excitation. Selective excitation of optical centers can be achieved due to existence of zero-phonon transitions corresponding to narrow homogeneous zero-phonon lines in the spectra of impurity centers in solids, which are hidden in broad inhomogeneous optical bands upon usual nonselective excitation. The fundamentals of zero-phonon transition spectroscopy are considered and the mechanism of removing the inhomogeneous broadening of optical spectra of ions and molecules in crystals and amorphous solids under selective laser excitation of luminescence and persistent hole burning in absorption spectra is presented in detail. Various applications of selective laser spectroscopy for fundamental and applied studies are discussed.

Stabilization of Quinapril by Incorporating Hydrogen Bonding Interactions

PubMed Central

Roy, B. N.; Singh, G. P.; Godbole, H. M.; Nehate, S. P.

2009-01-01

In the present study stability of various known solvates of quinapril hydrochloride has been compared with nitromethane solvate. Nitromethane solvate was found to be more stable compared to other known solvates. Single crystal X-ray diffraction analysis of quinapril nitromethane solvate shows intermolecular hydrogen bonding between quinapril molecule and nitromethane. Stabilization of quinapril by forming strong hydrogen bonding network as in case of co-crystals was further studied by forming co-crystal with tris(hydroxymethyl)amino methane. Quinapril free base forms a stable salt with tris(hydroxymethyl)amino methane not reported earlier. Quinapril tris(hydroxymethyl)amino methane salt found to be stable even at 80° for 72 h i.e. hardly any formation of diketopiperazine and diacid impurity. As expected single crystal X-ray diffraction analysis reveals tris(hydroxymethyl)amino methane salt of quinapril shows complex hydrogen bonding network between the two entities along with ionic bond. The properties of this stable salt - stable in solid as well as solution phase, might lead to an alternate highly stable formulation. PMID:20502545

Atomic force microscopy study on crystal growth of Cu 2+-doped L-arginine phosphate monohydrate crystals

NASA Astrophysics Data System (ADS)

Geng, Y. L.; Xu, D.; Wang, Y. L.; Du, W.; Liu, H. Y.; Zhang, G. H.; Wang, X. Q.; Sun, D. L.

2005-01-01

Sub-steps and defects of the {1 0 0} planes of Cu 2+-doped L-arginine phosphate monohydrate (LAP) crystals are observed by atomic force microscopy. Formation of sub-steps is not due to the stacking faults but a result of single LAP: Cu 2+ molecule acting as growth unit. Two-dimensional (2D) nuclei with the same height as sub-steps occur on the step-edges. Impurities of Cu 2+ ions cause steps bunch and macrosteps formation. Liquid inclusions in the form of long channels form when the macrosteps lose their stability. Numerous small 3D growth hillocks are found in the channels. The extra stress induced by the 3D islands can result in dislocations and steps mismatches.

Wall Conditioning Characterization in NSTX-U

NASA Astrophysics Data System (ADS)

Caron, D.; Soukhanovskii, V.; Scotti, F.; Weller, M.

2016-10-01

Impurities in tokamak plasmas can lead to disruptive instabilities due to radiative energy loss which impede access to high-confinements mode. One source of impurities in NSTX-U are water molecules trapped in graphite plasma facing components (PFCs), which make up the walls and divertors. Hydrogen and oxygen impurities are released into the plasma due to plasma surface interactions. Extreme ultraviolet (EUV) and visible spectrometers are used in conjunction with a residual gas analyzer (RGA) to characterize the source and amount of released impurities. A high resolution visible spectrometer measured H/D Balmer- α intensity ratio on the inner wall, the upper and lower divertors, and provided a hydrogen time history for shot-to-shot trends. The RGA provided partial pressure trends of masses 2 (H2) , 16 (O2) , and 18 (H2O). Trends of O VIII and C VI spectral line intensities from the core plasma were obtained from the EUV spectrometer. The trends are correlated with wall conditioning, namely helium glow discharge cleaning and boronization. Using these trends, impurity content monitoring and recommendations for wall conditioning can be implemented. Work supported by DOE under Contracts DE-AC52-07NA27344 and DE-AC02-09CH11466.

Role of oxygen impurities in synthesis of iron mononitride thin films

NASA Astrophysics Data System (ADS)

Niti, Seema, Gupta, Mukul

2018-04-01

In this work we have studied iron mononitride (FeN) thin films. FeN is debated for its structure and often a mixed phase is obtained experimentally. Even in single phases of FeN obtain so far, an additional phase was always found even though its volume fraction was minimal. Such phases have been claimed to stem from impurities due to partial oxidation taking place during the growth. In order to study the nature of such impurities, we have deliberately introduced oxygen during the growth of FeN in a magnetron sputtering process. We found that the presence of oxygen tends to distort the tetrahedral symmetry as envisaged in the N K edge absorption spectra. The effect of oxygen impurities is subtler on the long range ordering due to formation of a disordered phase. Obtained results can be used to find the pathways to prepare a single phase FeN compound and thereafter to resolve the debate about its structure and the magnetic ground state.

Trapped one-dimensional ideal Fermi gas with a single impurity

NASA Astrophysics Data System (ADS)

Astrakharchik, G. E.; Brouzos, I.

2013-08-01

Ground-state properties of a single impurity in a one-dimensional Fermi gas are investigated in uniform and trapped geometries. The energy of a trapped system is obtained (i) by generalizing the McGuire expression from a uniform to trapped system (ii) within the local density approximation (iii) using the perturbative approach in the case of a weakly interacting impurity and (iv) diffusion Monte Carlo method. We demonstrate that there is a closed formula based on the exact solution of the homogeneous case which provides a precise estimation for the energy of a trapped system even for a small number of fermions and arbitrary coupling constant of the impurity. Using this expression, we analyze energy contributions from kinetic, interaction, and potential components, as well as spatial properties such as the system size and the pair-correlation function. Finally, we calculate the frequency of the breathing mode. Our analysis is directly connected and applicable to the recent experiments in microtraps.

Single magnetic adsorbates on s-wave superconductors

NASA Astrophysics Data System (ADS)

Heinrich, Benjamin W.; Pascual, Jose I.; Franke, Katharina J.

2018-02-01

In superconductors, magnetic impurities induce a pair-breaking potential for Cooper pairs, which locally affects the Bogoliubov quasiparticles and gives rise to Yu-Shiba-Rusinov (YSR or Shiba, in short) bound states in the density of states (DoS). These states carry information on the magnetic coupling strength of the impurity with the superconductor, which determines the many-body ground state properties of the system. Recently, the interest in Shiba physics was boosted by the prediction of topological superconductivity and Majorana modes in magnetically coupled chains and arrays of Shiba impurities. Here, we review the physical insights obtained by scanning tunneling microscopy into single magnetic adsorbates on the s-wave superconductor lead (Pb). We explore the tunneling processes into Shiba states, show how magnetic anisotropy affects many-body excitations, and determine the crossing of the many-body ground state through a quantum phase transition. Finally, we discuss the coupling of impurities into dimers and chains and their relation to Majorana physics.

In-situ observation of impurity diffusion boundary layer in silicon Czochralski growth

NASA Astrophysics Data System (ADS)

Kakimoto, Koichi; Eguchi, Minoru; Watanabe, Hisao; Hibiya, Taketoshi

1990-01-01

In-situ observation of the impurity diffusion boundary layer during single crystal growth of indium-doped silicon was carried out by X-ray radiography. The difference in the transmitted X-ray image compared with molten silicon just beneath the crystal-melt interface was attributed to the concentration of indium impurities having a larger absorption coefficient. The intensity profile of the transmitted X-ray can be reproduced by a transmittance calculation that considers the meniscus shape and impurity distribution. The impurity distribution profile near the crystal-melt interface was estimated using the Burton-Prim-Slichter (BPS) equation. The observed impurity diffusion boundary layer thickness was about 0.5 mm. It was found that the boundary layer thickness was not constant in the radial direction, which cannot be explained by the BPS theory, since it is based on a one-dimensional calculation.

The Effect of Hydrogen Annealing on the Impurity Content of Alumina-Forming Alloys

NASA Technical Reports Server (NTRS)

Smialek, James L.

2000-01-01

Previously, the effect of hydrogen annealing on increasing the adhesion of Al2O3 scales had been related to the effective desulfurization that occurred during this process. The simultaneous reduction of other impurities has now been re-examined for up to 20 impurity elements in the case of five different alloys (NiCrAl, FeCrAl, PWA 1480, Rene'142, and Rene'N5). Hydrogen annealing produced measurable reductions in elemental concentration for B, C, Na, Mg, P, K, Sr, or Sn in varying degrees for at least one and up to three of these alloys. No single element was reduced by hydrogen annealing for all the alloys except sulfur. In many cases spalling occurred at low levels of these other impurities, while in other cases the scales were adherent at high levels of the impurities. No impurity besides sulfur was strongly correlated with adhesion.

Robustness against non-magnetic impurities in topological superconductors

NASA Astrophysics Data System (ADS)

Nagai, Y.; Ota, Y.; Machida, M.

2014-12-01

We study the robustness against non-magnetic impurities in a three-dimensional topological superconductor, focusing on an effective model (massive Dirac Bogoliubov-de Gennes (BdG) Hamiltonian with s-wave on-site pairing) of CuxBi2Se3 with the parameter set determined by the first-principles calculation. With the use of the self-consistent T- matrix approximation for impurity scattering, we discuss the impurity-concentration dependence of the zero-energy density of states. We show that a single material variable, measuring relativistic effects in the Dirac-BdG Hamiltonian, well characterizes the numerical results. In the nonrelativistic limit, the odd-parity fully-gapped topological superconductivity is fragile against non-magnetic impurities, since this superconductivity can be mapped onto the p-wave superconductivity. On the other hand, in the ultrarelativistic limit, the superconductivity is robust against the non-magnetic impurities, since the effective model has the s-wave superconductivity. We derive the effective Hamiltonian in the both limit.

Fermi-edge transmission resonance in graphene driven by a single Coulomb impurity.

PubMed

Karnatak, Paritosh; Goswami, Srijit; Kochat, Vidya; Pal, Atindra Nath; Ghosh, Arindam

2014-07-11

The interaction between the Fermi sea of conduction electrons and a nonadiabatic attractive impurity potential can lead to a power-law divergence in the tunneling probability of charge through the impurity. The resulting effect, known as the Fermi edge singularity (FES), constitutes one of the most fundamental many-body phenomena in quantum solid state physics. Here we report the first observation of FES for Dirac fermions in graphene driven by isolated Coulomb impurities in the conduction channel. In high-mobility graphene devices on hexagonal boron nitride substrates, the FES manifests in abrupt changes in conductance with a large magnitude ≈e(2)/h at resonance, indicating total many-body screening of a local Coulomb impurity with fluctuating charge occupancy. Furthermore, we exploit the extreme sensitivity of graphene to individual Coulomb impurities and demonstrate a new defect-spectroscopy tool to investigate strongly correlated phases in graphene in the quantum Hall regime.

Genesis and microstratigraphy of calcite coralloids analysed by high resolution imaging and petrography

NASA Astrophysics Data System (ADS)

Vanghi, V.; Frisia, S.; Borsato, A.

2017-08-01

The genesis of calcite coralloid speleothems from Lamalunga cave (Southern Italy) is here investigated from a purely petrographic perspective, which constitutes the basis for any subsequent chemical investigation. Lamalunga cave coralloids formed on bones and debris on the floor of the cave. They consist of elongated columnar crystals whose elongation progressively increases from the flanks to the tips of the coralloid, forming a succession of lens-shaped layers, which may be separated by micrite or impurity-rich layers. Organic molecules are preferentially concentrated toward the centre of convex lenses as highlighted by epifluorescence. Their occurrence on cave floor, lens-shaped morphology and concentration of impurities toward the apex of the convex lenses supports the hypothesis that their water supply was hydroaerosol, generated by the fragmentation of cave drips. Evaporation and degassing preferentially occurred on tips, enhancing the digitated morphology and trapping the organic molecules and impurities, carried by the hydroaerosol, between the growing crystals which became more elongated. Micrite layers, that cap some coralloid lenses, likely identify periods when decreasing in hydroaerosol resulted in stronger evaporation and higher supersaturation with respect to calcite of the parent film of fluid. This interpretation of coralloid formation implies that these speleothems can be used to extract hydroclimate information.

Surface-induced magnetism of the solids with impurities and vacancies

NASA Astrophysics Data System (ADS)

Morozovska, A. N.; Eliseev, E. A.; Glinchuk, M. D.; Blinc, R.

2011-04-01

Using the quantum-mechanical approach combined with the image charge method we calculated the lowest energy levels of the impurities and neutral vacancies with two electrons or holes located in the vicinity of flat surface of different solids. Unexpectedly we obtained that the magnetic triplet state is the ground state of the impurities and neutral vacancies in the vicinity of surface, while the nonmagnetic singlet is the ground state in the bulk, for e.g. He atom, Li+, Be++ ions, etc. The energy difference between the lowest triplet and singlet states strongly depends on the electron (hole) effective mass μ, dielectric permittivity of the solid ε2 and the distance from the surface z0. For z0=0 and defect charge ∣Z∣=2 the energy difference is more than several hundreds of Kelvins at μ=(0.5-1)me and ε2=2-10, more than several tens of Kelvins at μ=(0.1-0.2)me and ε2=5-10, and not more than several Kelvins at μ<0.1me and ε2>15 (me is the mass of a free electron). Pair interaction of the identical surface defects (two doubly charged impurities or vacancies with two electrons or holes) reveals the ferromagnetic spin state with the maximal exchange energy at the definite distance between the defects (∼5-25 nm). We estimated the critical concentration of surface defects and transition temperature of ferromagnetic long-range order appearance in the framework of percolation and mean field theories, and RKKY approach for semiconductors like ZnO. We obtained that the nonmagnetic singlet state is the lowest one for a molecule with two electrons formed by a pair of identical surface impurities (like surface hydrogen), while its next state with deep enough negative energy minimum is the magnetic triplet. The metastable magnetic triplet state appeared for such molecule at the surface indicates the possibility of metastable ortho-states of the hydrogen-like molecules, while they are absent in the bulk of material. The two series of spectral lines are expected due to the coexistence of ortho- and para-states of the molecules at the surface. We hope that obtained results could provide an alternative mechanism of the room temperature ferromagnetism observed in TiO2, HfO2, and In2O3 thin films with contribution of the oxygen vacancies. We expect that both anion and cation vacancies near the flat surface act as magnetic defects because of their triplet ground state and Hund's rule. The theoretical forecasts are waiting for experimental justification allowing for the number of the defects in the vicinity of surface is much larger than in the bulk of as-grown samples.

Chemical Interaction-Guided, Metal-Free Growth of Large-Area Hexagonal Boron Nitride on Silicon-Based Substrates.

PubMed

Behura, Sanjay; Nguyen, Phong; Debbarma, Rousan; Che, Songwei; Seacrist, Michael R; Berry, Vikas

2017-05-23

Hexagonal boron nitride (h-BN) is an ideal platform for interfacing with two-dimensional (2D) nanomaterials to reduce carrier scattering for high-quality 2D electronics. However, scalable, transfer-free growth of hexagonal boron nitride (h-BN) remains a challenge. Currently, h-BN-based 2D heterostructures require exfoliation or chemical transfer of h-BN grown on metals resulting in small areas or significant interfacial impurities. Here, we demonstrate a surface-chemistry-influenced transfer-free growth of large-area, uniform, and smooth h-BN directly on silicon (Si)-based substrates, including Si, silicon nitride (Si 3 N 4 ), and silicon dioxide (SiO 2 ), via low-pressure chemical vapor deposition. The growth rates increase with substrate electronegativity, Si < Si 3 N 4 < SiO 2 , consistent with the adsorption rates calculated for the precursor molecules via atomistic molecular dynamics simulations. Under graphene with high grain density, this h-BN film acts as a polymer-free, planar-dielectric interface increasing carrier mobility by 3.5-fold attributed to reduced surface roughness and charged impurities. This single-step, chemical interaction guided, metal-free growth mechanism of h-BN for graphene heterostructures establishes a potential pathway for the design of complex and integrated 2D-heterostructured circuitry.

Semiconducting behavior of substitutionally doped bilayer graphene

NASA Astrophysics Data System (ADS)

Mousavi, Hamze; Khodadadi, Jabbar; Grabowski, Marek

2018-02-01

In the framework of the Green's functions approach, random tight-binding model and using the coherent potential approximation, electronic characteristics of the bilayer graphene are investigated by exploring various forms of substitutional doping of a single or both layers of the system by either boron and (or) nitrogen atoms. The results for displacement of the Fermi level resemble the behavior of acceptor or donor doping in a conventional semiconductor, dependent on the impurity type and concentration. The particular pattern of doping of just one layer with one impurity type is most efficient for opening a gap within the energy bands which could be tuned directly by impurity concentration. Doping both layers at the same time, each with one impurity type, leads to an anomaly whereby the gap decreases with increasing impurity concentration.

Localized magnetism in liquid Al80Mn20 alloys: A first-principles investigation

NASA Astrophysics Data System (ADS)

Jakse, N.; LeBacq, O.; Pasturel, A.

2006-04-01

We present first-principles investigations of the formation of magnetic moments in liquid Al80Mn20 alloys as a function of temperature. We predict the existence of large magnetic moments on Mn atoms which are close to that of the single-impurity limit. The wide distribution of moments can be understood in terms of fluctuations in the local environment. Our calculations also predict that thermal expansion effects within the single-impurity model mainly explain the striking increase of magnetism with temperature.

Lowering the Spectral Detection Threshold for Molecular Impurities in Gas Mixtures by Interference Multiplexing

NASA Astrophysics Data System (ADS)

Ivanov, M. P.; Tolmachev, Yu. A.

2018-05-01

We consider the most feasible ways to significantly improve the sensitivity of spectroscopic methods for detection and measurement of trace concentrations of greenhouse gas molecules in the atmosphere. The proposed methods are based on combining light fluxes from a number of spectral components of the specified molecule on the same photodetector, taking into account the characteristic features of the transmission spectrum of devices utilizing multipath interference effects.

Development of RP UPLC-TOF/MS, stability indicating method for omeprazole and its related substances by applying two level factorial design; and identification and synthesis of non-pharmacopoeial impurities.

PubMed

Jadhav, Sushant Bhimrao; Kumar, C Kiran; Bandichhor, Rakeshwar; Bhosale, P N

2016-01-25

A new UPLC-TOF/MS compatible, reverse phase-stability indicating method was developed for determination of Omeprazole (OMP) and its related substances in pharmaceutical dosage forms by implementing Design of Experiment (DoE) i.e. two level full factorial Design (2(3)+3 center points=11 experiments) to understand the Critical Method Parameters (CMP) and its relation with Critical Method Attribute (CMA); to ensure robustness of the method. The separation of eleven specified impurities including conversion product of OMP related compound F (13) and G (14) i.e. Impurity-I (1), OMP related compound-I (11) and OMP 4-chloro analog (12) was achieved in a single method on Acquity BEH shield RP18 100 × 2.1 mm, 1.7 μm column, with inlet filter (0.2 μm) using gradient elution and detector wavelength at 305 nm and validated in accordance with ICH guidelines and found to be accurate, precise, reproducible, robust and specific. The drug was found to degrade extensively in heat, humidity and acidic conditions and forms unknown degradation products during stability studies. The same method was used for LC-MS analysis to identify m/z and fragmentation of maximum unknown impurities (Non-Pharmacopoeial) i.e. Impurity-I (1), Impurity-III (3), Impurity-V (5) and Impurity-VIII (9) formed during stability studies. Based on the results, degradation pathway for the drug has been proposed and synthesis of identified impurities i.e. impurities (Impurity-I (1), Impurity-III (3), Impurity-V (5) and Impurity-VIII (9)) are discussed in detail to ensure in-depth understanding of OMP and its related impurities and optimum performance during lifetime of the product. Copyright © 2015. Published by Elsevier B.V.

Habit modification of potassium acid phthalate (KAP) single crystals by impurities

NASA Astrophysics Data System (ADS)

Murugakoothan, P.; Mohan Kumar, R.; Ushasree, P. M.; Jayavel, R.; Dhanasekaran, R.; Ramasamy, P.

1999-12-01

Nonlinear optical materials potassium dihydrogen phosphate (KDP), urea and L-arginine phosphate (LAP)-doped KAP crystals were grown by the slow cooling method. The LAP-doped crystals show pronounced habit modification compared to KDP and urea doping. The effect of these impurities on growth kinetics, surface morphology, habit modification, structure, optical and mechanical properties have been studied. Among the three impurities, urea doping yields high mechanical stability and optical transmission and for KDP and LAP doping there is a decrease in optical transmission.

A facile one-step fluorescence method for the quantitation of low-content single base deamination impurity in synthetic oligonucleotides.

PubMed

Su, Xiaoye; Liang, Ruiting; Stolee, Jessica A

2018-06-05

Oligonucleotides are being researched and developed as potential drug candidates for the treatment of a broad spectrum of diseases. The characterization of antisense oligonucleotide (ASO) impurities caused by base mutations (e.g. deamination) which are closely related to the target ASO is a significant analytical challenge. Herein, we describe a novel one-step method, utilizing a strategy that combines fluorescence-ON detection with competitive hybridization, to achieve single base mutation quantitation in extensively modified synthetic ASOs. Given that this method is highly specific and sensitive (LoQ = 4 nM), we envision that it will find utility for screening other impurities as well as sequencing modified oligonucleotides. Copyright © 2018 Elsevier B.V. All rights reserved.

Development of adsorptive hybrid filters to enable two-step purification of biologics

PubMed Central

Peck, Michael; Voloshin, Alexei M.; Moreno, Angela M.; Tan, Zhijun; Hester, Jonathan; Borys, Michael C.; Li, Zheng Jian

2017-01-01

ABSTRACT Recent progress in mammalian cell culture process has resulted in significantly increased product titers, but also a substantial increase in process- and product-related impurities. Due to the diverse physicochemical properties of these impurities, there is constant need for new technologies that offer higher productivity and improved economics without sacrificing the process robustness required to meet final drug substance specifications. Here, we examined the use of new synthetic adsorptive hybrid filters (AHF) modified with the high binding capacity of quaternary amine (Emphaze™ AEX) and salt-tolerant biomimetic (Emphaze™ ST-AEX) ligands for clearance of process-related impurities like host cell protein (HCP), residual DNA, and virus. The potential to remove soluble aggregates was also examined. Our aim was to develop a mechanistic understanding of the interactions governing adsorptive removal of impurities during filtration by evaluating the effect of various filter types, feed streams, and process conditions on impurity removal. The ionic capacity of these filters was measured and correlated with their ability to remove impurities for multiple molecules. The ionic capacity of AHF significantly exceeded that of traditional adsorptive depth filters (ADF) by 40% for the Emphaze™ AEX and by 700% for the Emphaze™ ST-AEX, providing substantially higher reduction of soluble anionic impurities, including DNA, HCPs and model virus. Nevertheless, we determined that ADF with filter aid provided additional hydrophobic functionality that resulted in removal of higher molecular weight species than AHF. Implementing AHF demonstrated improved process-related impurity removal and viral clearance after Protein A chromatography and enabled a two-step purification process. The consequences of enhanced process performance are far reaching because it allows the downstream polishing train to be restructured and simplified, and chromatographic purity standards to be met with a reduced number of chromatographic steps. PMID:27929735

Root yield and quality of sugarbeet hybrids with pollinators selected for sodium, potassium, or amino-nitrogen concentration

USDA-ARS?s Scientific Manuscript database

Sodium, potassium, and amino-nitrogen, collectively referred to as impurities, are natural constituents of sugarbeet that impede sucrose extraction during factory operations. Lines selected specifically for low or high concentration of a single impurity component were crossed as pollinators with a ...

Impurity Induced Phase Competition and Supersolidity

NASA Astrophysics Data System (ADS)

Karmakar, Madhuparna; Ganesh, R.

2017-12-01

Several material families show competition between superconductivity and other orders. When such competition is driven by doping, it invariably involves spatial inhomogeneities which can seed competing orders. We study impurity-induced charge order in the attractive Hubbard model, a prototypical model for competition between superconductivity and charge density wave order. We show that a single impurity induces a charge-ordered texture over a length scale set by the energy cost of the competing phase. Our results are consistent with a strong-coupling field theory proposed earlier in which superconducting and charge order parameters form components of an SO(3) vector field. To discuss the effects of multiple impurities, we focus on two cases: correlated and random distributions. In the correlated case, the CDW puddles around each impurity overlap coherently leading to a "supersolid" phase with coexisting pairing and charge order. In contrast, a random distribution of impurities does not lead to coherent CDW formation. We argue that the energy lowering from coherent ordering can have a feedback effect, driving correlations between impurities. This can be understood as arising from an RKKY-like interaction, mediated by impurity textures. We discuss implications for charge order in the cuprates and doped CDW materials such as NbSe2.

Multiplicity of transmission coefficients in photonic crystal and split ring resonator waveguides with Kerr nonlinear impurities

NASA Astrophysics Data System (ADS)

Rai, Buddhi; McGurn, Arthur R.

2015-02-01

Photonic crystal and split ring resonator (SRR) metamaterial waveguides with Kerr nonlinear dielectric impurities are studied. The transmission coefficients for two guided modes of different frequencies scattering from the Kerr impurities are computed. The systems are shown to exhibit multiple transmission coefficient solutions arising from the Kerr nonlinearity. Multiple transmission coefficients occur when different input intensities into a waveguide result in the same transmitted output intensities past its nonlinear impurities. (In the case of a single incident guided mode the multiplicity of transmission coefficients is known as optical bistability.) The analytical conditions under which the transmission coefficients are single and multiple valued are determined, and specific examples of both single and multiple valued transmission coefficient scattering are presented. Both photonic crystal and split ring resonator systems are studied as the Kerr nonlinearity enters the photonic crystal and SRR systems in different ways. This allows for an interesting comparison of the differences in behaviors of these two types of system which are described by distinctly different mathematical structures. Both the photonic crystal and SRR models used in the calculations are based on a difference equation approach to the system dynamics. The difference equation approach has been extensively employed in previous papers to model the basic properties of these systems. The paper is a continuation of work on the optical bistability of single guided modes interacting with Kerr impurities in photonic crystals originally considered by McGurn [Chaos 13, 754 (2003), 10.1063/1.1568691] and work on the resonant scattering from Kerr impurities in photonic crystal waveguides considered by McGurn [J. Phys.: Condens. Matter 16, S5243 (2004), 10.1088/0953-8984/16/44/021]. It generalizes this work making the extension to the more complex interaction of two guided modes at different frequencies. It extends the two guided mode treatment by McGurn [Organ. Electron. 8, 227 (2007), 10.1016/j.orgel.2006.06.008] which was limited to a special case of one of the photonic crystal systems considered here.

Tunable reactivity of supported single metal atoms by impurity engineering of the MgO(001) support.

PubMed

Pašti, Igor A; Johansson, Börje; Skorodumova, Natalia V

2018-02-28

Development of novel materials may often require a rational use of high price components, like noble metals, in combination with the possibility to tune their properties in a desirable way. Here we present a theoretical DFT study of Au and Pd single atoms supported by doped MgO(001). By introducing B, C and N impurities into the MgO(001) surface, the interaction between the surface and the supported metal adatoms can be adjusted. Impurity atoms act as strong binding sites for Au and Pd adatoms and can help to produce highly dispersed metal particles. The reactivity of metal atoms supported by doped MgO(001), as probed by CO, is altered compared to their counterparts on pristine MgO(001). We find that Pd atoms on doped MgO(001) are less reactive than on perfect MgO(001). In contrast, Au adatoms bind CO much more strongly when placed on doped MgO(001). In the case of Au on N-doped MgO(001) we find that charge redistribution between the metal atom and impurity takes place even when not in direct contact, which enhances the interaction of Au with CO. The presented results suggest possible ways for optimizing the reactivity of oxide supported metal catalysts through impurity engineering.

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

Mezdrogina, M. M., E-mail: Margaret.m@mail.ioffe.ru; Vinogradov, A. Ya.; Kuzmin, R. V.

For ZnO films, nanorods, and bulk single crystals doped with Er{sup +} ions, it is shown that the effect of codopants introduced into the cation and ion sublattices and the observation of a high-intensity emission band at the wavelength λ{sub max} = 1535 nm are defined by the local environment of the Er{sup +} ion. Doping of the films and single crystals with Er{sup +} ions by diffusion brings about an infrared (IR) emission band with a low intensity because of an inadequate concentration of impurity ions. The emission intensity of this band can be raised by introducing additional Ag,more » Au, or N{sup +} impurities into the ZnO films. The UV-emission intensity of the Er-doped films and single crystals at λ{sub max} = 368–372 nm is identical to that of the undoped films. ZnO nanorods doped with Er only or together with Al or Ga codopants exhibit only one IR band (at λ{sub max} = 1535 nm), whose intensity decreases upon the introduction of codopants. Doping of the nanorods with the N{sup +} gaseous impurity during growth (930 < T < 960°C) and then with the Er{sup +} impurity by diffusion does not yield a substantial increase in the IR-emission intensity compared to the that of the corresponding band for nanorods not doped with the N{sup +} impurity. In the Er-doped nanorods, whose photoluminescence spectra exhibit a high-intensity band at λ{sub max} = 1535 nm, the UV emission band at λ{sub max} = 372 nm is practically lacking.« less

Single- or multi-flavor Kondo effect in graphene

NASA Astrophysics Data System (ADS)

Zhu, Zhen-Gang; Ding, Kai-He; Berakdar, Jamal

2010-06-01

Based on the tight-binding formalism, we investigate the Anderson and the Kondo model for an adatom magnetic impurity above graphene. Different impurity positions are analyzed. Employing a partial-wave representation we study the nature of the coupling between the impurity and the conducting electrons. The components from the two Dirac points are mixed while interacting with the impurity. Two configurations are considered explicitly: the adatom is above one atom (ADA), the other case is the adatom above the center the honeycomb (ADC). For ADA the impurity is coupled with one flavor for both A and B sublattice and both Dirac points. For ADC the impurity couples with multi-flavor states for a spinor state of the impurity. We show, explicitly for a 3d magnetic atom, dz2, (dxz,dyz), and (dx2- y2,dxy) couple respectively with the Γ1, Γ5(E1), and Γ6(E2) representations (reps) of C6v group in ADC case. The bases for these reps of graphene are also derived explicitly. For ADA we calculate the Kondo temperature.

Impurity-induced states in superconducting heterostructures

NASA Astrophysics Data System (ADS)

Liu, Dong E.; Rossi, Enrico; Lutchyn, Roman M.

2018-04-01

Heterostructures allow the realization of electronic states that are difficult to obtain in isolated uniform systems. Exemplary is the case of quasi-one-dimensional heterostructures formed by a superconductor and a semiconductor with spin-orbit coupling in which Majorana zero-energy modes can be realized. We study the effect of a single impurity on the energy spectrum of superconducting heterostructures. We find that the coupling between the superconductor and the semiconductor can strongly affect the impurity-induced states and may induce additional subgap bound states that are not present in isolated uniform superconductors. For the case of quasi-one-dimensional superconductor/semiconductor heterostructures we obtain the conditions for which the low-energy impurity-induced bound states appear.

Quasibound states in short SNS junctions with point defects

NASA Astrophysics Data System (ADS)

Bespalov, A. A.

2018-04-01

Using the Green functions technique, we study the subgap spectrum of short three-dimensional superconductor-normal metal-superconductor junctions containing one or two point impurities in the normal layer. We find that a single nonmagnetic or magnetic defect induces two quasibound Shiba-like states. If the defect is located close to the junction edge, the energies of these states oscillate as functions of the distance between the impurity and the edge. In the case of two nonmagnetic impurities, there are generally four quasibound states (two per spin projection). Their energies oscillate as functions of the distance between the impurities, and reach their asymptotic values when this distance becomes much larger than the Fermi wavelength. The contributions of the impurities to the Josephson current, local density of states, and to the normal-state conductance of the junction are analyzed.

Magnetic impurity effect on charge and magnetic order in doped La1.5Ca0.5CoO4

NASA Astrophysics Data System (ADS)

Horigane, K.; Hiraka, H.; Tomiyasu, K.; Ohoyama, K.; Louca, D.; Yamada, K.

2012-02-01

Neutron scattering experiments were performed on single crystals of magnetic impurity doped cobalt oxides La1.5Ca0.5CoO4 to characterize the charge and spin orders. We newly found contrasting impurity effects. Two types of magnetic peaks are observed at q = (0.5,0,L) with L = half-integer and integer in La1.5Ca0.5CoO4, while magnetic peak at L = half-integer (integer) was only observed in Mn (Fe)-substituted sample. Although Mn and Fe impurities degrade charge and magnetic order, Cr impurity stabilizes the ordering at x = 0.5. Based on the crystal structural analysis of Cr doped sample, we found that the excess oxygen and change of octahedron around Co3+ were realized in Cr doped sample.

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

Sharma, Munish, E-mail: munishsharmahpu@live.com; Jamdagni, Pooja; Ahluwalia, P. K.

We present a first principle study of interaction of toxic gas molecules (NO, NO{sub 2} and SO{sub 2}) with monolayer MoSe{sub 2}. The predicted order of sensitivity of gas molecule is NO{sub 2} > SO{sub 2} > NO. Adsorbed molecules strongly influence the electronic behaviour of monolayer MoSe{sub 2} by inducing impurity levels in the vicinity of Fermi energy. NO and SO{sub 2} is found to induce p-type doping effect while semiconductor to metallic transitions occur on NO{sub 2} adsorption. Our findings may guide the experimentalist for fabricating sensor devices based on MoSe{sub 2} monolayer.

Effect of impurities on the mechanical and electronic properties of Au, Ag, and Cu monatomic chain nanowires

NASA Astrophysics Data System (ADS)

Çakır, D.; Gülseren, O.

2011-08-01

In this study, we have investigated the interaction of various different atomic and molecular species (H, C, O, H2, and O2) with the monatomic chains of Au, Ag, and Cu via total-energy calculations using the plane-wave pseudopotential method based on density functional theory. The stability, energetics, mechanical, and electronic properties of the clean and contaminated Au, Ag, and Cu nanowires have been presented. We have observed that the interaction of H, C, or O atoms with the monatomic chains are much stronger than the one of H2 or O2 molecules. The atomic impurities can easily be incorporated into these nanowires; they form stable and strong bonds with these one-dimensional structures when they are inserted in or placed close to the nanowires. Moreover, the metal-atomic impurity bond is much stronger than the metal-metal bond. Upon elongation, the nanowires contaminated with atomic impurities usually break from the remote metal-metal bond. We have observed both metallic and semiconducting contaminated nanowires depending on the type of impurity, whereas all clean monatomic chains of Au, Cu, and Ag exhibit metallic behavior. Our findings indicate that the stability and the electronic properties of these monatomic chains can be tuned by using appropriate molecular or atomic additives.

Magnetic properties of ZnO nanoparticles.

PubMed

Garcia, M A; Merino, J M; Fernández Pinel, E; Quesada, A; de la Venta, J; Ruíz González, M L; Castro, G R; Crespo, P; Llopis, J; González-Calbet, J M; Hernando, A

2007-06-01

We experimentally show that it is possible to induce room-temperature ferromagnetic-like behavior in ZnO nanoparticles without doping with magnetic impurities but simply inducing an alteration of their electronic configuration. Capping ZnO nanoparticles ( approximately 10 nm size) with different organic molecules produces an alteration of their electronic configuration that depends on the particular molecule, as evidenced by photoluminescence and X-ray absorption spectroscopies and altering their magnetic properties that varies from diamagnetic to ferromagnetic-like behavior.

Water inhibits CO oxidation on gold cations in the gas phase. Structures and binding energies of the sequential addition of CO, H2O, O2, and N2 onto Au.

PubMed

Reveles, J Ulises; Saoud, Khaled M; El-Shall, M Samy

2016-10-19

We report a detailed experimental and theoretical study of the gas phase reactivity of Au + with CO, O 2 , N 2 and their mixtures in the presence of a trace amount of water impurity. The gold cation is found to strongly interact with CO and H 2 O molecules via successive addition reactions until reaching saturation. The stoichiometry of the formed complex is determined by the strength of the binding energy of the neutral molecule to the gold cation. CO binds the strongest to Au + , followed by H 2 O, N 2 and then O 2 . We found that the gold cation (Au + ) can activate the O 2 molecule within the Au + (CO) 2 (O 2 ) complex which could react with another CO molecule to form Au + (CO)(CO 2 ) + CO 2 . The product Au + (CO)(CO 2 ) is observed experimentally with a small intensity at room temperature. However, the presence of water leads to the formation of Au + (CO)(H 2 O)(O 2 ) instead of Au + (CO) 2 (O 2 ) due to the strong interaction between Au + and water. The current experiments and calculations might lead to a molecular level understanding of the interactions between the active sites, reactants and impurities which could pave the way for the design of efficient nanocatalysts.

Purification of Germanium Crystals by Zone Refining

NASA Astrophysics Data System (ADS)

Kooi, Kyler; Yang, Gang; Mei, Dongming

2016-09-01

Germanium zone refining is one of the most important techniques used to produce high purity germanium (HPGe) single crystals for the fabrication of nuclear radiation detectors. During zone refining the impurities are isolated to different parts of the ingot. In practice, the effective isolation of an impurity is dependent on many parameters, including molten zone travel speed, the ratio of ingot length to molten zone width, and number of passes. By studying the theory of these influential factors, perfecting our cleaning and preparation procedures, and analyzing the origin and distribution of our impurities (aluminum, boron, gallium, and phosphorous) identified using photothermal ionization spectroscopy (PTIS), we have optimized these parameters to produce HPGe. We have achieved a net impurity level of 1010 /cm3 for our zone-refined ingots, measured with van der Pauw and Hall-effect methods. Zone-refined ingots of this purity can be processed into a detector grade HPGe single crystal, which can be used to fabricate detectors for dark matter and neutrinoless double beta decay detection. This project was financially supported by DOE Grant (DE-FG02-10ER46709) and the State Governor's Research Center.

Numerical renormalization group calculation of impurity internal energy and specific heat of quantum impurity models

NASA Astrophysics Data System (ADS)

Merker, L.; Costi, T. A.

2012-08-01

We introduce a method to obtain the specific heat of quantum impurity models via a direct calculation of the impurity internal energy requiring only the evaluation of local quantities within a single numerical renormalization group (NRG) calculation for the total system. For the Anderson impurity model we show that the impurity internal energy can be expressed as a sum of purely local static correlation functions and a term that involves also the impurity Green function. The temperature dependence of the latter can be neglected in many cases, thereby allowing the impurity specific heat Cimp to be calculated accurately from local static correlation functions; specifically via Cimp=(∂Eionic)/(∂T)+(1)/(2)(∂Ehyb)/(∂T), where Eionic and Ehyb are the energies of the (embedded) impurity and the hybridization energy, respectively. The term involving the Green function can also be evaluated in cases where its temperature dependence is non-negligible, adding an extra term to Cimp. For the nondegenerate Anderson impurity model, we show by comparison with exact Bethe ansatz calculations that the results recover accurately both the Kondo induced peak in the specific heat at low temperatures as well as the high-temperature peak due to the resonant level. The approach applies to multiorbital and multichannel Anderson impurity models with arbitrary local Coulomb interactions. An application to the Ohmic two-state system and the anisotropic Kondo model is also given, with comparisons to Bethe ansatz calculations. The approach could also be of interest within other impurity solvers, for example, within quantum Monte Carlo techniques.

Negative quantum capacitance induced by midgap states in single-layer graphene.

PubMed

Wang, Lin; Wang, Yang; Chen, Xiaolong; Zhu, Wei; Zhu, Chao; Wu, Zefei; Han, Yu; Zhang, Mingwei; Li, Wei; He, Yuheng; Xiong, Wei; Law, Kam Tuen; Su, Dangsheng; Wang, Ning

2013-01-01

We demonstrate that single-layer graphene (SLG) decorated with a high density of Ag adatoms displays the unconventional phenomenon of negative quantum capacitance. The Ag adatoms act as resonant impurities and form nearly dispersionless resonant impurity bands near the charge neutrality point (CNP). Resonant impurities quench the kinetic energy and drive the electrons to the Coulomb energy dominated regime with negative compressibility. In the absence of a magnetic field, negative quantum capacitance is observed near the CNP. In the quantum Hall regime, negative quantum capacitance behavior at several Landau level positions is displayed, which is associated with the quenching of kinetic energy by the formation of Landau levels. The negative quantum capacitance effect near the CNP is further enhanced in the presence of Landau levels due to the magnetic-field-enhanced Coulomb interactions.

Negative Quantum Capacitance Induced by Midgap States in Single-layer Graphene

PubMed Central

Wang, Lin; Wang, Yang; Chen, Xiaolong; Zhu, Wei; Zhu, Chao; Wu, Zefei; Han, Yu; Zhang, Mingwei; Li, Wei; He, Yuheng; Xiong, Wei; Law, Kam Tuen; Su, Dangsheng; Wang, Ning

2013-01-01

We demonstrate that single-layer graphene (SLG) decorated with a high density of Ag adatoms displays the unconventional phenomenon of negative quantum capacitance. The Ag adatoms act as resonant impurities and form nearly dispersionless resonant impurity bands near the charge neutrality point (CNP). Resonant impurities quench the kinetic energy and drive the electrons to the Coulomb energy dominated regime with negative compressibility. In the absence of a magnetic field, negative quantum capacitance is observed near the CNP. In the quantum Hall regime, negative quantum capacitance behavior at several Landau level positions is displayed, which is associated with the quenching of kinetic energy by the formation of Landau levels. The negative quantum capacitance effect near the CNP is further enhanced in the presence of Landau levels due to the magnetic-field-enhanced Coulomb interactions. PMID:23784258

Universal trace pollutant detector for aircraft monitoring of the ozone layer and industrial areas

NASA Technical Reports Server (NTRS)

Filiouguine, I. V.; Kostiouchenko, S. V.; Koudriavtsev, N. N.

1994-01-01

A method of monitoring the trace impurities of nitrogen oxides based on controlling of luminescence of NO molecules excited by nanosecond gas discharge have been developed having pptv-ppbv sensitivity and temporal resolution less than 0.01 s.

Bonding and vibrations of CO molecules adsorbed at transition metal impurity sites on the MgO (001) surface. A density functional model cluster study

NASA Astrophysics Data System (ADS)

Neyman, K. M.; Rösch, N.

1993-11-01

First principles density functional cluster investigations of adsorption at the (001) surface of pure and doped magnesium oxide are carried out to characterize and compare the interaction of CO molecules with main group (Mg 2+) and d metal (Co 2+, Ni 2+, Cu 2+) surface cationic centers of the ionic substrate. The geometry of the adsorption complexes, the binding mechanism and spectroscopic manifestations of the surface species are analyzed. Special attention is payed to vibrational frequencies and intensities. The calculations qualitatively reproduce observed trends in the adsorption-induced frequency shifts for the series of the surface aggregates Mg 5cCO→Ni 5cCO→CO 5cCO and the corresponding change of the infrared intensities of the CO vibrational mode. For the transition metal impurity sites these results are rationalized in terms of a small, but notable Md πCOπ interaction.

Purification, crystal growth and characterization of CdSe single crystals

NASA Astrophysics Data System (ADS)

Burger, A.; Henderson, D. O.; Morgan, S. H.; Silberman, E.

1991-02-01

CdSe single crystals have been grown from the stoichiometric melt and from Se rich solutions. Here we report the first mid and far infrared spectra of CdSe crystals free of any known impurity bands. Previous studies of the lattice vibrational properties of CdSe crystals have shown the presence of two bands at 538 and 270 cm -1. Modifications in the purification and crystal growth conditions lead us to assign these two bands to a sulfur impurity. Low temperature photoluminescence spectra are also presented and discussed.

Fast Characterization of Magnetic Impurities in Single-Wall Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Chen, Feng; Xue, Y. Y.; Hadijiev, Viktor G.; Chu, C. W.; Nikolaev, Pasha; Arepalli, Sivaram

2003-01-01

We have demonstrated that the magnetic susceptibility measurement is a non-destructive, fast and accurate method to determine the residual metal catalysts in a few microgram single-wall carbon nanotube (SWCNT) sample. We have studied magnetic impurities in raw and purified SWCNT by magnetic susceptibility measurements, transmission electron microscopy, and thermogravimetry. The data suggest that the saturation magnetic moment and the effective field, which is caused by the interparticle interactions, decreases and increases respectively with the decrease of the particle size. Methods are suggested to overcome the uncertainty associated.

Nonequilibrium Quasiparticle Distribution Induced by Kondo Defects

NASA Astrophysics Data System (ADS)

Kroha, J.; Zawadowski, A.

2002-04-01

It is shown that in resistive nanowires out of equilibrium containing either single- or two-channel Kondo impurities the distribution function f(E,U) obeys scaling behavior in terms of the quasiparticle energy E and the bias voltage U. The numerically calculated f(E,U) curves explain quantitatively recent experiments on Cu and Au nanowires. The systematics of the impurity concentration cimp extracted from the comparison between theory and results on various Cu and Au samples strongly suggests that in these systems the scaling arises from magnetic Kondo impurities.

Characterization of zinc selenide single crystals

NASA Technical Reports Server (NTRS)

Gerhardt, Rosario A.

1996-01-01

ZnSe single crystals of high quality and low impurity levels are desired for use as substrates in optoelectronic devices. This is especially true when the device requires the formation of homoepitaxial layers. While ZnSe is commercially available, it is at present extremely expensive due to the difficulty of growing single crystal boules with low impurity content and the resultant low yields. Many researchers have found it necessary to heat treat the crystals in liquid Zn in order to remove the impurities, lower the resistivity and activate the photoluminescence at room temperature. The physical vapor transport method (PVT) has been successfully used at MSFC to grow many single crystals of II-VI semiconducting materials including ZnSe. The main goal at NASA has been to try to establish the effect of gravity on the growth parameters. To this effect, crystals have been grown vertically upwards or horizontally. Both (111) and (110) oriented ZnSe crystals have been obtained via unseeded PVT growth. Preliminary characterization of the horizontally grown crystals has revealed that Cu is a major impurity and that the low temperature photoluminescence spectra is dominated by the copper peak. The ratio of the copper peak to the free exciton peak is being used to determine variations in composition throughout the crystal. It was the intent of this project to map the copper composition of various crystals via photoluminescence first, then measure their electrical resistivity and capacitance as a function of frequency before proceeding with a heat treatment designed to remove the copper impurities. However, equipment difficulties with the photoluminescence set up, having to establish a procedure for measuring the electrical properties of the as-grown crystals and time limitations made us re-evaluate the project goals. Vertically grown samples designated as ZnSe-25 were chosen to be measured electrically since they were not expected to show as much variation in their composition through their cross-section as the horizontally grown samples.

Characterization of product-related low molecular weight impurities in therapeutic monoclonal antibodies using hydrophilic interaction chromatography coupled with mass spectrometry.

PubMed

Wang, Shunhai; Liu, Anita P; Yan, Yuetian; Daly, Thomas J; Li, Ning

2018-05-30

Traditional SDS-PAGE method and its modern equivalent CE-SDS method are both widely applied to assess the purity of therapeutic monoclonal antibody (mAb) drug products. However, structural identification of low molecular weight (LMW) impurities using those methods has been challenging and largely based on empirical knowledges. In this paper, we present that hydrophilic interaction chromatography (HILIC) coupled with mass spectrometry analysis is a novel and orthogonal method to characterize such LMW impurities present within a purified mAb drug product sample. We show here that after removal of N-linked glycans, the HILIC method separates mAb-related LMW impurities with a size-based elution order. The subsequent mass measurement from a high-resolution accurate mass spectrometer provides direct and unambiguous identification of a variety of low-abundance LMW impurities within a single LC-MS analysis. Free light chain, half antibody, H2L species (antibody possessing a single light chain) and protein backbone-truncated species can all be confidently identified and elucidated in great detail, including the truncation sites and associated post-translational modifications. It is worth noting that this study provides the first example where the H2L species can be directly detected in a mAb drug product sample by intact mass analysis without prior enrichment. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Inclusion property of Cs, Sr, and Ba impurities in LiCl crystal formed by layer-melt crystallization

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

Choi, Jung-Hoon; Cho, Yung-Zun; Lee, Tae-Kyo

Pyroprocessing is one of the promising technologies enabling the recycling of spent nuclear fuels from a commercial light water reactor (LWR). In general, pyroprocessing uses dry molten salts as electrolytes. In particular, LiCl waste salt after pyroprocessing contains highly radioactive I/II group fission products mainly composed of Cs, Sr, and Ba impurities. Therefore, it is beneficial to reuse LiCl salt in the pyroprocessing as an electrolyte for economic and environmental issues. Herein, to understand the inclusion property of impurities within LiCl crystal, the physical properties such as lattice parameter change, bulk modulus, and substitution enthalpy of a LiCl crystal havingmore » 0-6 at% Cs{sup +} or Ba{sup 2+} impurities under existence of 1 at% Sr{sup 2+} impurity were calculated via the first-principles density functional theory. The substitution enthalpy of LiCl crystals having 1 at% Sr{sup 2+} showed slightly decreased value than those without Sr{sup 2+} impurity. Therefore, through the substitution enthalpy calculation, it is expected that impurities will be incorporated within LiCl crystal as co-existed form rather than as a single component form. (authors)« less

Analysis of spin-Hamiltonian and molecular orbital coefficients of Cu2+ doped C8H11KO8 single crystal through EPR technique

NASA Astrophysics Data System (ADS)

Juliet sheela, K.; Krishnan, S. Radha; Shanmugam, V. M.; Subramanian, P.

2018-04-01

Electron paramagnetic resonance (EPR) studies have been investigated at X-band microwave frequency on Cu2+ ion incorporated into the single crystal of potassium succinate-succinic acid (KSSA) at room temperature. The angular variation of the EPR spectra has shown two magnetically in-equivalent Cu2+ sites in the KSSA single crystal system. The spin Hamiltonian parameters g and A are determined which reveals that the site I and site II occupied in rhombic and axial local field symmetry around the impurity ion. Among the two paramagnetic impurity ions, sites one occupies at substituitional position in the place of monovalent cation (K+) in the crystal whereas the other enters in its lattice interstitially by the correlation of EPR and crystal structure data. From the calculated principle values gxx, gyy, gzz and Axx, Ayy, Azz of both the sites, the admixture coefficients and molecular orbital coefficients were evaluated which gives the information of ground state wave function and types of bonding of impurity ions with the ligands.

Spin-polarized density-matrix functional theory of the single-impurity Anderson model

NASA Astrophysics Data System (ADS)

Töws, W.; Pastor, G. M.

2012-12-01

Lattice density functional theory (LDFT) is used to investigate spin excitations in the single-impurity Anderson model. In this method, the single-particle density matrix γijσ with respect to the lattice sites replaces the wave function as the basic variable of the many-body problem. A recently developed two-level approximation (TLA) to the interaction-energy functional W[γ] is extended to systems having spin-polarized density distributions and bond orders. This allows us to investigate the effect of external magnetic fields and, in particular, the important singlet-triplet gap ΔE, which determines the Kondo temperature. Applications to finite Anderson rings and square lattices show that the gap ΔE as well as other ground-state and excited-state properties are very accurately reproduced. One concludes that the spin-polarized TLA is reliable in all interaction regimes, from weak to strong correlations, for different hybridization strengths and for all considered impurity valence states. In this way the efficiency of LDFT to account for challenging electron-correlation effects is demonstrated.

Single crystal growth, characterization and high-pressure Raman spectroscopy of impurity-free magnesite (MgCO3)

NASA Astrophysics Data System (ADS)

Liang, Wen; Li, Zeming; Yin, Yuan; Li, Rui; Chen, Lin; He, Yu; Dong, Haini; Dai, Lidong; Li, Heping

2018-05-01

The understanding of the physical and chemical properties of magnesite (MgCO3) under deep-mantle conditions is highly important to capture the essence of deep-carbon storage in Earth's interior. To develop standard rating scales, the impurity-free magnesite single crystal, paying particular attention to the case of avoiding adverse impacts of Ca2+, Fe2+, and Mn2+ impurities in natural magnesite, is undoubtedly necessary for all research of magnesite, including crystalline structural phase transitions, anisotropic elasticity and conductivity, and equation of state (EoS). Thus, a high-quality single crystal of impurity-free magnesite was grown successfully for the first time using the self-flux method under high pressure-temperature conditions. The size of the magnesite single crystal, observed in a plane-polarized microscope, exceeds 200 μm, and the crystal exhibits a rhombohedral structure to cleave along the (101) plane. In addition, its composition of Mg0.999 ± 0.001CO3 was quantified through electron probing analysis. The structural property was investigated by means of single crystal X-ray diffraction and the unit cell dimensions obtained in the rhombohedral symmetry of the R\\bar {3}c space group are a = 4.6255 (3) and c = 14.987 (2), and the final R = 0.0243 for 718 reflections. High-pressure Raman spectroscopy of the magnesite single crystal was performed up to 27 GPa at ambient temperature. All Raman active bands, ν i, without any splitting increased almost linearly with increasing pressure. In combination with the high-pressure Raman results {{d/ν _i}}{{{d}P}} and the bulk modulus K T (103 GPa) reported from magnesite EoS studies, the mode Grüneisen parameters (1.49, 1.40, 0.26, and 0.27) of each vibration ( T, L, ν 4, and ν 1) were calculated.

Unbinding slave spins in the Anderson impurity model

NASA Astrophysics Data System (ADS)

Guerci, Daniele; Fabrizio, Michele

2017-11-01

We show that a generic single-orbital Anderson impurity model, lacking, for instance, any kind of particle-hole symmetry, can be exactly mapped without any constraint onto a resonant level model coupled to two Ising variables, which reduce to one if the hybridization is particle-hole symmetric. The mean-field solution of this model is found to be stable to unphysical spontaneous magnetization of the impurity, unlike the saddle-point solution in the standard slave-boson representation. Remarkably, the mean-field estimate of the Wilson ratio approaches the exact value RW=2 in the Kondo regime.

Non-Fermi Liquid Behavior in the Single-Impurity Mixed Valence Problem

NASA Astrophysics Data System (ADS)

Zhang, Guang-Ming; Su, Zhao-Bin; Yu, Lu

An effective Hamiltonian of the Anderson single-impurity model with finite-range Coulomb interactions is derived near a particular limit, which is analogous to the Toulouse limit of the ordinary Kondo problem, and the physical properties around the mixed valence quantum critical point are calculated. At this quantum critical point, the local moment is only partially quenched and X-ray edge singularities are exhibited. Around this point, a new type of non-Fermi liquid behavior is predicted with an extra specific heat Cimp ~ T1/4 + AT ln T and spin-susceptibility χimp ~T-3/4 + B ln T.

Drift and separation in collisionality gradients

DOE PAGES

Ochs, I. E.; Rax, J. M.; Gueroult, R.; ...

2017-07-20

Here we identify a single-particle drift resulting from collisional interactions with a background species, in the presence of a collisionality gradient and background net flow. We also analyze this drift in different limits, showing how it reduces to the well known impurity pinch for high-Zi impurities. We find that in the low-temperature, singly ionized limit, the magnitude of the drift becomes mass-dependent and energy-dependent. Furthermore, by solving for the resulting diffusion-advection motion, we propose a mass-separation scheme that takes advantage of this drift, and analyze the separative capability as a function of collisionally dissipated energy.

Drift and separation in collisionality gradients

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

Ochs, I. E.; Rax, J. M.; Gueroult, R.

Here we identify a single-particle drift resulting from collisional interactions with a background species, in the presence of a collisionality gradient and background net flow. We also analyze this drift in different limits, showing how it reduces to the well known impurity pinch for high-Zi impurities. We find that in the low-temperature, singly ionized limit, the magnitude of the drift becomes mass-dependent and energy-dependent. Furthermore, by solving for the resulting diffusion-advection motion, we propose a mass-separation scheme that takes advantage of this drift, and analyze the separative capability as a function of collisionally dissipated energy.

The cluster Ir4 and its interaction with a hydrogen impurity. A density functional study.

PubMed

Bussai, Chuenchit; Krüger, Sven; Vayssilov, Georgi N; Rösch, Notker

2005-07-07

To contribute to the understanding of how iridium particles act as catalysts for hydrogenation and dehydrogenation of hydrocarbons, we have determined structures and binding energies of various isomers of Ir(4) as well as HIr(4) on the basis of relativistic density functional theory. The most stable isomer of Ir(4) showed a square planar structure with eight unpaired electrons. The tetrahedral structure, experimentally suggested for supported species, was calculated 49 kJ mol(-1) less stable. Hydrogen coordinates preferentially to a single Ir center of the planar cluster with a binding energy of up to 88 kJ mol(-1) with respect to the atom in the H(2) molecule. Terminal interaction of hydrogen with an Ir(4) tetrahedron causes the cluster to open to a butterfly structure. We calculated terminal binding of hydrogen at different Ir(4) isomers to be more stable than bridge coordination, at variance with earlier studies.

Entanglement entropy in a boundary impurity model.

PubMed

Levine, G C

2004-12-31

Boundary impurities are known to dramatically alter certain bulk properties of (1+1)-dimensional strongly correlated systems. The entanglement entropy of a zero temperature Luttinger liquid bisected by a single impurity is computed using a novel finite size scaling or bosonization scheme. For a Luttinger liquid of length 2L and UV cutoff epsilon, the boundary impurity correction (deltaSimp) to the logarithmic entanglement entropy (Sent proportional, variant lnL/epsilon scales as deltaSimp approximately yrlnL/epsilon, where yr is the renormalized backscattering coupling constant. In this way, the entanglement entropy within a region is related to scattering through the region's boundary. In the repulsive case (g<1), deltaSimp diverges (negatively) suggesting that the entropy vanishes. Our results are consistent with the recent conjecture that entanglement entropy decreases irreversibly along renormalization group flow.

[Development and application of reference materials containing mixed degradation products of amoxicillin and ampicillin].

PubMed

Li, Wei; Zhang, Wei-Qing; Li, Xiang; Hu, Chang-Qin

2014-09-01

Reference materials containing mixed degradation products of amoxicillin and ampicillin were developed after optimization of preparation processes. The target impurities were obtained by controlled stress testing, and each major component was identified with HPLC-MS and compared with single traceable reference standard each. The developed reference materials were applied to system suitability test for verifying HPLC system performed in accordance with set forth in China Pharmacopeia and identification of major impurities in samples based on retention and spectra information, which have advantages over the methods put forth in foreign pharmacopoeias. The development and application of the reference materials offer an effective way for rapid identification of impurities in chromatograms, and provide references for analyzing source of impurities and evaluation of drug quality.

Method for Determination of Less Than 5 ppm Oxygen in Sodium Samples

NASA Technical Reports Server (NTRS)

Reid, R. S.; Martin, J. J.; Schmidt, G. L.

2005-01-01

Alkali metals used in pumped loops or heat pipes must be sufficiently free of nonmetallic impurities to ensure long heat rejection system life. Life issues are well established for alkali metal systems. Impurities can form ternary compounds between the container and working fluid, leading to corrosion. This Technical Memorandum discusses the consequences of impurities and candidate measurement techniques to determine whether impurities have been reduced to suf.ciently low levels within a single-phase liquid metal loop or a closed two-phase heat transfer system, such as a heat pipe. These techniques include the vanadium wire equilibration, neutron activation analysis, plug traps, distillation, and chemical analysis. Conceptual procedures for performing vanadium wire equilibration purity measurements on sodium contained in a heat pipe are discussed in detail.

Separation and characterization of unknown impurities and isomers in flomoxef sodium by LC-IT-TOF MS and study of their negative-ion fragmentation regularities.

PubMed

Yu, Xu; Wang, Fan; Li, Jiani; Shan, Weiguang; Zhu, Bingqi; Wang, Jian

2017-06-05

Thirteen unknown impurities in flomoxef sodium were separated and characterized by liquid chromatography coupled with high resolution ion trap/time-of-flight mass spectrometry (LC-IT-TOF MS)with positive and negative modes of electrospray ionization method for further improvement of official monographs in pharmacopoeias. The fragmentation patterns of impurities in flomoxef in the negative ion mode were studied in detail, and new negative-ion fragmentation regularities were discovered. Chromatographic separation was performed on a Kromasil C18 column (250mm×4.6mm, 5μm). The mobile phase consisted of (A) ammonium formate aqueous solution (10mM)-methanol (84:16, v/v) and (B) ammonium formate aqueous solution (10mM)-methanol (47:53, v/v). In order to determine the m/z values of the molecular ions and formulas of all detected impurities, full scan LC-MS in both positive and negative ion modes was firstly executed to obtain the m/z value of the molecules. Then LC-MS 2 and LC-MS 3 were carried out on target compounds to obtain as much structural information as possible. Complete fragmentation patterns of impurities were studied and used to obtain information about the structures of these impurities. Structures of thirteen unknown degradation products in flomoxef sodium were deduced based on the high resolution MS n data with both positive and negative modes. The forming mechanisms of degradation products in flomoxef sodium were also studied. Copyright © 2017. Published by Elsevier B.V.

Bogolon-mediated electron capture by impurities in hybrid Bose-Fermi systems

NASA Astrophysics Data System (ADS)

Boev, M. V.; Kovalev, V. M.; Savenko, I. G.

2018-04-01

We investigate the processes of electron capture by a Coulomb impurity center residing in a hybrid system consisting of spatially separated two-dimensional layers of electron and Bose-condensed dipolar exciton gases coupled via the Coulomb forces. We calculate the probability of the electron capture accompanied by the emission of a single Bogoliubov excitation (bogolon), similar to regular phonon-mediated scattering in solids. Furthermore, we study the electron capture mediated by the emission of a pair of bogolons in a single capture event and show that these processes not only should be treated in the same order of the perturbation theory, but also they give a more important contribution than single-bogolon-mediated capture, in contrast with regular phonon scattering.

Modeling of non-stationary local response on impurity penetration in plasma

NASA Astrophysics Data System (ADS)

Tokar, M. Z.; Koltunov, M.

2012-04-01

In fusion devices, strongly localized intensive sources of impurities may arise unexpectedly, e.g., if the wall is excessively demolished by hot plasma particles, or can be created deliberately through impurity seeding. The spreading of impurities from such sources both along and perpendicular to the magnetic field is affected by coulomb collisions with background particles, ionization, acceleration by electric field, etc. Simultaneously, the plasma itself can be significantly disturbed by these interactions. To describe self-consistently the impurity spreading process and the plasma response, three-dimensional fluid equations for the particle, parallel momentum, and energy balances of various plasma components are solved by reducing them to ordinary differential equations for the time evolution of several parameters characterizing the solutions in principal details: the maximum densities of impurity ions of different charges, the dimensions both along and across the magnetic field of the shells occupied by these particles, the characteristic temperatures of all plasma components, and the densities of the main ions and electrons in different shells. The results of modeling for penetration of lithium singly charged particles in tokamak edge plasma are presented. A new mechanism for the condensation phenomenon and formation of cold dense plasma structures, implying an outstanding role of coulomb collisions between main and impurity ions, is proposed.

Effect of ionization suppression by trace impurities in mobile phase water on the accuracy of quantification by high-performance liquid chromatography/mass spectrometry.

PubMed

Herath, H M D R; Shaw, P N; Cabot, P; Hewavitharana, A K

2010-06-15

The high-performance liquid chromatography (HPLC) column is capable of enrichment/pre-concentration of trace impurities in the mobile phase during the column equilibration, prior to sample injection and elution. These impurities elute during gradient elution and result in significant chromatographic peaks. Three types of purified water were tested for their impurity levels, and hence their performances as mobile phase, in HPLC followed by total ion current (TIC) mode of MS. Two types of HPLC-grade water produced 3-4 significant peaks in solvent blanks while LC/MS-grade water produced no peaks (although peaks were produced by LC/MS-grade water also after a few days of standing). None of the three waters produced peaks in HPLC followed by UV-Vis detection. These peaks, if co-eluted with analyte, are capable of suppressing or enhancing the analyte signal in a MS detector. As it is not common practice to run solvent blanks in TIC mode, when quantification is commonly carried out using single ion monitoring (SIM) or single or multiple reaction monitoring (SRM or MRM), the effect of co-eluting impurities on the analyte signal and hence on the accuracy of the results is often unknown to the analyst. Running solvent blanks in TIC mode, regardless of the MS mode used for quantification, is essential in order to detect this problem and to take subsequent precautions. Copyright (c) 2010 John Wiley & Sons, Ltd.

Silicon Materials Task of the Low Cost Solar Array Project, Phase 3. Effect of Impurities and Processing on Silicon Solar Cells

NASA Technical Reports Server (NTRS)

Hopkins, R. H.; Davis, J. R.; Blais, P. D.; Rohatgi, A.; Campbell, R. B.; Rai-Choudhury, P.; Stapleton, R. E.; Mollenkopf, H. C.; Mccormick, J. R.

1979-01-01

The effects of impurities, various thermochemical processes, and any impurity process interactions on the performance of terrestrial silicon solar cells are defined. Determinations of the segregation coefficients of tungsten, tantalum, and cobalt for the Czochralski pulling of silicon single crystals are reported. Sensitive neutron activation analysis was used to determine the metal impurity content of the silicon while atomic absorption was used to measure the metal content of the residual liquid from which the doped crystals were grown. Gettering of Ti doped silicon wafers improved cell performance by one to two percent for the highest temperatures and longest times. The HCl is more effective than POCl3 treatments for deactivating Ti but POCl3 and HCl produced essentially identical results for Mo or Fe.

Adsorption of gas molecules on Cu impurities embedded monolayer MoS2: A first- principles study

NASA Astrophysics Data System (ADS)

Zhao, B.; Li, C. Y.; Liu, L. L.; Zhou, B.; Zhang, Q. K.; Chen, Z. Q.; Tang, Z.

2016-09-01

Adsorption of small gas molecules (O2, NO, NO2 and NH3) on transition-metal Cu atom embedded monolayer MoS2 was investigated by first-principles calculations based on the density-functional theory (DFT). The embedded Cu atom is strongly constrained on the sulfur vacancy of monolayer MoS2 with a high diffusion barrier. The stable adsorption geometry, charge transfer and electronic structures of these gas molecules on monolayer MoS2 embedded with transition-metal Cu atom are discussed in detail. It is found that the monolayer MoS2 with embedded Cu atom can effectively capture these gas molecules with high adsorption energy. The NH3 molecule acts as electron donor after adsorption, which is different from the other gas molecules (O2, NO, and NO2). The results suggest that MoS2-Cu system may be promising for future applications in gas molecules sensing and catalysis, which is similar to those of the transition-metal embedded graphene.

Photoluminescence of vapor and solution grown ZnTe single crystals

NASA Astrophysics Data System (ADS)

Biao, Y.; Azoulay, M.; George, M. A.; Burger, A.; Collins, W. E.; Silberman, E.; Su, C.-H.; Volz, M. E.; Szofran, F. R.; Gillies, D. C.

1994-04-01

ZnTe single crystals grown by horizontal physical vapor transport (PVT) and by vertical traveling heater method (THM) from a Te solution were characterized by photoluminescence (PL) at 10.6 K and by atomic force microscopy (AFM). Copper was identified by PL as a major impurity existing in both crystals, forming a substitutional acceptor, Cu Zn. The THM ZnTe crystals were found to contain more Cu impurity than the PVT ZnTe crystals. The formation of Cu Zn-V Te complexes and the effects of annealing, oxygen contamination and intentional Cu doping were also studied. Finally, the surface morphology analyzed by AFM was correlated to the PL results.

Correlated impurities and intrinsic spin-liquid physics in the kagome material herbertsmithite

DOE PAGES

Han, Tian-Heng; Norman, M. R.; Wen, J. -J.; ...

2016-08-18

Low energy inelastic neutron scattering on single crystals of the kagome spin-liquid compound ZnCu 3(OD) 6Cl 2 (herbertsmithite) reveals in this paper antiferromagnetic correlations between impurity spins for energy transfers h(with stroke)ω < 0.8 meV (~ J/20). The momentum dependence differs significantly from higher energy scattering which arises from the intrinsic kagome spins. The low energy fluctuations are characterized by diffuse scattering near wave vectors (100) and (00 3/2), which is consistent with antiferromagnetic correlations between pairs of nearest-neighbor Cu impurities on adjacent triangular (Zn) interlayers. The corresponding impurity lattice resembles a simple cubic lattice in the dilute limit belowmore » the percolation threshold. Such an impurity model can describe prior neutron, NMR, and specific heat data. The low energy neutron data are consistent with the presence of a small spin gap (Δ ~ 0.7 meV) in the kagome layers, similar to that recently observed by NMR. Finally, the ability to distinguish the scattering due to Cu impurities from that of the planar kagome Cu spins provides an important avenue for probing intrinsic spin-liquid physics.« less

Microwave Induced Direct Bonding of Single Crystal Silicon Wafers

NASA Technical Reports Server (NTRS)

Budraa, N. K.; Jackson, H. W.; Barmatz, M.

1999-01-01

We have heated polished doped single-crystal silicon wafers in a single mode microwave cavity to temperatures where surface to surface bonding occurred. The absorption of microwaves and heating of the wafers is attributed to the inclusion of n-type or p-type impurities into these substrates. A cylindrical cavity TM (sub 010) standing wave mode was used to irradiate samples of various geometry's at positions of high magnetic field. This process was conducted in vacuum to exclude plasma effects. This initial study suggests that the inclusion of impurities in single crystal silicon significantly improved its microwave absorption (loss factor) to a point where heating silicon wafers directly can be accomplished in minimal time. Bonding of these substrates, however, occurs only at points of intimate surface to surface contact. The inclusion of a thin metallic layer on the surfaces enhances the bonding process.

Luminescence and radiation resistance of undoped NaI crystals

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

Shiran, N., E-mail: shiran@isc.kharkov.com; Boiaryntseva, I.; Gektin, A.

2014-11-15

Highlights: • The performance of NaI scintillators depends on luminescence properties. • A criterion of crystals’ purity level is radiation colorability at room temperature. • The traces of the most dangerous impurities were detected. • Crucial role in efficiency of pure NaI scintillator play the crystal perfection. - Abstract: Undoped NaI single crystal is an excellent scintillator at low temperature. However, scintillation parameters of different quality crystals vary in a wide range, significantly exceeding measurement error. Experimental data demonstrate the features of luminescence, radiation induced coloration, and afterglow dependence on the quality of nominally pure crystals. It is found thatmore » defects level that allows to elucidate artefacts introduced by traces of harmful impurities corresponds to 3 × 10{sup 15} cm{sup −3} that significantly overhead accuracy of chemical and absorption analysis. It is shown that special raw material treatment before and during the single crystal growth allows to reach NaI purity level that avoids impurities influence to the basic luminescence data.« less

Development and validation of a single robust HPLC method for the characterization of a pharmaceutical starting material and impurities from three suppliers using three separate synthetic routes.

PubMed

Sheldon, E M; Downar, J B

2000-08-15

Novel approaches to the development of analytical procedures for monitoring incoming starting material in support of chemical/pharmaceutical processes are described. High technology solutions were utilized for timely process development and preparation of high quality clinical supplies. A single robust HPLC method was developed and characterized for the analysis of the key starting material from three suppliers. Each supplier used a different process for the preparation of this material and, therefore, each suppliers' material exhibited a unique impurity profile. The HPLC method utilized standard techniques acceptable for release testing in a QC/manufacturing environment. An automated experimental design protocol was used to characterize the robustness of the HPLC method. The method was evaluated for linearity, limit of quantitation, solution stability, and precision of replicate injections. An LC-MS method that emulated the release HPLC method was developed and the identities of impurities were mapped between the two methods.

Absorption Coefficient of Alkaline Earth Halides.

DTIC Science & Technology

1980-04-01

not observed at low energy level , are developed at high power levels . No matter how low the absorption is. the effect is objectionable at high-energy... levels . As a natural consequence, the magnitude of the absorption coefficient is the key parameter in selecting laser window materials. Over the past...Presence of impurities can complicate the exponential tail. particularly at low absorption levels . The impurities may enter 12 the lattice singly or

A Non-Perturbative Treatment of Quantum Impurity Problems in Real Lattices

NASA Astrophysics Data System (ADS)

Allerdt, Andrew C.

Historically, the RKKY or indirect exchange, interaction has been accepted as being able to be described by second order perturbation theory. A typical universal expression is usually given in this context. This approach, however, fails to incorporate many body effects, quantum fluctuations, and other important details. In Chapter 2, a novel numerical approach is developed to tackle these problems in a quasi-exact, non-perturbative manner. Behind the method lies the main concept of being able to exactly map an n-dimensional lattice problem onto a 1-dimensional chain. The density matrix renormalization group algorithm is then employed to solve the newly cast Hamiltonian. In the following chapters, it is demonstrated that conventional RKKY theory does not capture the crucial physics. It is found that the Kondo effect, i.e. the screening of an impurity spin, tends to dominate over a ferromagnetic interaction between impurity spins. Furthermore, it is found that the indirect exchange interaction does not decay algebraically. Instead, there is a crossover upon increasing JK, where impurities favor forming their own independent Kondo states after just a few lattice spacings. This is not a trivial result, as one may naively expect impurities to interact when their conventional Kondo clouds overlap. The spin structure around impurities coupled to the edge of a 2D topological insulator is investigated in Chapter 7. Modeled after materials such as silicine, germanene, and stanene, it is shown with spatial resolution of the lattice that the specific impurity placement plays a key role. Effects of spin-orbit interactions are also discussed. Finally, in the last chapter, transition metal complexes are studied. This really shows the power and versatility of the method developed throughout the work. The spin states of an iron atom in the molecule FeN4C 10 are calculated and compared to DFT, showing the importance of inter-orbital coulomb interactions. Using dynamical DMRG, the density of states for the 3d-orbitals can also be obtained.

Silicon as a model ion trap: Time domain measurements of donor Rydberg states

PubMed Central

Vinh, N. Q.; Greenland, P. T.; Litvinenko, K.; Redlich, B.; van der Meer, A. F. G.; Lynch, S. A.; Warner, M.; Stoneham, A. M.; Aeppli, G.; Paul, D. J.; Pidgeon, C. R.; Murdin, B. N.

2008-01-01

One of the great successes of quantum physics is the description of the long-lived Rydberg states of atoms and ions. The Bohr model is equally applicable to donor impurity atoms in semiconductor physics, where the conduction band corresponds to the vacuum, and the loosely bound electron orbiting a singly charged core has a hydrogen-like spectrum according to the usual Bohr–Sommerfeld formula, shifted to the far-infrared because of the small effective mass and high dielectric constant. Manipulation of Rydberg states in free atoms and ions by single and multiphoton processes has been tremendously productive since the development of pulsed visible laser spectroscopy. The analogous manipulations have not been conducted for donor impurities in silicon. Here, we use the FELIX pulsed free electron laser to perform time-domain measurements of the Rydberg state dynamics in phosphorus- and arsenic-doped silicon and we have obtained lifetimes consistent with frequency domain linewidths for isotopically purified silicon. This implies that the dominant decoherence mechanism for excited Rydberg states is lifetime broadening, just as for atoms in ion traps. The experiments are important because they represent a step toward coherent control and manipulation of atomic-like quantum levels in the most common semiconductor and complement magnetic resonance experiments in the literature, which show extraordinarily long spin lattice relaxation times—key to many well known schemes for quantum computing qubits—for the same impurities. Our results, taken together with the magnetic resonance data and progress in precise placement of single impurities, suggest that doped silicon, the basis for modern microelectronics, is also a model ion trap.

Development of visual peak selection system based on multi-ISs normalization algorithm to apply to methamphetamine impurity profiling.

PubMed

Lee, Hun Joo; Han, Eunyoung; Lee, Jaesin; Chung, Heesun; Min, Sung-Gi

2016-11-01

The aim of this study is to improve resolution of impurity peaks using a newly devised normalization algorithm for multi-internal standards (ISs) and to describe a visual peak selection system (VPSS) for efficient support of impurity profiling. Drug trafficking routes, location of manufacture, or synthetic route can be identified from impurities in seized drugs. In the analysis of impurities, different chromatogram profiles are obtained from gas chromatography and used to examine similarities between drug samples. The data processing method using relative retention time (RRT) calculated by a single internal standard is not preferred when many internal standards are used and many chromatographic peaks present because of the risk of overlapping between peaks and difficulty in classifying impurities. In this study, impurities in methamphetamine (MA) were extracted by liquid-liquid extraction (LLE) method using ethylacetate containing 4 internal standards and analyzed by gas chromatography-flame ionization detection (GC-FID). The newly developed VPSS consists of an input module, a conversion module, and a detection module. The input module imports chromatograms collected from GC and performs preprocessing, which is converted with a normalization algorithm in the conversion module, and finally the detection module detects the impurities in MA samples using a visualized zoning user interface. The normalization algorithm in the conversion module was used to convert the raw data from GC-FID. The VPSS with the built-in normalization algorithm can effectively detect different impurities in samples even in complex matrices and has high resolution keeping the time sequence of chromatographic peaks the same as that of the RRT method. The system can widen a full range of chromatograms so that the peaks of impurities were better aligned for easy separation and classification. The resolution, accuracy, and speed of impurity profiling showed remarkable improvement. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

ICP-MS: Analytical Method for Identification and Detection of Elemental Impurities.

PubMed

Mittal, Mohini; Kumar, Kapil; Anghore, Durgadas; Rawal, Ravindra K

2017-01-01

Aim of this article is to review and discuss the currently used quantitative analytical method ICP-MS, which is used for quality control of pharmaceutical products. ICP-MS technique has several applications such as determination of single elements, multi element analysis in synthetic drugs, heavy metals in environmental water, trace element content of selected fertilizers and dairy manures. ICP-MS is also used for determination of toxic and essential elements in different varieties of food samples and metal pollutant present in the environment. The pharmaceuticals may generate impurities at various stages of development, transportation and storage which make them risky to be administered. Thus, it is essential that these impurities must be detected and quantified. ICP-MS plays an important function in the recognition and revealing of elemental impurities. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Plasma rotation measurement in small tokamaks using an optical spectrometer and a single photomultiplier as detector.

PubMed

Severo, J H F; Nascimento, I C; Kuznetov, Yu K; Tsypin, V S; Galvão, R M O; Tendler, M

2007-04-01

The method for plasma rotation measurement in the tokamak TCABR is reported in this article. During a discharge, an optical spectrometer is used to scan sequentially spectral lines of plasma impurities and spectral lines of a calibration lamp. Knowing the scanning velocity of the diffraction grating of the spectrometer with adequate precision, the Doppler shifts of impurity lines are determined. The photomultiplier output voltage signals are recorded with adequate sampling rate. With this method the residual poloidal and toroidal plasma rotation velocities were determined, assuming that they are the same as those of the impurity ions. The results show reasonable agreement with the neoclassical theory and with results from similar tokamaks.

Validation of the manufacturing process used to produce long-acting recombinant factor IX Fc fusion protein

PubMed Central

McCue, J; Osborne, D; Dumont, J; Peters, R; Mei, B; Pierce, G F; Kobayashi, K; Euwart, D

2014-01-01

Recombinant factor IX Fc (rFIXFc) fusion protein is the first of a new class of bioengineered long-acting factors approved for the treatment and prevention of bleeding episodes in haemophilia B. The aim of this work was to describe the manufacturing process for rFIXFc, to assess product quality and to evaluate the capacity of the process to remove impurities and viruses. This manufacturing process utilized a transferable and scalable platform approach established for therapeutic antibody manufacturing and adapted for production of the rFIXFc molecule. rFIXFc was produced using a process free of human- and animal-derived raw materials and a host cell line derived from human embryonic kidney (HEK) 293H cells. The process employed multi-step purification and viral clearance processing, including use of a protein A affinity capture chromatography step, which binds to the Fc portion of the rFIXFc molecule with high affinity and specificity, and a 15 nm pore size virus removal nanofilter. Process validation studies were performed to evaluate identity, purity, activity and safety. The manufacturing process produced rFIXFc with consistent product quality and high purity. Impurity clearance validation studies demonstrated robust and reproducible removal of process-related impurities and adventitious viruses. The rFIXFc manufacturing process produces a highly pure product, free of non-human glycan structures. Validation studies demonstrate that this product is produced with consistent quality and purity. In addition, the scalability and transferability of this process are key attributes to ensure consistent and continuous supply of rFIXFc. PMID:24811361

Effect of atomic disorder on the magnetic phase separation.

PubMed

Groshev, A G; Arzhnikov, A K

2018-05-10

The effect of disorder on the magnetic phase separation between the antiferromagnetic and incommensurate helical [Formula: see text] and [Formula: see text] phases is investigated. The study is based on the quasi-two-dimensional single-band Hubbard model in the presence of atomic disorder (the [Formula: see text] Anderson-Hubbard model). A model of binary alloy disorder is considered, in which the disorder is determined by the difference in energy between the host and impurity atomic levels at a fixed impurity concentration. The problem is solved within the theory of functional integration in static approximation. Magnetic phase diagrams are obtained as functions of the temperature, the number of electrons and impurity concentration with allowance for phase separation. It is shown that for the model parameters chosen, the disorder caused by impurities whose atomic-level energy is greater than that of the host atomic levels, leads to qualitative changes in the phase diagram of the impurity-free system. In the opposite case, only quantitative changes occur. The peculiarities of the effect of disorder on the phase separation regions of the quasi-two-dimensional Hubbard model are discussed.

High-frequency EPR of surface impurities on nanodiamond

NASA Astrophysics Data System (ADS)

Peng, Zaili; Stepanov, Viktor; Takahashi, Susumu

Diamond is a fascinating material, hosting nitrogen-vacancy (NV) defect centers with unique magnetic and optical properties. There have been many reports that suggest the existence of paramagnetic impurities near surface of various kinds of diamonds. Electron paramagnetic resonance (EPR) investigation of mechanically crushed nanodiamonds (NDs) as well as detonation NDs revealed g 2 like signals that are attributed to structural defects and dangling bonds near the diamond surface. In this presentation, we investigate paramagnetic impurities in various sizes of NDs using high-frequency (HF) continuous wave (cw) and pulsed EPR spectroscopy. Strong size dependence on the linewidth of HF cw EPR spectra reveals the existence of paramagnetic impurities in the vicinity of the diamond surface. We also study the size dependence of the spin-lattice and spin-spin relaxation times (T1 and T2) of single substitutional nitrogen defects in NDs Significant deviations from the temperature dependence of the phonon-assisted T1 process were observed in the ND samples, and were attributed to the contribution from the surface impurities. This work was supported by the Searle Scholars Program and the National Science Foundation (DMR-1508661 and CHE-1611134).

Impurity-induced anisotropic semiconductor-semimetal transition in monolayer biased black phosphorus

NASA Astrophysics Data System (ADS)

Bui, D. H.; Yarmohammadi, Mohsen

2018-07-01

Taking into account the electron-impurity interaction within the continuum approximation of tight-binding model, the Born approximation, and the Green's function method, the main features of anisotropic electronic phase transition are investigated in monolayer biased black phosphorus (BP). To this end, we concentrated on the disordered electronic density of states (DOS), which gives useful information for electro-optical devices. Increasing the impurity concentration in both unbiased and biased impurity-infected single-layer BP, in addition to the decrease of the band gap, independent of the direction, leads to the midgap states and an extra Van Hove singularity inside and outside of the band gap, respectively. Furthermore, strong impurity scattering potentials lead to a semiconductor-semimetal transition and one more Van Hove singularity in x-direction of unbiased BP and surprisingly, this transition does not occur in biased BP. We found that there is no phase transition in y-direction. Since real applications require structures with modulated band gaps, we have studied the influence of different bias voltages on the disordered DOS in both directions, resulting in the increase of the band gap.

Effect of atomic disorder on the magnetic phase separation

NASA Astrophysics Data System (ADS)

Groshev, A. G.; Arzhnikov, A. K.

2018-05-01

The effect of disorder on the magnetic phase separation between the antiferromagnetic and incommensurate helical and phases is investigated. The study is based on the quasi-two-dimensional single-band Hubbard model in the presence of atomic disorder (the Anderson–Hubbard model). A model of binary alloy disorder is considered, in which the disorder is determined by the difference in energy between the host and impurity atomic levels at a fixed impurity concentration. The problem is solved within the theory of functional integration in static approximation. Magnetic phase diagrams are obtained as functions of the temperature, the number of electrons and impurity concentration with allowance for phase separation. It is shown that for the model parameters chosen, the disorder caused by impurities whose atomic-level energy is greater than that of the host atomic levels, leads to qualitative changes in the phase diagram of the impurity-free system. In the opposite case, only quantitative changes occur. The peculiarities of the effect of disorder on the phase separation regions of the quasi-two-dimensional Hubbard model are discussed.

Observation of Spin Polarons in a Tunable Fermi Liquid of Ultracold Atoms

NASA Astrophysics Data System (ADS)

Zwierlein, Martin

2009-05-01

We have observed spin polarons, dressed spin down impurities in a spin up Fermi sea of ultracold atoms via tomographic RF spectroscopy. Feshbach resonances allow to freely tune the interactions between the two spin states involved. A single spin down atom immersed in a Fermi sea of spin up atoms can do one of two things: For strong attraction, it can form a molecule with exactly one spin up partner, but for weaker interaction it will spread its attraction and surround itself with a collection of majority atoms. This spin down atom dressed with a spin up cloud constitutes the spin- or Fermi polaron. We have observed a striking spectroscopic signature of this quasi-particle for various interaction strengths, a narrow peak in the spin down spectrum that emerges above a broad background. The spectra allow us to directly measure the polaron energy and the quasi-particle residue Z. The polarons are found to be only weakly interacting with each other, and can thus be identified with the quasi-particles of Landau's Fermi liquid theory. At a critical interaction strength, we observe a transition from spin one-half polarons to spin zero molecules. At this point the Fermi liquid undergoes a phase transition into a superfluid Bose liquid.

The influence of dopants on the nucleation of semiconductor nanocrystals from homogeneous solution.

PubMed

Bryan, J Daniel; Schwartz, Dana A; Gamelin, Daniel R

2005-09-01

The influence of Co2+ ions on the homogeneous nucleation of ZnO is examined. Using electronic absorption spectroscopy as a dopant-specific in-situ spectroscopic probe, Co2+ ions are found to be quantitatively excluded from the ZnO critical nuclei but incorporated nearly statistically in the subsequent growth layers, resulting in crystallites with pure ZnO cores and Zn(1-x)Co(x)O shells. Strong inhibition of ZnO nucleation by Co2+ ions is also observed. These results are explained using the classical nucleation model. Statistical analysis of nucleation inhibition data allows estimation of the critical nucleus size as 25 +/- 4 Zn2+ ions. Bulk calorimetric data allow the activation barrier for ZnO nucleation containing a single Co2+ impurity to be estimated as 5.75 kcal/mol cluster greater than that of pure ZnO, corresponding to a 1.5 x 10(4)-fold reduction in the ZnO nucleation rate constant upon introduction of a single Co2+ impurity. These data and analysis offer a rare view into the role of composition in homogeneous nucleation processes, and specifically address recent experiments targeting formation of semiconductor quantum dots containing single magnetic impurity ions at their precise centers.

Estimation of snow albedo reduction by light absorbing impurities using Monte Carlo radiative transfer model

NASA Astrophysics Data System (ADS)

Sengupta, D.; Gao, L.; Wilcox, E. M.; Beres, N. D.; Moosmüller, H.; Khlystov, A.

2017-12-01

Radiative forcing and climate change greatly depends on earth's surface albedo and its temporal and spatial variation. The surface albedo varies greatly depending on the surface characteristics ranging from 5-10% for calm ocean waters to 80% for some snow-covered areas. Clean and fresh snow surfaces have the highest albedo and are most sensitive to contamination with light absorbing impurities that can greatly reduce surface albedo and change overall radiative forcing estimates. Accurate estimation of snow albedo as well as understanding of feedbacks on climate from changes in snow-covered areas is important for radiative forcing, snow energy balance, predicting seasonal snowmelt, and run off rates. Such information is essential to inform timely decision making of stakeholders and policy makers. Light absorbing particles deposited onto the snow surface can greatly alter snow albedo and have been identified as a major contributor to regional climate forcing if seasonal snow cover is involved. However, uncertainty associated with quantification of albedo reduction by these light absorbing particles is high. Here, we use Mie theory (under the assumption of spherical snow grains) to reconstruct the single scattering parameters of snow (i.e., single scattering albedo ῶ and asymmetry parameter g) from observation-based size distribution information and retrieved refractive index values. The single scattering parameters of impurities are extracted with the same approach from datasets obtained during laboratory combustion of biomass samples. Instead of using plane-parallel approximation methods to account for multiple scattering, we have used the simple "Monte Carlo ray/photon tracing approach" to calculate the snow albedo. This simple approach considers multiple scattering to be the "collection" of single scattering events. Using this approach, we vary the effective snow grain size and impurity concentrations to explore the evolution of snow albedo over a wide wavelength range (300 nm - 2000 nm). Results will be compared with the SNICAR model to better understand the differences in snow albedo computation between plane-parallel methods and the statistical Monte Carlo methods.

Defects and impurities induced structural and electronic changes in pyrite CoS2: first principles studies.

PubMed

Li, Shengwen; Zhang, Yanning; Niu, Xiaobin

2018-05-03

Cobalt pyrite (CoS2) and related materials are attracting much attention due to their potential use in renewable energy applications. In this work, first-principles studies were performed to investigate the effects of various neutral defects and ion dopants on the structural, energetic, magnetic and electronic properties of the bulk CoS2. Our theoretical results show that the concentrations of single cobalt (VCo) and sulfur (VS) vacancies in CoS2 samples can be high under S-rich and S-poor conditions, respectively. Although the single vacancies induce defect states near the gap edge, they are still half-metallic. We find that the substitution of one S with the O atom does not obviously change the structural, magnetic and electronic features near the Fermi level of the system. Most transition metal impurities (MnCo, FeCo, and MoCo) and Group IV and V anion impurities (CS, SiS, NS, PS, and AsS) create impurity states that are deep and/or near the gap edge. However, NiCo and Group VII elements (FS, ClS, and BrS) cause very localized gap states close to the Fermi level in the minority spin channel, which may modify their electrochemical performances. Our extensive calculations provide instructive information for the design and optimization of CoS2-related energy materials.

Preface: Special Topic on Single-Molecule Biophysics

NASA Astrophysics Data System (ADS)

Makarov, Dmitrii E.; Schuler, Benjamin

2018-03-01

Single-molecule measurements are now almost routinely used to study biological systems and processes. The scope of this special topic emphasizes the physics side of single-molecule observations, with the goal of highlighting new developments in physical techniques as well as conceptual insights that single-molecule measurements bring to biophysics. This issue also comprises recent advances in theoretical physical models of single-molecule phenomena, interpretation of single-molecule signals, and fundamental areas of statistical mechanics that are related to single-molecule observations. A particular goal is to illustrate the increasing synergy between theory, simulation, and experiment in single-molecule biophysics.

Determination of Organic Impurities in Anthraquinone Color Additives D&C Violet No. 2 and D&C Green No. 6 by Ultra-High Performance Liquid Chromatography.

PubMed

Yang, H H Wendy

2017-01-01

A new practical and time-saving ultra-high performance liquid chromatography (UHPLC) method has been developed for determining the organic impurities in the anthraquinone color additives D&C Violet No. 2 and D&C Green No. 6. The impurities determined are p-toluidine, 1-hydroxyanthraquinone, 1,4-dihydroxyanthraquinone, and two subsidiary colors. The newly developed UHPLC method uses a 1.7-μ particle size C-18 column, 0.1 M ammonium acetate and acetonitrile as eluents, and photodiode array detection. For the quantification of the impurities, six-point calibration curves were used with correlation coefficients that ranged from 0.9974 to 0.9998. Recoveries of impurities ranged from 99 to 104%. Relative standard deviations ranged from 0.81 to 4.29%. The limits of detection for the impurities ranged from 0.0067% to 0.216%. Samples from sixteen batches of each color additive were analyzed, and the results favorably compared with the results obtained by gravity-elution column chromatography, thin-layer chromatography, and isooctane extraction. Unlike with those other methods, use of the UHPLC method permits all of the impurities to be determined in a single analysis, while also reducing the amount of organic waste and saving time and labor. The method is expected to be implemented by the U.S. Food and Drug Administration for analysis of color additive samples submitted for batch certification.

Room temperature aluminum antimonide radiation detector and methods thereof

DOEpatents

Lordi, Vincenzo; Wu, Kuang Jen J.; Aberg, Daniel; Erhart, Paul; Coombs, III, Arthur W; Sturm, Benjamin W

2015-03-03

In one embodiment, a method for producing a high-purity single crystal of aluminum antimonide (AlSb) includes providing a growing environment with which to grow a crystal, growing a single crystal of AlSb in the growing environment which comprises hydrogen (H.sub.2) gas to reduce oxide formation and subsequent incorporation of oxygen impurities in the crystal, and adding a controlled amount of at least one impurity to the growing environment to effectively incorporate at least one dopant into the crystal. In another embodiment, a high energy radiation detector includes a single high-purity crystal of AlSb, a supporting structure for the crystal, and logic for interpreting signals obtained from the crystal which is operable as a radiation detector at a temperature of about 25.degree. C. In one embodiment, a high-purity single crystal of AlSb includes AlSb and at least one dopant selected from a group consisting of selenium (Se), tellurium (Te), and tin (Sn).

Liquid xenon purification, de-radonation (and de-kryptonation)

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

Pocar, Andrea, E-mail: pocar@umass.edu; Physics Division, Lawrence Livermore National Laboratory, Livermore, California 94550

Liquid xenon detectors are at the forefront of rare event physics, including searches for neutrino-less double beta decay and WIMP dark matter. The xenon for these experiments needs to be purified from chemical impurities such as electronegative atoms and molecules, which absorb ionization electrons, and VUV (178 nm) scintillation light-absorbing chemical species. In addition, superb purification from radioactive impurities is required. Particularly challenging are radioactive noble isotopes ({sup 85}Kr,{sup 39,42}Ar,{sup 220,222}Rn). Radon is a particularly universal problem, due to the extended decay sequence of its daughters and its ubiquitous presence in detector materials. Purification and de-radonation of liquid xenon aremore » addressed with particular focus on the experience gained with the EXO-200 neutrino-less double beta decay detector.« less

Transition metal substitutions for Cu in BSCCO: An instructive probe of high temperature superconductivity

NASA Astrophysics Data System (ADS)

Schneider, Clinton W.

1998-12-01

Single crystals of the high temperature superconductor Bisb2Srsb2Casb1(Cusb{1-x}Msb{x})sb2)Osb{8+delta} have been grown for M = Zn, Ni, Co, Fe, and Pd in order to probe the effect of transition metal impurities on superconducting properties. Samples have been characterized by XRD, electron microprobe, and transport measurements. Measurement of resistance is used to determine the depression of Tsb{c} due to the impurities. We determine a value dTsb{c}/dx = -7.8K/at/for all substituents, independent of magnetic moment. Considered in terms of the Abrikosov-Gorkov theory for impurity scattering in superconductors, this result agrees with a d-wave order parameter and strong coupling.

Molecular Kondo effect in flat-band lattices

NASA Astrophysics Data System (ADS)

Tran, Minh-Tien; Nguyen, Thuy Thi

2018-04-01

The Kondo effect of a single magnetic impurity embedded in the Lieb lattice is studied by the numerical renormalization group. When the band flatness is present in the local density of states at the impurity site, it quenches the participation of all dispersive electrons in the Kondo singlet formation and reduces the many-body Kondo problem to a two-electron molecular Kondo problem. A quantum entanglement of two spins, which is the two-electron molecular analog of the many-body Kondo singlet, is stable at low temperature, and the impurity contributions to thermodynamical and dynamical quantities are qualitatively different from that obtained in the many-body Kondo effect. The conditions for existence of the molecular Kondo effect in narrow band systems are also presented.

Measurement of the attenuation length of argon scintillation light in the ArDM LAr TPC

NASA Astrophysics Data System (ADS)

Calvo, J.; Cantini, C.; Crivelli, P.; Daniel, M.; Di Luise, S.; Gendotti, A.; Horikawa, S.; Molina-Bueno, L.; Montes, B.; Mu, W.; Murphy, S.; Natterer, G.; Nguyen, K.; Periale, L.; Quan, Y.; Radics, B.; Regenfus, C.; Romero, L.; Rubbia, A.; Santorelli, R.; Sergiampietri, F.; Viant, T.; Wu, S.

2018-01-01

We report on a measurement of the attenuation length for the scintillation light in the tonne size liquid argon target of the ArDM dark matter experiment. The data was recorded in the first underground operation of the experiment in single-phase operational mode. The results were achieved by comparing the light yield spectra from 39Ar and 83mKr to a description of the ArDM setup with a model of full light ray tracing. A relatively low value close to 0.5 m was found for the attenuation length of the liquid argon bulk to its own scintillation light. We interpret this result as a presence of optically active impurities in the liquid argon which are not filtered by the installed purification systems. We also present analyses of the argon gas employed for the filling and discuss cross sections in the vacuum ultraviolet of various molecules in respect to purity requirements in the context of large liquid argon installations.

Adsorption of CO2 on Fe-doped graphene nano-ribbons: Investigation of transport properties

NASA Astrophysics Data System (ADS)

Othman, W.; Fahed, M.; Hatim, S.; Sherazi, A.; Berdiyorov, G.; Tit, N.

2017-07-01

Density functional theory combined with the non-equilibrium Green’s function formalism is used to study the conductance response of Fe-doped graphene nano-ribbons (GNRs) to CO2 gas adsorption. A single Fe atom is either adsorbed on GNR’s surface (aFe-graphene) or it substitutes the carbon atom (sFe-graphene). Metal atom doping reduces the electronic transmission of pristine graphene due to the localization of electronic states near the impurity site. Moreover, the aFe-graphene is found to be less sensitive to the CO2 molecule attachment as compared to the sFe-graphene system. These behaviours are not only consolidated but rather confirmed by calculating the IV characteristics from which both surface resistance and its sensitivity to the gas are estimated. Since the change in the conductivity is one of the main outputs of sensors, our findings will be useful in developing efficient graphene-based solid-state gas sensors.

Role of thermal two-phonon scattering for impurity dynamics in a low-dimensional Bose-Einstein condensate

NASA Astrophysics Data System (ADS)

Lausch, Tobias; Widera, Artur; Fleischhauer, Michael

2018-03-01

We numerically study the relaxation dynamics of a single, heavy impurity atom interacting with a finite one- or two-dimensional, ultracold Bose gas. While there is a clear separation of time scales between processes resulting from single- and two-phonon scattering in three spatial dimensions, the thermalization in lower dimensions is dominated by two-phonon processes. This is due to infrared divergences in the corresponding scattering rates in the thermodynamic limit, which are a manifestation of the Mermin-Wagner-Hohenberg theorem. This makes it necessary to include second-order phonon scattering above a crossover temperature T2ph . T2ph scales inversely with the system size and is much smaller than currently experimentally accessible.

Impurity bound states in d-wave superconductors with subdominant order parameters

NASA Astrophysics Data System (ADS)

Mashkoori, Mahdi; Björnson, Kristofer; Black-Schaffer, Annica

Single magnetic impurity induces intra-gap bound states in conventional s-wave superconductors (SCs) but, in d-wave SCs only virtual bound states can be induced. However, in small cuprate islands a fully gapped spectrum has recently been discovered. In this work, we investigate the real bound states due to potential and magnetic impurities in the two candidate fully gapped states for this system: the topologically trivial d + is -wave state and the topologically non-trivial d + id' -wave (chiral d-wave state). Using the analytic T-matrix formalism and self-consistent numerical tight-binding lattice calculations, we show that potential and magnetic impurities create entirely different intra-gap bound states in d + is -wave and chiral d-wave SCs. Therefore, our results suggest that the bound states mainly depend on the subdominant order parameter. Considering that recent experiments have demonstrated an access to adjustable coupling J, impurities thus offer an intriguing way to clearly distinguish between the chiral d-wave and topologically trivial d + is -wave state. This work was supported by Swedish Research Council, Swedish Foundation for Strategic Research, the Wallenberg Academy Fellows program and the Göran Gustafsson Foundation. The computations were performed on resources provided by SNIC at LUNARC.

Log-rise of the resistivity in the holographic Kondo model

NASA Astrophysics Data System (ADS)

Padhi, Bikash; Tiwari, Apoorv; Setty, Chandan; Phillips, Philip W.

2018-03-01

We study a single-channel Kondo effect using a recently developed [1-4] holographic large-N technique. In order to obtain resistivity of this model, we introduce a probe field. The gravity dual of a localized fermionic impurity in 1 +1 -dimensional host matter is constructed by embedding a localized two-dimensional Anti-de Sitter (AdS2 )-brane in the bulk of three-dimensional AdS3 . This helps us construct an impurity charge density which acts as a source to the bulk equation of motion of the probe gauge field. The functional form of the charge density is obtained independently by solving the equations of motion for the fields confined to the AdS2 -brane. The asymptotic solution of the probe field is dictated by the impurity charge density, which in turn affects the current-current correlation functions and hence the resistivity. Our choice of parameters tunes the near-boundary impurity current to be marginal, resulting in a log T behavior in the UV resistivity, as is expected for the Kondo problem. The resistivity at the IR fixed point turns out to be zero, signaling a complete screening of the impurity.

Symmetry transition via tetravalent impurity and investigations on magnetic properties of Li0.5Fe2.5O4

NASA Astrophysics Data System (ADS)

Kounsalye, Jitendra S.; Kharat, Prashant B.; Chavan, Apparao R.; Humbe, Ashok V.; Borade, R. M.; Jadhav, K. M.

2018-04-01

The present study, deals with the phase symmetry transformation of lithium ferrite after introducing tetravalent (Ti4+) impurity. The sol-gel auto combustion technique was adopted for the synthesis of nanoparticle samples with generic chemical formula Li0.5Fe2.5O4 and Li0.55Ti0.10Fe2.35O4. The synthesized nanoparticles were characterized by X-ray diffraction (XRD) technique for structural analysis. The XRD patterns show the single phase cubic structure without any impurity phase but the P4332 to Fd-3m transformation was observed after introducing Ti4+ impurity. The Nano size of the synthesized particles was confirmed by crystallite size ( 20nm) calculated using Debye-Scherrer's formula. The Fourier transform infrared spectroscopy (FTIR) studies shows shifting of band frequencies which reflect the structural changes after tetravalent substitutional impurities. The magnetic properties were studied through pulse field hysteresis loop (M-H loop) technique at room temperature, the M-H loops showdecrease in magnetic properties afternonmagnetic Ti4+ ion substitution. This is attributed to transition of inverse spinel structure of lithium ferrite to random spinel structure.

Occurrence and Characterization Microstructure of Iron Impurities in Halloysite.

PubMed

Liu, Rong; Yan, Chunjie; Wang, Hongquan; Xiao, Guoqi; Tu, Dong

2015-09-01

The quality of the clays and over all halloysite are mostly associated with minor amounts of ferruginous impurities content, since this element gives an undesirable reddish color to the halloysite mineral. Hence, finding out the modes of occurrence of iron in halloysite is of prime importance in the value addition and optimum utilization of halloysite. In order to analyze the occurrence of iron impurities in halloysite, Transmission Electron Microscopy (TEM), X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) were combined with wet chemical analysis methods to study the low-grade halloysite. The results indicated that the mineral phases of iron impurities in the concentrates are mainly composed of amounts of magnetite, goethite and hematite. Two types of occurrences for iron impurities have been found. One is single crystalline mineral consist in the halloysite, which contains three different phases of Goethite FeO(OH) (44.75%), Magnetite Fe3O4 (27.43%) and Hematite Fe2O3 (31.96%). The other is amorphous Fe-Al-Si glial materials. This study is of significance in the theoretical research on the halloysite mineralogy and in the developmental practice of halloysite in coal measures.

Barium Transport Process in Impregnated Dispenser Cathodes.

DTIC Science & Technology

1982-01-25

experiments were carried out on pure tungsten. The tung- sten was either in the form of thin foils (6 mm on a side) or single crystal disks (6 mm in...temperature reveal the presence of car- bon, silicon , calcium, and nitrogen impurities, with only trace amounts (ɚ%) of calcium and nitrogen. Carbon is not...expected to be present at diffusion temperatures but forms as an overlayer only upon cooling [6]. We hope to re- duce silicon impurity levels by use of

Weak ferromagnetism along the third-order axis of the FeBO3 crystals caused by Fe2+ impurity ions

NASA Astrophysics Data System (ADS)

Ovchinnikov, S. G.; Rudenko, V. V.; Vorotynov, A. M.

2018-05-01

Using the single-ion approximation, the weak ferromagnetic moment σZ(Fe2+) along the third-order axis of FeBO3 crystals, which is caused by the contribution of Fe2+ ions, has been investigated in the framework of the model Fe2+ impurity ion -BO3 vacancy. The extreme low-temperature behavior of the total magnetic moment due to the strong dependence of the Fe2+ion contribution is predicted.

Tunneling current noise spectra of biased impurity with a phonon mode

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

Maslova, N. S.; Arseev, P. I.; Mantsevich, V. N., E-mail: vmantsev@gmail.com

We report the results of theoretical investigations of the tunneling current noise spectra through a single-level impurity both in the presence and in the absence of electron–phonon interaction based on the nonequilibrium Green’s functions formalism. We show that due to the quantum nature of tunneling, the Fano factor is dramatically different from the Poisson limit both in the presence and in the absence of inelastic processes. The results are demonstrated to be sensitive to the tunneling contact parameters.

Local nature of impurity induced spin-orbit torques

NASA Astrophysics Data System (ADS)

Nikolaev, Sergey; Kalitsov, Alan; Chshiev, Mairbec; Mryasov, Oleg

Spin-orbit torques are of a great interest due to their potential applications for spin electronics. Generally, it originates from strong spin orbit coupling of heavy 4d/5d elements and its mechanism is usually attributed either to the Spin Hall effect or Rashba spin-orbit coupling. We have developed a quantum-mechanical approach based on the non-equilibrium Green's function formalism and tight binding Hamiltonian model to study spin-orbit torques and extended our theory for the case of extrinsic spin-orbit coupling induced by impurities. For the sake of simplicity, we consider a magnetic material on a two dimensional lattice with a single non-magnetic impurity. However, our model can be easily extended for three dimensional layered heterostructures. Based on our calculations, we present the detailed analysis of the origin of local spin-orbit torques and persistent charge currents around the impurity, that give rise to spin-orbit torques even in equilibrium and explain the existence of anisotropy.

Validation of the manufacturing process used to produce long-acting recombinant factor IX Fc fusion protein.

PubMed

McCue, J; Osborne, D; Dumont, J; Peters, R; Mei, B; Pierce, G F; Kobayashi, K; Euwart, D

2014-07-01

Recombinant factor IX Fc (rFIXFc) fusion protein is the first of a new class of bioengineered long-acting factors approved for the treatment and prevention of bleeding episodes in haemophilia B. The aim of this work was to describe the manufacturing process for rFIXFc, to assess product quality and to evaluate the capacity of the process to remove impurities and viruses. This manufacturing process utilized a transferable and scalable platform approach established for therapeutic antibody manufacturing and adapted for production of the rFIXFc molecule. rFIXFc was produced using a process free of human- and animal-derived raw materials and a host cell line derived from human embryonic kidney (HEK) 293H cells. The process employed multi-step purification and viral clearance processing, including use of a protein A affinity capture chromatography step, which binds to the Fc portion of the rFIXFc molecule with high affinity and specificity, and a 15 nm pore size virus removal nanofilter. Process validation studies were performed to evaluate identity, purity, activity and safety. The manufacturing process produced rFIXFc with consistent product quality and high purity. Impurity clearance validation studies demonstrated robust and reproducible removal of process-related impurities and adventitious viruses. The rFIXFc manufacturing process produces a highly pure product, free of non-human glycan structures. Validation studies demonstrate that this product is produced with consistent quality and purity. In addition, the scalability and transferability of this process are key attributes to ensure consistent and continuous supply of rFIXFc. © 2014 The Authors. Haemophilia Published by John Wiley & Sons Ltd.

Identification, isolation, and synthesis of seven novel impurities of anti-diabetic drug Repaglinide.

PubMed

Kancherla, Prasad; Keesari, Srinivas; Alegete, Pallavi; Khagga, Mukkanti; Das, Parthasarathi

2018-01-01

Seven unknown impurities in Repaglinide bulk drug batches at below 0.1% (ranging from 0.05 to 0.10%) were detected by an ultra-performance liquid chromatographic (UPLC) method. These impurities were isolated from the crude sample of Repaglinide using preparative high performance liquid chromatography (prep-HPLC). Based on liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI/MS) study, the chemical structures of seven new impurities (8, 9, 10, 11, 13, 14, and 16) were presumed and characterized as 4-(cyanomethyl)-2-ethoxybenzoic acid (8), 4-(cyanomethyl)-2-ethoxy-N-(3-methyl-1-(2-(piperidin-1-yl)phenyl)butyl)benzamide (9), 4-(2-amino-2-oxoethyl)-2-ethoxy-N-(3-methyl-1-(2-(piperidin-1-yl)phenyl)butyl) benzamide (10) and 2-(3-ethoxy-4-((3-methyl-1-(2-(piperidin-1-yl)phenyl)butyl) carbamoyl) phenyl) acetic acid (11) and 4-(cyanomethyl)-N-cyclohexyl-2-ethoxybenzamide (13), 2-(4-(cyclohexylcarbamoyl)-3-ethoxyphenyl) acetic acid (14) and N-cyclohexyl-4-(2-(cyclohexylamino)-2-oxoethyl)-2-ethoxybenzamide (16). The complete spectral analysis, proton nuclear magnetic resonance ( 1 H NMR), 13 C NMR, MS, and infrared (IR) confirmed the proposed chemical structures of impurities. Identification, structural characterization, formation, and their synthesis was first reported in this study. The impurity 11 was crystallized and structure was solved by single crystal X-ray diffraction. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Protein Crystals Grow Purer in Space: Physics of Phenomena

NASA Technical Reports Server (NTRS)

Chernov, Alex A.

2000-01-01

This presentation will summarize the quantitative experimental and theoretical results obtained by B.R. Thomas, P.G. Vekilov, D.C. Carter, A.M. Holmes, W.K. Widierow and the Author, the team with expertise in physics, biochemistry, crystallography and engineering. Impurities inhomogeneously trapped by a growing crystal - e.g., producing sectorial structure and/or striations - may induce macroscopic internal stress in it if an impurity molecule has slightly (less than 10%) different shape or volume than the regular one(s) they replace. We tested for the first time plasticity and measured Young modulus E of the triclinic, not cross-linked lysozyme by triple point bending technique. Triclinic lysozyme crystals are purely elastic with E similar or equal to 1/5 (raised dot) 10 (exp 9) partial derivative yn/sq cm. The strength limit, sigma (sub c) similar or equal to 10 (exp -3)E similar or equal to Epsilon (sub c), where sigma (sub c) and epsilon (sub c) are critical stress and strain, respectively. Scaling E and sigma (sub c) with the lattice spacing suggests similar binding stiffness in inorganic and biomolecular crystals. The inhomogeneous internal stress may be resolved in these brittle crystals either by cracking or by creation of misoriented mosaic blocks during, not after growth. If each impurity molecule induces in the lattice elementary strain epsilon (sub 0) similar or equal to 3 (raised dot) 10 (exp -2) (this is maximal elementary strain that can arise at the supersaturation DELTA mu/kT similar or equal to 2 and macroscopic molecular concentration difference between subsequent macrolayers or growth sectors is partial derivativeC similar or equal to 5 (raised dot) 10 (exp -3), the internal strain epsilon similar or equal to epsilon (sub 0) partial derivative C similar or equal to 10 (exp -4). Mosaic misorientation resolving such strain is approximately 30 arcsec. Tenfold increase of impurity concentration may cause cracking. Estimates of stress in an isometric sectorial crystal show that lysozyme crystals can tolerate the stress till the size of 0.5mm. Dissolving mosaic lysozyme crystal shows that the mosaicity, indeed, is absent below that size.

Protein Crystal Growth Dynamics and Impurity Incorporation

NASA Technical Reports Server (NTRS)

Chernov, Alex A.; Thomas, Bill

2000-01-01

The general concepts and theories of crystal growth are proven to work for biomolecular crystallization. This allowed us to extract basic parameters controlling growth kinetics - free surface energy, alpha, and kinetic coefficient, beta, for steps. Surface energy per molecular site in thermal units, alpha(omega)(sup 2/3)/kT approx. = 1, is close to the one for inorganic crystals in solution (omega is the specific molecular volume, T is the temperature). Entropic restrictions on incorporation of biomolecules into the lattice reduce the incorporation rate, beta, by a factor of 10(exp 2) - 10(exp 3) relative to inorganic crystals. A dehydration barrier of approx. 18kcal/mol may explain approx. 10(exp -6) times difference between frequencies of adding a molecule to the lattice and Brownian attempts to do so. The latter was obtained from AFM measurements of step and kink growth rates on orthorhombic lysozyme. Protein and many inorganic crystals typically do not belong to the Kossel type, thus requiring a theory to account for inequivalent molecular positions within its unit cell. Orthorhombic lysozyme will serve as an example of how to develop such a theory. Factors deteriorating crystal quality - stress and strain, mosaicity, molecular disorder - will be reviewed with emphasis on impurities. Dimers in ferritin and lysozyme and acetylated lysozyme, are microheterogeneous i.e. nearly isomorphic impurities that are shown to be preferentially trapped by tetragonal lysozyme and ferritin crystals, respectively. The distribution coefficient, K defined as a ratio of the (impurity/protein) ratios in crystal and in solution is a measure of trapping. For acetylated lysoyzme, K = 2.15 or, 3.42 for differently acetylated forms, is independent of both the impurity and the crystallizing protein concentration. The reason is that impurity flux to the surface is constant while the growth rate rises with supersaturation. About 3 times lower dimer concentration in space grown ferritin and lysozyme crystals might be examples explaining higher quality of the space grown protein crystal. Depletion of solution with respect to isomorphic impurities around a growing crystal may be K times deeper than with respect to the crystallizing protein.

Theory of p-type Zinc Oxide

NASA Astrophysics Data System (ADS)

Zhang, Shengbai

2002-03-01

Recent advances in bipolar doping of wide gap semiconductors challenge our understanding of impurity and defect properties in these materials, as theories based on equilibrium thermodynamics cannot keep up with these recent developments. For ZnO, the puzzling experimental results involve doping with nitrogen(M. Joseph, H. Tabata, and T. Kawai, Jpn. J. Appl. Phys. 38), L1205 (1999)., arsenic(Y. R. Ryu, S. Zhu, D. C. Look, J. M. Wrobel, H. M. Jeong, and H. W. White, J. Crys. Growth 216), 330 (2000)., and phosphorus(T. Aoki, Y. Hatanaka, and D. C. Look, Appl. Phys. Lett. 76), 3257 (2000).. In this talk, I will discuss some recent theoretical efforts trying to explain the experiments by first-principles total energy calculations. I will first discuss the acceptor level positions for group I and group V impurities. A general trend is observed(C. H. Park, S. B. Zhang, and S.-H. Wei, submitted to Phys. Rev. B.) that substitutional group V impurities on O range from relatively deep (e.g. N) to very deep (e.g. P and As) with high formation energies, whereas substitutional group I impurities on Zn are shallow acceptors. However, substitutional group I impurities are unstable against the formation of interstitials that are donors. A careful examination of N doping in Ref. [1] suggests that one can kinetically suppress the formation of N2 molecules by engineering dopant sources/footnoteY. Yan, S. B. Zhang, and S. T. Pantelides, Phys. Rev. Lett. 86, 5723 (2001).. This leads to significantly enhanced N solubility and hence p-type ZnO. For As [2], our preliminary studies show that the formation energy of AsO is so high that it is an exothermic process to form low-energy complexes that act effectively as relatively shallow acceptors.

Depinning of the transverse domain wall trapped at magnetic impurities patterned in planar nanowires: Control of the wall motion using low-intensity and short-duration current pulses

NASA Astrophysics Data System (ADS)

Paixão, E. L. M.; Toscano, D.; Gomes, J. C. S.; Monteiro, M. G.; Sato, F.; Leonel, S. A.; Coura, P. Z.

2018-04-01

Understanding and controlling of domain wall motion in magnetic nanowires is extremely important for the development and production of many spintronic devices. It is well known that notches are able to pin domain walls, but their pinning potential strength are too strong and it demands high-intensity current pulses to achieve wall depinning in magnetic nanowires. However, traps of pinning can be also originated from magnetic impurities, consisting of located variations of the nanowire's magnetic properties, such as exchange stiffness constant, saturation magnetization, anisotropy constant, damping parameter, and so on. In this work, we have performed micromagnetic simulations to investigate the depinning mechanism of a transverse domain wall (TDW) trapped at an artificial magnetic defect using spin-polarized current pulses. In order to create pinning traps, a simplified magnetic impurity model, only based on a local reduction of the exchange stiffness constant, have been considered. In order to provide a background for experimental studies, we have varied the parameter related to the pinning potential strength of the magnetic impurity. By adjusting the pinning potential of magnetic impurities and choosing simultaneously a suitable current pulse, we have found that it is possible to obtain domain wall depinning by applying low-intensity and short-duration current pulses. Furthermore, it was considered a planar magnetic nanowire containing a linear distribution of equally-spaced magnetic impurities and we have demonstrated the position control of a single TDW by applying sequential current pulses; that means the wall movement from an impurity to another.

Ce and La single- and double-substitutional defects in yttrium aluminum garnet: first-principles study.

PubMed

Muñoz-García, Ana Belén; Seijo, Luis

2011-02-10

The atomistic structure, energetics, and electronic structure of single-substitutional Ce and La defects and double-substitutional Ce-La defects in Ce,La-codoped yttrium aluminum garnet (YAG) Y(3)Al(5)O(12) have been studied by means of first-principles periodic boundary conditions density functional theory calculations. Single substitution of Y by Ce or by La produces atomistic expansions around the impurities, which are significantly smaller than the ionic radii mismatches and the overall lattice distortions are found to be confined within their second coordination spheres. In double-substitutional defects, the impurities tend to be as close as possible. La-codoping Ce:YAG provokes an anisotropic expansion around Ce defects. The Ce impurity introduces 4f occupied states in the 5.0 eV computed gap of YAG, peaking 0.25 eV above the top of the valence band, and empty 4f, 5d, and 6s states starting at 3.8 eV in the gap and spreading over the conduction band. La-codoping produces very small effects on the electronic structure of Ce:YAG, the most visible one being the decrease in covalent bonding with one of the oxygen atoms, which shifts 0.05 Å away from Ce and gets 0.04 Å closer to La in the most stable Ce-La double-substitutional defect.

Impurities near an antiferromagnetic-singlet quantum critical point

DOE PAGES

Mendes-Santos, T.; Costa, N. C.; Batrouni, G.; ...

2017-02-15

Heavy-fermion systems and other strongly correlated electron materials often exhibit a competition between antiferromagnetic (AF) and singlet ground states. We examine the effect of impurities in the vicinity of such an AF-singlet quantum critical point (QCP), through an appropriately defined “impurity susceptibility” χimp, using exact quantum Monte Carlo simulations. Our key finding is a connection within a single calculational framework between AF domains induced on the singlet side of the transition and the behavior of the nuclear magnetic resonance (NMR) relaxation rate 1/T1. Furthermore, we show that local NMR measurements provide a diagnostic for the location of the QCP, whichmore » agrees remarkably well with the vanishing of the AF order parameter and large values of χimp.« less

The Ni and Co substitutions in iron chalcogenide single crystals

NASA Astrophysics Data System (ADS)

Bezusyy, V. L.; Gawryluk, D. J.; Malinowski, A.; Berkowski, M.; Cieplak, Marta Z.

2015-03-01

We study the ab-plane resistivity and Hall effect in Fe1-yMyTe0.65Se0.35 single crystals with M =Co or Ni, and y up to 0.2. The crystals are grown by Bridgman's method. The low-temperature Hall coefficient RH changes sign to negative for crystals with y exceeding 0.135 (Co) and 0.06 (Ni), consistent with the electron doping induced by these impurities. However, the RH remains positive for all samples at high T, suggesting that remnant hole pockets survive the doping, but the holes become localized at low T in heavily doped crystals. Superconducting transition temperature (Tc) approaches zero for y = 0.14 (Co), and 0.03 (Ni), while the resistivity at the Tc onset is only weakly affected by Co doping, but it increases strongly for the Ni. These results suggest that in case of Co impurity the Tc suppression may be attributed to electron doping. On the other hand, the Ni substitution, in addition to electron doping, induces strong localization effects at small impurity contents. Using two-band conduction model we argue that the localization of electron carriers is responsible for strong superconductivity suppression by Ni impurity. Supported by EC through the FunDMS Advanced Grant of the ERC (FP7 Ideas), by the Polish NCS Grant 2011/01/B/ST3/00462, and by the French-Polish Program PICS 2012. Performed in the laboratories co-financed by NanoFun Project POIG.02.02.00-00-025/09.

Cucurbituril mediated single molecule detection and identification via recognition tunneling.

PubMed

Xiao, Bohuai; Liang, Feng; Liu, Simin; Im, JongOne; Li, Yunchuan; Liu, Jing; Zhang, Bintian; Zhou, Jianghao; He, Jin; Chang, Shuai

2018-06-08

Recognition tunneling (RT) is an emerging technique for investigating single molecules in a tunnel junction. We have previously demonstrated its capability of single molecule detection and identification, as well as probing the dynamics of intermolecular bonding at the single molecule level. Here by introducing cucurbituril as a new class of recognition molecule, we demonstrate a powerful platform for electronically investigating the host-guest chemistry at single molecule level. In this report, we first investigated the single molecule electrical properties of cucurbituril in a tunnel junction. Then we studied two model guest molecules, aminoferrocene and amantadine, which were encapsulated by cucurbituril. Small differences in conductance and lifetime can be recognized between the host-guest complexes with the inclusion of different guest molecules. By using a machine learning algorithm to classify the RT signals in a hyper dimensional space, the accuracy of guest molecule recognition can be significantly improved, suggesting the possibility of using cucurbituril molecule for single molecule identification. This work enables a new class of recognition molecule for RT technique and opens the door for detecting a vast variety of small molecules by electrical measurements.

Creation of Rydberg Polarons in a Bose Gas

NASA Astrophysics Data System (ADS)

Camargo, F.; Schmidt, R.; Whalen, J. D.; Ding, R.; Woehl, G.; Yoshida, S.; Burgdörfer, J.; Dunning, F. B.; Sadeghpour, H. R.; Demler, E.; Killian, T. C.

2018-02-01

We report spectroscopic observation of Rydberg polarons in an atomic Bose gas. Polarons are created by excitation of Rydberg atoms as impurities in a strontium Bose-Einstein condensate. They are distinguished from previously studied polarons by macroscopic occupation of bound molecular states that arise from scattering of the weakly bound Rydberg electron from ground-state atoms. The absence of a p -wave resonance in the low-energy electron-atom scattering in Sr introduces a universal behavior in the Rydberg spectral line shape and in scaling of the spectral width (narrowing) with the Rydberg principal quantum number, n . Spectral features are described with a functional determinant approach (FDA) that solves an extended Fröhlich Hamiltonian for a mobile impurity in a Bose gas. Excited states of polyatomic Rydberg molecules (trimers, tetrameters, and pentamers) are experimentally resolved and accurately reproduced with a FDA.

Evaluation of the Kinetic Property of Single-Molecule Junctions by Tunneling Current Measurements.

PubMed

Harashima, Takanori; Hasegawa, Yusuke; Kiguchi, Manabu; Nishino, Tomoaki

2018-01-01

We investigated the formation and breaking of single-molecule junctions of two kinds of dithiol molecules by time-resolved tunneling current measurements in a metal nanogap. The resulting current trajectory was statistically analyzed to determine the single-molecule conductance and, more importantly, to reveal the kinetic property of the single-molecular junction. These results suggested that combining a measurement of the single-molecule conductance and statistical analysis is a promising method to uncover the kinetic properties of the single-molecule junction.

Determination of dye/protein ratios in a labeling reaction between a cyanine dye and bovine serum albumin by micellar electrokinetic chromatography using a diode laser-induced fluorescence detection.

PubMed

Jing, Peng; Kaneta, Takashi; Imasaka, Totaro

2002-08-01

The degree of labeling, i.e., dye/protein ratio (D/P) is important for characterizing properties of dye labeling with proteins. A method for the determination of this ratio between a fluorescent cyanine dye and bovine serum albumin (BSA), based on the separation of the labeling mixture using micellar electrokinetic chromatography with diode laser-induced fluorescence detection, is described. Two methods for the determination of D/P were examined in this study. In these methods, a hydrolysis product and impurities, which are usually unfavorable compounds that are best excluded for protein analysis, were utilized to determine the amounts of dye bound to BSA. One is a direct method in which a ratio of the peak area of BSA to the total peak area of all the products produced in the labeling reaction was used for determining the average number of dye molecules bound to a single BSA molecule. The other is an indirect determination, which is based on diminution of all peak areas related to the products except for the labeled BSA. These methods were directly compared by means of a spectrophotometric method. The experimental results show that the indirect method is both reliable and sensitive. Therefore, D/P values can be determined at trace levels using the indirect method.

Controlled chain polymerisation and chemical soldering for single-molecule electronics.

PubMed

Okawa, Yuji; Akai-Kasaya, Megumi; Kuwahara, Yuji; Mandal, Swapan K; Aono, Masakazu

2012-05-21

Single functional molecules offer great potential for the development of novel nanoelectronic devices with capabilities beyond today's silicon-based devices. To realise single-molecule electronics, the development of a viable method for connecting functional molecules to each other using single conductive polymer chains is required. The method of initiating chain polymerisation using the tip of a scanning tunnelling microscope (STM) is very useful for fabricating single conductive polymer chains at designated positions and thereby wiring single molecules. In this feature article, developments in the controlled chain polymerisation of diacetylene compounds and the properties of polydiacetylene chains are summarised. Recent studies of "chemical soldering", a technique enabling the covalent connection of single polydiacetylene chains to single functional molecules, are also introduced. This represents a key step in advancing the development of single-molecule electronics.

Confined ion energy >200 keV and increased fusion yield in a DPF with monolithic tungsten electrodes and pre-ionization

NASA Astrophysics Data System (ADS)

Lerner, Eric J.; Hassan, Syed M.; Karamitsos, Ivana; Von Roessel, Fred

2017-10-01

To reduce impurities in the dense plasma focus FF-1 device, we used monolithic tungsten electrodes with pre-ionization. With this new set-up, we demonstrated a three-fold reduction of impurities by mass and a ten-fold reduction by ion number. FF-1 produced a 50% increase in fusion yield over our previous copper electrodes, both for a single shot and for a mean of ten consecutive shots with the same conditions. These results represent a doubling of fusion yield as compared with any other plasma focus device with the same 60 kJ energy input. In addition, FF-1 produced a new single-shot record of 240 ± 20 keV for mean ion energy, a record for any confined fusion plasma, using any device, and a 50% improvement in ten-shot mean ion energy. With a deuterium-nitrogen mix and corona-discharge pre-ionization, we were also able to reduce the standard deviation in the fusion yield to about 15%, a four-fold reduction over the copper-electrode results. We intend to further reduce impurities with new experiments using microwave treatment of tungsten electrodes, followed by the use of beryllium electrodes.

Physical properties of the WAIS Divide ice core

USGS Publications Warehouse

Fitzpatrick, Joan J.; Voigt, Donald E.; Fegyveresi, John M.; Stevens, Nathan T.; Spencer, Matthew K.; Cole-Dai, Jihong; Alley, Richard B.; Jardine, Gabriella E.; Cravens, Eric; Wilen, Lawrence A.; Fudge, T. J.; McConnell, Joseph R.

2014-01-01

The WAIS (West Antarctic Ice Sheet) Divide deep ice core was recently completed to a total depth of 3405 m, ending ∼50 m above the bed. Investigation of the visual stratigraphy and grain characteristics indicates that the ice column at the drilling location is undisturbed by any large-scale overturning or discontinuity. The climate record developed from this core is therefore likely to be continuous and robust. Measured grain-growth rates, recrystallization characteristics, and grain-size response at climate transitions fit within current understanding. Significant impurity control on grain size is indicated from correlation analysis between impurity loading and grain size. Bubble-number densities and bubble sizes and shapes are presented through the full extent of the bubbly ice. Where bubble elongation is observed, the direction of elongation is preferentially parallel to the trace of the basal (0001) plane. Preferred crystallographic orientation of grains is present in the shallowest samples measured, and increases with depth, progressing to a vertical-girdle pattern that tightens to a vertical single-maximum fabric. This single-maximum fabric switches into multiple maxima as the grain size increases rapidly in the deepest, warmest ice. A strong dependence of the fabric on the impurity-mediated grain size is apparent in the deepest samples.

Protein purification in multicompartment electrolyzers for crystal growth of r-DNA products in microgravity

NASA Technical Reports Server (NTRS)

Righetti, Pier Giorgio; Casale, Elena; Carter, Daniel; Snyder, Robert S.; Wenisch, Elisabeth; Faupel, Michel

1990-01-01

Recombinant-DNA (deoxyribonucleic acid) (r-DNA) proteins, produced in large quantities for human consumption, are now available in sufficient amounts for crystal growth. Crystallographic analysis is the only method now available for defining the atomic arrangements within complex biological molecules and decoding, e.g., the structure of the active site. Growing protein crystals in microgravity has become an important aspect of biology in space, since crystals that are large enough and of sufficient quality to permit complete structure determinations are usually obtained. However even small amounts of impurities in a protein preparation are anathema for the growth of a regular crystal lattice. A multicompartment electrolyzer with isoelectric, immobiline membranes, able to purify large quantities of r-DNA proteins is described. The electrolyzer consists of a stack of flow cells, delimited by membranes of very precise isoelectric point (pI, consisting of polyacrylamide supported by glass fiber filters containing Immobiline buffers and titrants to uniquely define a pI value) and very high buffering power, able to titrate all proteins tangent or crossing such membranes. By properly selecting the pI values of two membranes delimiting a flow chamber, a single protein can be kept isoelectric in a single flow chamber and thus, be purified to homogeneity (by the most stringent criterion, charge homogeneity).

Recombination reactions of 5-eV O(3P) atoms on a MgF2 surface

NASA Technical Reports Server (NTRS)

Orient, O. J.; Chutjian, A.; Murad, E.

1990-01-01

A source of hyperthermal, ground-state, impurity-free, atomic oxygen of an energy variable in the range 2-100 eV has been developed. Experimental results are presented of emission spectra in the wavelength range 250-850 nm produced by collisions of 5-eV O(3P) atoms with adsorbed NO and CO molecules on a MgF2 surface.

Interaction of ions, atoms, and small molecules with quantized vortex lines in superfluid (4)He.

PubMed

Mateo, David; Eloranta, Jussi; Williams, Gary A

2015-02-14

The interaction of a number of impurities (H2, Ag, Cu, Ag2, Cu2, Li, He3 (+), He(*) ((3)S), He2 (∗) ((3)Σu), and e(-)) with quantized rectilinear vortex lines in superfluid (4)He is calculated by using the Orsay-Trento density functional theory (DFT) method at 0 K. The Donnelly-Parks (DP) potential function binding ions to the vortex is combined with DFT data, yielding the impurity radius as well as the vortex line core parameter. The vortex core parameter at 0 K (0.74 Å) obtained either directly from the vortex line geometry or through the DP potential fitting is smaller than previously suggested but is compatible with the value obtained from re-analysis of the Rayfield-Reif experiment. All of the impurities have significantly higher binding energies to vortex lines below 1 K than the available thermal energy, where the thermally assisted escape process becomes exponentially negligible. Even at higher temperatures 1.5-2.0 K, the trapping times for larger metal clusters are sufficiently long that the previously observed metal nanowire assembly in superfluid helium can take place at vortex lines. The binding energy of the electron bubble is predicted to decrease as a function of both temperature and pressure, which allows adjusting the trap depth for either permanent trapping or to allow thermally assisted escape. Finally, a new scheme for determining the trapping of impurities on vortex lines by optical absorption spectroscopy is outlined and demonstrated for He(*).

Interaction of ions, atoms, and small molecules with quantized vortex lines in superfluid 4He

NASA Astrophysics Data System (ADS)

Mateo, David; Eloranta, Jussi; Williams, Gary A.

2015-02-01

The interaction of a number of impurities (H2, Ag, Cu, Ag2, Cu2, Li, He3 + , He* (3S), He2∗ (3Σu), and e-) with quantized rectilinear vortex lines in superfluid 4He is calculated by using the Orsay-Trento density functional theory (DFT) method at 0 K. The Donnelly-Parks (DP) potential function binding ions to the vortex is combined with DFT data, yielding the impurity radius as well as the vortex line core parameter. The vortex core parameter at 0 K (0.74 Å) obtained either directly from the vortex line geometry or through the DP potential fitting is smaller than previously suggested but is compatible with the value obtained from re-analysis of the Rayfield-Reif experiment. All of the impurities have significantly higher binding energies to vortex lines below 1 K than the available thermal energy, where the thermally assisted escape process becomes exponentially negligible. Even at higher temperatures 1.5-2.0 K, the trapping times for larger metal clusters are sufficiently long that the previously observed metal nanowire assembly in superfluid helium can take place at vortex lines. The binding energy of the electron bubble is predicted to decrease as a function of both temperature and pressure, which allows adjusting the trap depth for either permanent trapping or to allow thermally assisted escape. Finally, a new scheme for determining the trapping of impurities on vortex lines by optical absorption spectroscopy is outlined and demonstrated for He*.

Impurity optical absorption spectra of ZnGa 2Se 4:Ni 2+ single crystals

NASA Astrophysics Data System (ADS)

Kim, Wha-Tek; Jin, Moon-Seog; Cheon, Seung-Ho; Kim, Yong-Geun; Park, Byong-Seo

1990-04-01

The optical absorption of single crystals of ZnGa 2Se 4:Ni 2+ grown by the chemical transport reaction method was investigated in the temperature region 20-300 K. In the single crystals the impurity optical absorption peaks due to the transitions 3T1( 3F) → 3T2( 3F), 3T1( 3F) → 3A2( 3F) and 3T1( 3F) → 3T1( 3P) of the Ni 2+ ions sited in the host lattice of the ZnGa 2Se 4 single crystal with Td symmetry appeared at 4444, 7874 and 11 600 cm -1, respectively. The crystal-field parameter and the Racah parameter were given by Dq = 340 cm -1 and B = 615 cm -1, respectively. The peak due to the transition 3T1( 3F) → 3T1( 3P) split into four levels by first order spin-orbit-coupling effects of Ni 2+ ions in the lower temperature below 150 K. The spin-orbit-coupling parameter was found to be λ = -400 cm -1.

Distilling quantum entanglement via mode-matched filtering

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

Huang Yuping; Kumar, Prem

We propose an avenue toward distillation of quantum entanglement that is implemented by directly passing the entangled qubits through a mode-matched filter. This approach can be applied to a common class of entanglement impurities appearing in photonic systems, where the impurities inherently occupy different spatiotemporal modes than the entangled qubits. As a specific application, we show that our method can be used to significantly purify the telecom-band entanglement generated via the Kerr nonlinearity in single-mode fibers where a substantial amount of Raman-scattering noise is concomitantly produced.

The infrared spectrum of matrix isolated hydrogen and deuterium

NASA Technical Reports Server (NTRS)

Warren, J. A.; Smith, G. R.; Guillory, W. A.

1980-01-01

The induced infrared spectra of H2 and D2, trapped in matrices of Ar, Kr, N2, CO, have been investigated. It is found that in Ar and Kr, the pure rotation spectrum is always readily observable. Portions of the fundamental region, however, are induced by impurities, while the entire spectrum is impurity induced in N2 matrices. These results are discussed in light of a recent Raman study of this system, and in comparison with several single crystal studies. Effective rotational and vibrational constants for matrix isolated H2 are also given.

Temperature and hydrostatic pressure effects on single dopant states in hollow cylindrical core-shell quantum dot

NASA Astrophysics Data System (ADS)

El-Yadri, M.; Aghoutane, N.; El Aouami, A.; Feddi, E.; Dujardin, F.; Duque, C. A.

2018-05-01

This work reports on theoretical investigation of the temperature and hydrostatic pressure effects on the confined donor impurity in a AlGaAs-GaAs hollow cylindrical core-shell quantum dot. The charges are assumed to be completely confined to the interior of the shell with approximately rigid walls. Within the framework of the effective-mass approximation and by using a variational approach, we have computed the donor binding energies as a function of the shell size in order to study the behavior of the electron-impurity attraction for a very small thickness under the influence of both temperature and hydrostatic pressure. Our results show that the temperature and hydrostatic pressure have a significant influence on the impurity binding energy for large shell quantum dots. It will be shown that the binding energy is more pronounced with increasing pressure and decreasing temperature for any impurity position and quantum dot size. The photoionization cross section is also analyzed by considering only the in-plane incident radiation polarization. Its behavior is investigated as a function of photon energy for different values of pressure and temperature. The opposite effects caused by temperature and hydrostatic pressure reveal a big practical interest and offer an alternative way to tuning of correlated electron-impurity transitions in optoelectronic devices.

Influence of impurities and contact scale on the lubricating properties of bovine submaxillary mucin (BSM) films on a hydrophobic surface.

PubMed

Nikogeorgos, Nikolaos; Madsen, Jan Busk; Lee, Seunghwan

2014-10-01

Lubricating properties of bovine submaxillary mucin (BSM) on a compliant, hydrophobic surface were studied as influenced by impurities, in particular bovine serum albumin (BSA), at macro and nanoscale contacts by means of pin-on-disk tribometry and friction force microscopy (FFM), respectively. At both contact scales, the purity of BSM and the presence of BSA were quantitatively discriminated. The presence of BSA was responsible for higher frictional forces observed from BSM samples containing relatively larger amount of BSA. But, the mechanisms contributing to higher friction forces by BSA were different at different contact scales. At the macroscale contact, higher friction forces were caused by faster and dominant adsorption of BSA into the contacting area under a continuous cycle of desorption and re-adsorption of the macromolecules from tribostress. Nevertheless, all BSMs lowered the interfacial friction forces due to large contact area and a large number of BSM molecules in the contact area. At the nanoscale contact, however, no significant desorption of the macromolecules is expected in tribological contacts because of too small contact area and extremely small number of BSM molecules involved in the contact area. Instead, increasingly higher friction forces with increasing amount of BSA in BSM layer are attributed to higher viscosity caused by BSA in the layer. Comparable size of AFM probes with BSM molecules allowed them to penetrate through the BSM layers and to scratch on the underlying substrates, and thus induced higher friction forces compared to the sliding contact on bare substrates. Copyright © 2014 Elsevier B.V. All rights reserved.

Cobalt adatoms on graphene: Effects of anisotropies on the correlated electronic structure

NASA Astrophysics Data System (ADS)

Mozara, R.; Valentyuk, M.; Krivenko, I.; Şaşıoǧlu, E.; Kolorenč, J.; Lichtenstein, A. I.

2018-02-01

Impurities on surfaces experience a geometric symmetry breaking induced not only by the on-site crystal-field splitting and the orbital-dependent hybridization, but also by different screening of the Coulomb interaction in different directions. We present a many-body study of the Anderson impurity model representing a Co adatom on graphene, taking into account all anisotropies of the effective Coulomb interaction, which we obtained by the constrained random-phase approximation. The most pronounced differences are naturally displayed by the many-body self-energy projected onto the single-particle states. For the solution of the Anderson impurity model and analytical continuation of the Matsubara data, we employed new implementations of the continuous-time hybridization expansion quantum Monte Carlo and the stochastic optimization method, and we verified the results in parallel with the exact diagonalization method.

Optical properties of an indium doped CdSe nanocrystal: A density functional approach

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

Salini, K.; Mathew, Vincent, E-mail: vincent@cukerala.ac.in; Mathew, Thomas

2016-05-06

We have studied the electronic and optical properties of a CdSe nanocrystal doped with n-type impurity atom. First principle calculations of the CdSe nanocrystal based on the density functional theory (DFT), as implemented in the Vienna Ab Initio Simulation Package (VASP) was used in the calculations. We have introduced a single Indium impurity atom into CdSe nanocrystal with 1.3 nm diameter. Nanocrystal surface dangling bonds are passivated with hydrogen atom. The band-structure, density of states and absorption spectra of the doped and undopted nanocrystals were discussed. Inclusion of the n-type impurity atom introduces an additional electron in conduction band, and significantlymore » alters the electronic and optical properties of undoped CdSe nanocrystal. Indium doped CdSe nannocrystal have potential applications in optoelectronic devices.« less

Formation of dust grains with impurities in red giant winds

NASA Technical Reports Server (NTRS)

Dominik, Carsten

1994-01-01

Among the several proposed carriers of diffuse interstellar bands (DIB's) are impurities in small dust grains, especially in iron oxide grains (Huffman 1977) and silicate grains (Huffman 1970). Most promising are single ion impurities since they can reproduce the observed band widths (Whittet 1992). These oxygen-rich grains are believed to originate mostly in the mass flows from red giants and in supernovae ejecta (e.g. Gehrz 1989). A question of considerable impact for the origin of DIB's is therefore, whether these grains are produced as mainly clean crystals or as some dirty materials. A formalism has been developed that allows tracking of the heterogeneous growth of a dust grain and its internal structure during the dust formation process. This formalism has been applied to the dust formation in the outflow from a red giant star.

Scanning tunnelling spectroscopy as a probe of multi-Q magnetic states of itinerant magnets

DOE PAGES

Gastiasoro, Maria N.; Eremin, Ilya; Fernandes, Rafael M.; ...

2017-02-08

The combination of electronic correlations and Fermi surfaces with multiple nesting vectors can lead to the appearance of complex multi-Q magnetic ground states, hosting unusual states such as chiral density waves and quantum Hall insulators. Distinguishing single-Q and multi-Q magnetic phases is however a notoriously difficult experimental problem. Here we propose theoretically that the local density of states (LDOS) near a magnetic impurity, whose orientation may be controlled by an external magnetic field, can be used to map out the detailed magnetic configuration of an itinerant system and distinguish unambiguously between single-Q and multi-Q phases. We demonstrate this concept bymore » computing and contrasting the LDOS near a magnetic impurity embedded in three different magnetic ground states relevant to iron-based superconductors—one single-Q and two double-Q phases. Our results open a promising avenue to investigate the complex magnetic configurations in itinerant systems via standard scanning tunnelling spectroscopy, without requiring spin-resolved capability.« less

Impurity-assisted electric control of spin-valley qubits in monolayer MoS2

NASA Astrophysics Data System (ADS)

Széchenyi, G.; Chirolli, L.; Pályi, A.

2018-07-01

We theoretically study a single-electron spin-valley qubit in an electrostatically defined quantum dot in a transition metal dichalcogenide monolayer, focusing on the example of MoS2. Coupling of the qubit basis states for coherent control is challenging, as it requires a simultaneous flip of spin and valley. Here, we show that a tilted magnetic field together with a short-range impurity, such as a vacancy, a substitutional defect, or an adatom, can give rise to a coupling between the qubit basis states. This mechanism renders the in-plane g-factor nonzero, and allows to control the qubit with an in-plane ac electric field, akin to electrically driven spin resonance. We evaluate the dependence of the in-plane g-factor and the electrically induced qubit Rabi frequency on the type and position of the impurity. We reveal highly unconventional features of the coupling mechanism, arising from symmetry-forbidden intervalley scattering, in the case when the impurity is located at a S site. Our results provide design guidelines for electrically controllable qubits in two-dimensional semiconductors.

Nonstoichiometry and luminescent properties of ZnSe crystals grown from the melt at high pressures

NASA Astrophysics Data System (ADS)

Khanh, Tran; Mozhevitina, Elena; Khomyakov, Andrew; Avetisov, Roman; Davydov, Albert; Chegnov, Vladimir; Antonov, Vladimir; Kobeleva, Svetlana; Zhavoronkov, Nikolai; Avetissov, Igor

2017-01-01

50 mm diameter ZnSe crystals have been grown from the melt by a vertical Bridgman technique at 100 atm argon pressure in a graphite crucible. 3D impurities concentration and nonstoichiometry mappings of the grown crystals have been defined by ICP-MS and a direct physic-chemical method, correspondingly. Photoluminescence mapping of the analyzed crystal has been done. It was found out that along the crystal height the nonstoichiometry changed from Se excess over stoichiometrical composition in the cone (bottom) part to Zn excess in the tail (upper) part passing through the stoichiometrical composition in the cylindrical part of the crystal. Metal impurities concentrated in the upper part of the crystal. The gas-forming impurities (H, C, O, N, F) had stochastic distribution but Cl impurity concentrated in the crystal peripheral part (near the crucible walls). It was found out that the as-grown crystal had a single wide PL peal with maximum of 583 nm. A proposal about complex structure luminescent center based on Cl dopant an overstoichiometric Se has been made.

Discrete breathers in an electric lattice with an impurity: Birth, interaction, and death

NASA Astrophysics Data System (ADS)

Gómez-Rojas, A.; Halevi, P.

2018-02-01

We have simulated aspects of intrinsic localized modes or discrete breathers in a modulated lumped transmission line with nonlinear varactors and a defect unit cell. As the inductance or capacitance of this cell is increased, a transition from instability to stability takes place. Namely, there exist threshold values of the inductance or capacitance of a lattice impurity for a breather to be able to attach to. A resistive defect can also anchor a breather. Moreover, by either gradually lowering all the source resistances, or else increasing the modulation frequency, multiple secondary ILMs can be spontaneously generated at host sites (with only a single inductive or capacitive defect). Further, if two impurities are subcritically spaced (the separation increasing with the amplitude of the modulation voltage), a breather can pop up midway, with no breathers at the impurity sites themselves. Finally, an ILM can pull closer its neighbors on both sides, only to perish once these ILMs have gotten sufficiently close. To our knowledge, these effects have not been reported for any discrete nonlinear system.

Discrete breathers in an electric lattice with an impurity: Birth, interaction, and death.

PubMed

Gómez-Rojas, A; Halevi, P

2018-02-01

We have simulated aspects of intrinsic localized modes or discrete breathers in a modulated lumped transmission line with nonlinear varactors and a defect unit cell. As the inductance or capacitance of this cell is increased, a transition from instability to stability takes place. Namely, there exist threshold values of the inductance or capacitance of a lattice impurity for a breather to be able to attach to. A resistive defect can also anchor a breather. Moreover, by either gradually lowering all the source resistances, or else increasing the modulation frequency, multiple secondary ILMs can be spontaneously generated at host sites (with only a single inductive or capacitive defect). Further, if two impurities are subcritically spaced (the separation increasing with the amplitude of the modulation voltage), a breather can pop up midway, with no breathers at the impurity sites themselves. Finally, an ILM can pull closer its neighbors on both sides, only to perish once these ILMs have gotten sufficiently close. To our knowledge, these effects have not been reported for any discrete nonlinear system.

Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology

PubMed Central

2011-01-01

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution. PMID:21338175

Single-molecule dynamics in nanofabricated traps

NASA Astrophysics Data System (ADS)

Cohen, Adam

2009-03-01

The Anti-Brownian Electrokinetic trap (ABEL trap) provides a means to immobilize a single fluorescent molecule in solution, without surface attachment chemistry. The ABEL trap works by tracking the Brownian motion of a single molecule, and applying feedback electric fields to induce an electrokinetic motion that approximately cancels the Brownian motion. We present a new design for the ABEL trap that allows smaller molecules to be trapped and more information to be extracted from the dynamics of a single molecule than was previously possible. In particular, we present strategies for extracting dynamically fluctuating mobilities and diffusion coefficients, as a means to probe dynamic changes in molecular charge and shape. If one trapped molecule is good, many trapped molecules are better. An array of single molecules in solution, each immobilized without surface attachment chemistry, provides an ideal test-bed for single-molecule analyses of intramolecular dynamics and intermolecular interactions. We present a technology for creating such an array, using a fused silica plate with nanofabricated dimples and a removable cover for sealing single molecules within the dimples. With this device one can watch the shape fluctuations of single molecules of DNA or study cooperative interactions in weakly associating protein complexes.

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

Maughan, Bret; Zahl, Percy; Sutter, Peter

Switching the magnetic properties of organic semiconductors on a metal surface has thus far largely been limited to molecule-by-molecule tip-induced transformations in scanned probe experiments. Here we demonstrate with molecular resolution that collective control of activated Kondo screening can be achieved in thin-films of the organic semiconductor titanyl phthalocyanine on Cu(110) to obtain tunable concentrations of Kondo impurities. Using low-temperature scanning tunneling microscopy and spectroscopy, we show that a thermally activated molecular distortion dramatically shifts surface–molecule coupling and enables ensemble-level control of Kondo screening in the interfacial spin system. This is accompanied by the formation of a temperature-dependent Abrikosov–Suhl–Kondo resonancemore » in the local density of states of the activated molecules. This enables coverage-dependent control over activation to the Kondo screening state. Finally, our study thus advances the versatility of molecular switching for Kondo physics and opens new avenues for scalable bottom-up tailoring of the electronic structure and magnetic texture of organic semiconductor interfaces at the nanoscale.« less

Ensemble control of Kondo screening in molecular adsorbates

DOE PAGES

Maughan, Bret; Zahl, Percy; Sutter, Peter; ...

2017-04-06

Switching the magnetic properties of organic semiconductors on a metal surface has thus far largely been limited to molecule-by-molecule tip-induced transformations in scanned probe experiments. Here we demonstrate with molecular resolution that collective control of activated Kondo screening can be achieved in thin-films of the organic semiconductor titanyl phthalocyanine on Cu(110) to obtain tunable concentrations of Kondo impurities. Using low-temperature scanning tunneling microscopy and spectroscopy, we show that a thermally activated molecular distortion dramatically shifts surface–molecule coupling and enables ensemble-level control of Kondo screening in the interfacial spin system. This is accompanied by the formation of a temperature-dependent Abrikosov–Suhl–Kondo resonancemore » in the local density of states of the activated molecules. This enables coverage-dependent control over activation to the Kondo screening state. Finally, our study thus advances the versatility of molecular switching for Kondo physics and opens new avenues for scalable bottom-up tailoring of the electronic structure and magnetic texture of organic semiconductor interfaces at the nanoscale.« less

Non-equilibrium STLS approach to transport properties of single impurity Anderson model

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

Rezai, Raheleh, E-mail: R_Rezai@sbu.ac.ir; Ebrahimi, Farshad, E-mail: Ebrahimi@sbu.ac.ir

In this work, using the non-equilibrium Keldysh formalism, we study the effects of the electron–electron interaction and the electron-spin correlation on the non-equilibrium Kondo effect and the transport properties of the symmetric single impurity Anderson model (SIAM) at zero temperature by generalizing the self-consistent method of Singwi, Tosi, Land, and Sjolander (STLS) for a single-band tight-binding model with Hubbard type interaction to out of equilibrium steady-states. We at first determine in a self-consistent manner the non-equilibrium spin correlation function, the effective Hubbard interaction, and the double-occupancy at the impurity site. Then, using the non-equilibrium STLS spin polarization function in themore » non-equilibrium formalism of the iterative perturbation theory (IPT) of Yosida and Yamada, and Horvatic and Zlatic, we compute the spectral density, the current–voltage characteristics and the differential conductance as functions of the applied bias and the strength of on-site Hubbard interaction. We compare our spectral densities at zero bias with the results of numerical renormalization group (NRG) and depict the effects of the electron–electron interaction and electron-spin correlation at the impurity site on the aforementioned properties by comparing our numerical result with the order U{sup 2} IPT. Finally, we show that the obtained numerical results on the differential conductance have a quadratic universal scaling behavior and the resulting Kondo temperature shows an exponential behavior. -- Highlights: •We introduce for the first time the non-equilibrium method of STLS for Hubbard type models. •We determine the transport properties of SIAM using the non-equilibrium STLS method. •We compare our results with order-U2 IPT and NRG. •We show that non-equilibrium STLS, contrary to the GW and self-consistent RPA, produces the two Hubbard peaks in DOS. •We show that the method keeps the universal scaling behavior and correct exponential behavior of Kondo temperature.« less

Reversible Aptamer-Au Plasmon Rulers for Secreted Single Molecules

DOE PAGES

Lee, Somin Eunice; Chen, Qian; Bhat, Ramray; ...

2015-06-03

Plasmon rulers, consisting of pairs of gold nanoparticles, allow single-molecule analysis without photobleaching or blinking; however, current plasmon rulers are irreversible, restricting detection to only single events. Here, we present a reversible plasmon ruler, comprised of coupled gold nanoparticles linked by a single aptamer, capable of binding individual secreted molecules with high specificity. We show that the binding of target secreted molecules to the reversible plasmon ruler is characterized by single-molecule sensitivity, high specificity, and reversibility. Lastly, such reversible plasmon rulers should enable dynamic and adaptive live-cell measurement of secreted single molecules in their local microenvironment.

Single-Molecule Plasmon Sensing: Current Status and Future Prospects

PubMed Central

2017-01-01

Single-molecule detection has long relied on fluorescent labeling with high quantum-yield fluorophores. Plasmon-enhanced detection circumvents the need for labeling by allowing direct optical detection of weakly emitting and completely nonfluorescent species. This review focuses on recent advances in single molecule detection using plasmonic metal nanostructures as a sensing platform, particularly using a single particle–single molecule approach. In the past decade two mechanisms for plasmon-enhanced single-molecule detection have been demonstrated: (1) by plasmonically enhancing the emission of weakly fluorescent biomolecules, or (2) by monitoring shifts of the plasmon resonance induced by single-molecule interactions. We begin with a motivation regarding the importance of single molecule detection, and advantages plasmonic detection offers. We describe both detection mechanisms and discuss challenges and potential solutions. We finalize by highlighting the exciting possibilities in analytical chemistry and medical diagnostics. PMID:28762723

Perturbation theory of a superconducting 0 - π impurity quantum phase transition.

PubMed

Žonda, M; Pokorný, V; Janiš, V; Novotný, T

2015-03-06

A single-level quantum dot with Coulomb repulsion attached to two superconducting leads is studied via the perturbation expansion in the interaction strength. We use the Nambu formalism and the standard many-body diagrammatic representation of the impurity Green functions to formulate the Matsubara self-consistent perturbation expansion. We show that at zero temperature second order of the expansion in its spin-symmetric version yields a nearly perfect agreement with the numerically exact calculations for the position of the 0 - π phase boundary at which the Andreev bound states reach the Fermi energy as well as for the values of single-particle quantities in the 0-phase. We present results for phase diagrams, level occupation, induced local superconducting gap, Josephson current, and energy of the Andreev bound states with the precision surpassing any (semi)analytical approaches employed thus far.

The growth of zinc selenide single crystals by physical vapor transport in microgravity

NASA Technical Reports Server (NTRS)

Anderson, Elmer E.; Rosenberger, Franz E.; Cheng, Hai-Yuin

1990-01-01

Growth and characterization studies will be performed on zinc selenide single crystals. The high temperature outgassing behavior of the silica ampoule material will be studied in order to develop a cleaning and bake-out procedure that will minimize the amount of impurities introduced into the vapor from the ampoule materials and in particular during the seal-off procedure. The outgassing behavior of the ZnSe starting material will be studied during high vacuum refinement at elevated temperatures in order to develop a temperature pressure program that will optimize the removal of impurities while minimizing a shift in stoichiometry due to preferred evaporation of the higher fugacity component. The mass spectrometer system was completed, and after calibration, will be used to perform the above tasks. The system and its operation is described in detail.

Single crystal growth, crystalline structure investigation and high-pressure behavior of impurity-free siderite (FeCO3)

NASA Astrophysics Data System (ADS)

Liang, Wen; Yin, Yuan; Li, Zeming; Li, Rui; Li, Lin; He, Yu; Dong, Haini; Li, Zengsheng; Yan, Shuai; Zhai, Shuangmeng; Li, Heping

2018-03-01

Single crystals of impurity-free siderite were grown successfully using high-temperature-pressure annealing. The size of crystals ranged up to 100 µm, and they exhibited a rhomboid shape upon cleavage along the (101) plane. The composition of Fe0.9988±0.0011CO3 was quantified using electron probe analysis. Accurate crystalline structural data were investigated by means of single crystal X-ray diffraction (XRD) and the unit cell dimensions obtained in the rhombohedral symmetry of the R\\bar {3}c space group were a = 4.6861(3) and c = 15.362(2), and the final R = 0.0499. Using in situ synchrotron XRD, the high-pressure behavior of impurity-free siderite was investigated up to 20 GPa at ambient temperature. The pressure-volume (P-V) EoS was fitted by a third-order Birch-Murnaghan equation, and the isothermal bulk modulus was K 0 = 97.5(11) GPa for K 0' = 4. High-pressure Raman spectroscopy was performed at up to 30 GPa at ambient temperature, and the Raman bands shifted as the increase of pressure ({{d/ν _i}}{{{d}P}} ) was determined. In combination with the high-pressure Raman results and the bulk modulus K 0, the mode Grüneisen parameters of each vibration were calculated. Meanwhile, high-temperature Raman spectroscopy was carried out at up to 300 °C and the Raman band shift ({{d/ν _i}}{{{d}t}} ) was also quantified.

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.

Ordered array of CoPc-vacancies filled with single-molecule rotors

NASA Astrophysics Data System (ADS)

Xie, Zheng-Bo; Wang, Ya-Li; Tao, Min-Long; Sun, Kai; Tu, Yu-Bing; Yuan, Hong-Kuan; Wang, Jun-Zhong

2018-05-01

We report the highly ordered array of CoPc-vacancies and the single-molecule rotors inside the vacancies. When CoPc molecules are deposited on Cd(0001) at low-temperature, three types of molecular vacancies appeared randomly in the CoPc monolayer. Annealing the sample to higher temperature leads to the spontaneous phase separation and self-organized arrangement of the vacancies. Highly ordered arrays of two-molecule vacancies and single-molecule vacancies have been obtained. In particular, there is a rotating CoPc molecule inside each single-molecule vacancy, which constitutes the array of single-molecule rotors. These results provide a new routine to fabricate the nano-machines on a large scale.

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.

The Molecular Structure of the Han-Based Liquid Propellants

DTIC Science & Technology

1990-08-01

Temperature. pressur. and the presence of impurities or Wffixninanrs cause changes in the microcopic otganizAion of the mLixures. The size and stnrcture ok’ thm...unique and anomalous fluid. WVIr a small quantity of an iomc compound is introduced, it causes water molecules to marmrage fnxn their original custer...ehmnolamire. ethyldiethanolamine, and trziehanolamine. The boiling point of the pure, anhydrous, compounds are 89, 161, 246. and 340’ C, respectively

REFINING FLUORINATED COMPOUNDS

DOEpatents

Linch, A.L.

1963-01-01

This invention relates to the method of refining a liquid perfluorinated hydrocarbon oil containing fluorocarbons from 12 to 28 carbon atoms per molecule by distilling between 150 deg C and 300 deg C at 10 mm Hg absolute pressure. The perfluorinated oil is washed with a chlorinated lower aliphatic hydrocarbon, which mairtains a separate liquid phase when mixed with the oil. Impurities detrimental to the stability of the oil are extracted by the chlorinated lower aliphatic hydrocarbon. (AEC)

Accurate quantification of microRNA via single strand displacement reaction on DNA origami motif.

PubMed

Zhu, Jie; Feng, Xiaolu; Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can

2013-01-01

DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs.

Hydrogel Droplet Microfluidics for High-Throughput Single Molecule/Cell Analysis.

PubMed

Zhu, Zhi; Yang, Chaoyong James

2017-01-17

Heterogeneity among individual molecules and cells has posed significant challenges to traditional bulk assays, due to the assumption of average behavior, which would lose important biological information in heterogeneity and result in a misleading interpretation. Single molecule/cell analysis has become an important and emerging field in biological and biomedical research for insights into heterogeneity between large populations at high resolution. Compared with the ensemble bulk method, single molecule/cell analysis explores the information on time trajectories, conformational states, and interactions of individual molecules/cells, all key factors in the study of chemical and biological reaction pathways. Various powerful techniques have been developed for single molecule/cell analysis, including flow cytometry, atomic force microscopy, optical and magnetic tweezers, single-molecule fluorescence spectroscopy, and so forth. However, some of them have the low-throughput issue that has to analyze single molecules/cells one by one. Flow cytometry is a widely used high-throughput technique for single cell analysis but lacks the ability for intercellular interaction study and local environment control. Droplet microfluidics becomes attractive for single molecule/cell manipulation because single molecules/cells can be individually encased in monodisperse microdroplets, allowing high-throughput analysis and manipulation with precise control of the local environment. Moreover, hydrogels, cross-linked polymer networks that swell in the presence of water, have been introduced into droplet microfluidic systems as hydrogel droplet microfluidics. By replacing an aqueous phase with a monomer or polymer solution, hydrogel droplets can be generated on microfluidic chips for encapsulation of single molecules/cells according to the Poisson distribution. The sol-gel transition property endows the hydrogel droplets with new functionalities and diversified applications in single molecule/cell analysis. The hydrogel can act as a 3D cell culture matrix to mimic the extracellular environment for long-term single cell culture, which allows further heterogeneity study in proliferation, drug screening, and metastasis at the single-cell level. The sol-gel transition allows reactions in solution to be performed rapidly and efficiently with product storage in the gel for flexible downstream manipulation and analysis. More importantly, controllable sol-gel regulation provides a new way to maintain phenotype-genotype linkages in the hydrogel matrix for high throughput molecular evolution. In this Account, we will review the hydrogel droplet generation on microfluidics, single molecule/cell encapsulation in hydrogel droplets, as well as the progress made by our group and others in the application of hydrogel droplet microfluidics for single molecule/cell analysis, including single cell culture, single molecule/cell detection, single cell sequencing, and molecular evolution.

Electron beam controlled covalent attachment of small organic molecules to graphene

NASA Astrophysics Data System (ADS)

Markevich, Alexander; Kurasch, Simon; Lehtinen, Ossi; Reimer, Oliver; Feng, Xinliang; Müllen, Klaus; Turchanin, Andrey; Khlobystov, Andrei N.; Kaiser, Ute; Besley, Elena

2016-01-01

The electron beam induced functionalization of graphene through the formation of covalent bonds between free radicals of polyaromatic molecules and C&z.dbd;C bonds of pristine graphene surface has been explored using first principles calculations and high-resolution transmission electron microscopy. We show that the energetically strongest attachment of the radicals occurs along the armchair direction in graphene to carbon atoms residing in different graphene sub-lattices. The radicals tend to assume vertical position on graphene substrate irrespective of direction of the bonding and the initial configuration. The ``standing up'' molecules, covalently anchored to graphene, exhibit two types of oscillatory motion - bending and twisting - caused by the presence of acoustic phonons in graphene and dispersion attraction to the substrate. The theoretically derived mechanisms are confirmed by near atomic resolution imaging of individual perchlorocoronene (C24Cl12) molecules on graphene. Our results facilitate the understanding of controlled functionalization of graphene employing electron irradiation as well as mechanisms of attachment of impurities via the processing of graphene nanoelectronic devices by electron beam lithography.The electron beam induced functionalization of graphene through the formation of covalent bonds between free radicals of polyaromatic molecules and C&z.dbd;C bonds of pristine graphene surface has been explored using first principles calculations and high-resolution transmission electron microscopy. We show that the energetically strongest attachment of the radicals occurs along the armchair direction in graphene to carbon atoms residing in different graphene sub-lattices. The radicals tend to assume vertical position on graphene substrate irrespective of direction of the bonding and the initial configuration. The ``standing up'' molecules, covalently anchored to graphene, exhibit two types of oscillatory motion - bending and twisting - caused by the presence of acoustic phonons in graphene and dispersion attraction to the substrate. The theoretically derived mechanisms are confirmed by near atomic resolution imaging of individual perchlorocoronene (C24Cl12) molecules on graphene. Our results facilitate the understanding of controlled functionalization of graphene employing electron irradiation as well as mechanisms of attachment of impurities via the processing of graphene nanoelectronic devices by electron beam lithography. Electronic supplementary information (ESI) available: A table showing the calculated binding energies and magnetic moments for all studied molecular radicals; details of samples preparation and characterization; time series of TEM images showing transformations of a C24Cl12 molecule on graphene under electron irradiation. See DOI: 10.1039/c5nr07539d

Quasiparticle Approach to Molecules Interacting with Quantum Solvents.

PubMed

Lemeshko, Mikhail

2017-03-03

Understanding the behavior of molecules interacting with superfluid helium represents a formidable challenge and, in general, requires approaches relying on large-scale numerical simulations. Here, we demonstrate that experimental data collected over the last 20 years provide evidence that molecules immersed in superfluid helium form recently predicted angulon quasiparticles [Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001]. Most important, casting the many-body problem in terms of angulons amounts to a drastic simplification and yields effective molecular moments of inertia as straightforward analytic solutions of a simple microscopic Hamiltonian. The outcome of the angulon theory is in good agreement with experiment for a broad range of molecular impurities, from heavy to medium-mass to light species. These results pave the way to understanding molecular rotation in liquid and crystalline phases in terms of the angulon quasiparticle.

Ab initio nonadiabatic molecular dynamics of the ultrafast electron injection from a PbSe quantum dot into the TiO2 surface.

PubMed

Long, Run; Prezhdo, Oleg V

2011-11-30

Following recent experiments [Science 2010, 328, 1543; PNAS 2011, 108, 965], we report an ab initio nonadiabatic molecular dynamics (NAMD) simulation of the ultrafast photoinduced electron transfer (ET) from a PbSe quantum dot (QD) into the rutile TiO(2) (110) surface. The system forms the basis for QD-sensitized semiconductor solar cells and demonstrates that ultrafast interfacial ET is instrumental for achieving high efficiencies in solar-to-electrical energy conversion. The simulation supports the observation that the ET successfully competes with energy losses due to electron-phonon relaxation. The ET proceeds by the adiabatic mechanism because of strong donor-acceptor coupling. High frequency polar vibrations of both QD and TiO(2) promote the ET, since these modes can rapidly influence the donor-acceptor state energies and coupling. Low frequency vibrations generate a distribution of initial conditions for ET, which shows a broad variety of scenarios at the single-molecule level. Compared to the molecule-TiO(2) interfaces, the QD-TiO(2) system exhibits pronounced differences that arise due to the larger size and higher rigidity of QDs relative to molecules. Both donor and acceptor states are more delocalized in the QD system, and the ET is promoted by optical phonons, which have relatively low frequencies in the QD materials composed of heavy elements. In contrast, in molecular systems, optical phonons are not thermally accessible under ambient conditions. Meanwhile, TiO(2) acceptor states resemble surface impurities due to the local influence of molecular chromophores. At the same time, the photoinduced ET at both QD-TiO(2) and molecule-TiO(2) interfaces is ultrafast and occurs by the adiabatic mechanism, as a result of strong donor-acceptor coupling. The reported state-of-the-art simulation generates a detailed time-domain atomistic description of the interfacial ET process that is fundamental to a wide variety of applications.

Impurity-generated non-Abelions

NASA Astrophysics Data System (ADS)

Simion, G.; Kazakov, A.; Rokhinson, L. P.; Wojtowicz, T.; Lyanda-Geller, Y. B.

2018-06-01

Two classes of topological superconductors and Majorana modes in condensed matter systems are known to date: one in which disorder induced by impurities strongly suppresses topological superconducting gap and is detrimental to Majorana modes, and another where Majorana fermions are protected by a disorder-robust topological superconductor gap. Observation and control of Majorana fermions and other non-Abelions often requires a symmetry of an underlying system leading to a gap in the single-particle or quasiparticle spectra. In semiconductor structures, impurities that provide charge carriers introduce states into the gap and enable conductance and proximity-induced superconductivity via the in-gap states. Thus a third class of topological superconductivity and Majorana modes emerges, in which topological superconductivity and Majorana fermions appear exclusively when impurities generate in-gap states. We show that impurity-enabled topological superconductivity is realized in a quantum Hall ferromagnet, when a helical domain wall is coupled to an s -wave superconductor. As an example of emergence of topological superconductivity in quantum Hall ferromagnets, we consider the integer quantum Hall effect in Mn-doped CdTe quantum wells. Recent experiments on transport through the quantum Hall ferromagnet domain wall in this system indicated a vital role of impurities in the conductance, but left unresolved the question whether impurities preclude generation of Majorana fermions and other non-Abelions in such systems in general. Here, solving a general quantum-mechanical problem of impurity bound states in a system of spin-orbit coupled Landau levels, we demonstrate that impurity-induced Majorana modes emerge at boundaries between topological and conventional superconducting states generated in a domain wall due to proximity to an s superconductor. We consider both short-range disorder and a smooth random potential. The phase diagram of the system is defined by characteristic disorder, gate voltage induced angular momentum splitting of impurity levels, and by a proximity superconducting gap. The phase diagram exhibits two ranges of gate voltage with conventional superconducting order separated by a gate voltage range with topological superconductivity. We show that electrostatic control of domain walls in an integer quantum Hall ferromagnet allows manipulation of Majorana fermions. Ferromagnetic transitions in the fractional quantum Hall regime may lead to the formation and electrostatic control of higher order non-Abelian excitations.

Single-molecule detection: applications to ultrasensitive biochemical analysis

NASA Astrophysics Data System (ADS)

Castro, Alonso; Shera, E. Brooks

1995-06-01

Recent developments in laser-based detection of fluorescent molecules have made possible the implementation of very sensitive techniques for biochemical analysis. We present and discuss our experiments on the applications of our recently developed technique of single-molecule detection to the analysis of molecules of biological interest. These newly developed methods are capable of detecting and identifying biomolecules at the single-molecule level of sensitivity. In one case, identification is based on measuring fluorescence brightness from single molecules. In another, molecules are classified by determining their electrophoretic velocities.

A validated stability-indicating LC method for the separation of enantiomer and potential impurities of Linezolid using polar organic mode.

PubMed

Satyanarayana Raju, T; Vishweshwari Kutty, O; Ganesh, V; Yadagiri Swamy, P

2012-08-01

Although a number of methods are available for evaluating Linezolid and its possible impurities, a common method for separation if its potential impurities, degradants and enantiomer in a single method with good efficiency remain unavailable. With the objective of developing an advanced method with shorter runtimes, a simple, precise, accurate stability-indicating LC method was developed for the determination of purity of Linezolid drug substance and drug products in bulk samples and pharmaceutical dosage forms in the presence of its impurities and degradation products. This method is capable of separating all the related substances of Linezolid along with the chiral impurity. This method can also be used for the estimation of assay of Linezolid in drug substance as well as in drug product. The method was developed using Chiralpak IA (250 mm×4.6 mm, 5 μm) column. A mixture of acetonitrile, ethanol, n-butyl amine and trifluoro acetic acid in 96:4:0.10:0.16 (v/v/v/v) ratio was used as a mobile phase. The eluted compounds were monitored at 254 nm. Linezolid was subjected to the stress conditions of oxidative, acid, base, hydrolytic, thermal and photolytic degradation. The degradation products were well resolved from main peak and its impurities, proving the stability-indicating power of the method. The developed method was validated as per International Conference on Harmonization (ICH) guidelines with respect to specificity, limit of detection, limit of quantification, precision, linearity, accuracy, robustness and system suitability.

Systematics of electronic and magnetic properties in the transition metal doped Sb2Te3 quantum anomalous Hall platform

NASA Astrophysics Data System (ADS)

Islam, M. F.; Canali, C. M.; Pertsova, A.; Balatsky, A.; Mahatha, S. K.; Carbone, C.; Barla, A.; Kokh, K. A.; Tereshchenko, O. E.; Jiménez, E.; Brookes, N. B.; Gargiani, P.; Valvidares, M.; Schatz, S.; Peixoto, T. R. F.; Bentmann, H.; Reinert, F.; Jung, J.; Bathon, T.; Fauth, K.; Bode, M.; Sessi, P.

2018-04-01

The quantum anomalous Hall effect (QAHE) has recently been reported to emerge in magnetically doped topological insulators. Although its general phenomenology is well established, the microscopic origin is far from being properly understood and controlled. Here, we report on a detailed and systematic investigation of transition metal (TM) doped Sb2Te3 . By combining density functional theory calculations with complementary experimental techniques, i.e., scanning tunneling microscopy, resonant photoemission, and x-ray magnetic circular dichroism, we provide a complete spectroscopic characterization of both electronic and magnetic properties. Our results reveal that the TM dopants not only affect the magnetic state of the host material, but also significantly alter the electronic structure by generating impurity-derived energy bands. Our findings demonstrate the existence of a delicate interplay between electronic and magnetic properties in TM doped topological insulators. In particular, we find that the fate of the topological surface states critically depends on the specific character of the TM impurity: while V- and Fe-doped Sb2Te3 display resonant impurity states in the vicinity of the Dirac point, Cr and Mn impurities leave the energy gap unaffected. The single-ion magnetic anisotropy energy and easy axis, which control the magnetic gap opening and its stability, are also found to be strongly TM impurity dependent and can vary from in plane to out of plane depending on the impurity and its distance from the surface. Overall, our results provide general guidelines for the realization of a robust QAHE in TM doped Sb2Te3 in the ferromagnetic state.

An impurity-induced gap system as a quantum data bus for quantum state transfer

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

Chen, Bing, E-mail: chenbingphys@gmail.com; Li, Yong; Song, Z.

2014-09-15

We introduce a tight-binding chain with a single impurity to act as a quantum data bus for perfect quantum state transfer. Our proposal is based on the weak coupling limit of the two outermost quantum dots to the data bus, which is a gapped system induced by the impurity. By connecting two quantum dots to two sites of the data bus, the system can accomplish a high-fidelity and long-distance quantum state transfer. Numerical simulations for finite system show that the numerical and analytical results of the effective coupling strength agree well with each other. Moreover, we study the robustness ofmore » this quantum communication protocol in the presence of disorder in the couplings between the nearest-neighbor quantum dots. We find that the gap of the system plays an important role in robust quantum state transfer.« less

Enhanced Impurity-Free Intermixing Bandgap Engineering for InP-Based Photonic Integrated Circuits

NASA Astrophysics Data System (ADS)

Cui, Xiao; Zhang, Can; Liang, Song; Zhu, Hong-Liang; Hou, Lian-Ping

2014-04-01

Impurity-free intermixing of InGaAsP multiple quantum wells (MQW) using sputtering Cu/SiO2 layers followed by rapid thermal processing (RTP) is demonstrated. The bandgap energy could be modulated by varying the sputtering power and time of Cu, RTP temperature and time to satisfy the demands for lasers, modulators, photodetector, and passive waveguides for the photonic integrated circuits with a simple procedure. The blueshift of the bandgap wavelength of MQW is experimentally investigated on different sputtering and annealing conditions. It is obvious that the introduction of the Cu layer could increase the blueshift more greatly than the common impurity free vacancy disordering technique. A maximum bandgap blueshift of 172 nm is realized with an annealing condition of 750°C and 200s. The improved technique is promising for the fabrication of the active/passive optoelectronic components on a single wafer with simple process and low cost.

Silicon materials task of the low-cost solar array project. Phase 4: Effects of impurities and processing on silicon solar cells

NASA Technical Reports Server (NTRS)

Hopkins, R. H.; Hanes, M. H.; Davis, J. R.; Rohatgi, A.; Raichoudhury, P.; Mollenkopf, H. C.

1981-01-01

The results of the study form a basis for silicon producers, wafer manufacturers, and cell fabricators to develop appropriate cost-benefit relationships for the use of less pure, less costly solar grade silicon. Cr is highly mobile in silicon even at temperatures as low as 600 C. Contrasting with earlier data for Mo, Ti, and V, Cr concentrations vary from place to place in polycrystalline silicon wafers and the electrically-active Cr concentration in the polysilicon is more than an order of magnitude smaller than would be projected from single crystal impurity data. We hypothesize that Cr diffuses during ingot cooldown after growth, preferentially segregates to grain and becomes electrically deactivated. Accelerated aging data from Ni-contaminated silicon imply that no significant impurity-induced cell performance reduction should be expected over a twenty year device lifetime.

A spectroscopic system for time- and space-resolved studies of impurities on the EXTRAP-T2 reversed field pinch

NASA Astrophysics Data System (ADS)

Sallander, J.

1998-06-01

The radial distribution of impurity line emission in the EXTRAP-T2 reversed field pinch (RFP) is studied with a five viewing chord, absolutely calibrated, spectrometer system. The light is analyzed with a single 0.5 m grating spectrometer. Different parts of the entrance slit are used for different channels. This arrangement makes it possible to use the system over a wide wavelength range, from 2500 to 6500 Å, without having to recalibrate the relative sensitivity for the different channels. The rather short plasma pulses of 10-15 ms require a high time resolution. The use of photomultiplier tubes provides a time resolution of 10 μs which is limited by the transient recorders used. The result is a robust, low-cost system that produces reliable measurements of the radial dependence of emission from a wide range of impurity ions.

Nonequilibrium theory of tunneling into a localized state in a superconductor

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

Martin, Ivar; Mozyrsky, Dmitry

2014-09-01

A single static magnetic impurity in a fully gapped superconductor leads to the formation of an intragap quasiparticle bound state. At temperatures much below the superconducting transition, the energy relaxation and spin dephasing of the state are expected to be exponentially suppressed. The presence of such a state can be detected in electron tunneling experiments as a pair of conductance peaks at positive and negative biases. Here we show that, for an arbitrarily weak tunneling strength, the peaks have to be symmetric with respect to the applied bias. This is in contrast to the standard result in which the tunnelingmore » conductance is proportional to the local (in general, particle-hole asymmetric) density of states. The asymmetry can be recovered if one allows for either a finite density of impurity states, or if impurities are coupled to another, nonsuperconducting, equilibrium bath.« less

Soliton-impurity interaction in two Ablowitz-Ladik chains with different coupling

NASA Astrophysics Data System (ADS)

Kamburova, R. S.; Primatarowa, M. T.

2014-12-01

The interaction of solitons with point defects in a system of coupled Ablowitz- Ladik (AL) chains is studied numerically. The system is a discrete analog of coupled nonlinear Schrodinger equations. Two types of interchain coupling are investigated: one which admits reduction of the system to the standard integrable AL model (dispersive coupling) and one which couples opposite sites of the chains and does not admit reduction to the AL model (nondispersive coupling). The action of the two coupling types is additive and they can compensate each other in some cases. We have obtained that the single-peak bound soliton-defect solution (attractive impurity) is stable against perturbations, while the double-peak bound soliton-defect solution (repulsive impurity) is unstable and can be easily destroyed. Linear point defects do not influence the period of energy transfer and it is close to the period for the homogeneous case.

Efficient DFT+U calculations of ballistic electron transport: Application to Au monatomic chains with a CO impurity

NASA Astrophysics Data System (ADS)

Sclauzero, Gabriele; Dal Corso, Andrea

2013-02-01

An efficient method for computing the Landauer-Büttiker conductance of an open quantum system within DFT+U is presented. The Hubbard potential is included in electronic-structure and transport calculations as a simple renormalization of the nonlocal pseudopotential coefficients by restricting the integration for the onsite occupations within the cutoff spheres of the pseudopotential. We apply the methodology to the case of an Au monatomic chain in the presence of a CO molecule adsorbed on it. We show that the Hubbard U correction removes the spurious magnetization in the pristine Au chain at the equilibrium spacing, as well as the unphysical contribution of d electrons to the conductance, resulting in a single (spin-degenerate) transmission channel and a more realistic conductance of 1G0. We find that the conductance reduction due to CO adsorption is much larger for the atop site than for the bridge site, so that the general picture of electron transport in stretched Au chains given by the local density approximation remains valid at the equilibrium Au-Au spacing within DFT+U.

Imaging the effects of individual zinc impurity atoms on superconductivity in Bi2Sr2CaCu2O8+delta

PubMed

Pan; Hudson; Lang; Eisaki; Uchida; Davis

2000-02-17

Although the crystal structures of the copper oxide high-temperature superconductors are complex and diverse, they all contain some crystal planes consisting of only copper and oxygen atoms in a square lattice: superconductivity is believed to originate from strongly interacting electrons in these CuO2 planes. Substituting a single impurity atom for a copper atom strongly perturbs the surrounding electronic environment and can therefore be used to probe high-temperature superconductivity at the atomic scale. This has provided the motivation for several experimental and theoretical studies. Scanning tunnelling microscopy (STM) is an ideal technique for the study of such effects at the atomic scale, as it has been used very successfully to probe individual impurity atoms in several other systems. Here we use STM to investigate the effects of individual zinc impurity atoms in the high-temperature superconductor Bi2Sr2CaCu2O8+delta. We find intense quasiparticle scattering resonances at the Zn sites, coincident with strong suppression of superconductivity within approximately 15 A of the scattering sites. Imaging of the spatial dependence of the quasiparticle density of states in the vicinity of the impurity atoms reveals the long-sought four-fold symmetric quasiparticle 'cloud' aligned with the nodes of the d-wave superconducting gap which is believed to characterize superconductivity in these materials.

Complexity of Quantum Impurity Problems

NASA Astrophysics Data System (ADS)

Bravyi, Sergey; Gosset, David

2017-12-01

We give a quasi-polynomial time classical algorithm for estimating the ground state energy and for computing low energy states of quantum impurity models. Such models describe a bath of free fermions coupled to a small interacting subsystem called an impurity. The full system consists of n fermionic modes and has a Hamiltonian {H=H_0+H_{imp}}, where H 0 is quadratic in creation-annihilation operators and H imp is an arbitrary Hamiltonian acting on a subset of O(1) modes. We show that the ground energy of H can be approximated with an additive error {2^{-b}} in time {n^3 \\exp{[O(b^3)]}}. Our algorithm also finds a low energy state that achieves this approximation. The low energy state is represented as a superposition of {\\exp{[O(b^3)]}} fermionic Gaussian states. To arrive at this result we prove several theorems concerning exact ground states of impurity models. In particular, we show that eigenvalues of the ground state covariance matrix decay exponentially with the exponent depending very mildly on the spectral gap of H 0. A key ingredient of our proof is Zolotarev's rational approximation to the {√{x}} function. We anticipate that our algorithms may be used in hybrid quantum-classical simulations of strongly correlated materials based on dynamical mean field theory. We implemented a simplified practical version of our algorithm and benchmarked it using the single impurity Anderson model.

Kondo Effect of U Impurities in Dilute (YU)2Zn17

NASA Astrophysics Data System (ADS)

Takagi, Shigeru; Suzuki, Hiroyuki; Anzai, Kousuke

2001-10-01

Extending previous work on single-site properties of U ions in (LaU)2Zn17, we have investigated, from ρ(T), χ(T) and Cp(T) on single crystals, (Y1-xUx)2Zn17 with x=0.025 and 0.050, which has almost the same unit-cell volume as an antiferromagnetic heavy-electron compound U2Zn17. Remarkable features in the dilute-impurity limit have been clarified, which include Kondo behavior of ρ(T), large and almost isotropic χimp(T), and strongly enhanced Cimp(T)/T with gigantic γimp=2.02 2.05 J/K2·mole-U as T→0 due to a low characteristic energy-scale of the system. It is shown that gross features of the data are explained in terms of the conventional Kondo effect in the presence of the crystal field with the U3+ \\varGamma6 doublet ground state. It is also shown that the variation of γ with the unit-cell volume in related systems is not explained as a volume effect on TK and that even the behavior of fictitious “paramagnetic” U2Zn17 is not described as a collection of U impurities in dilute (YU)2Zn17.

Protein Crystallization

NASA Technical Reports Server (NTRS)

Chernov, Alexander A.

2005-01-01

Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.

Spectroscopic characterization of Venus at the single molecule level.

PubMed

David, Charlotte C; Dedecker, Peter; De Cremer, Gert; Verstraeten, Natalie; Kint, Cyrielle; Michiels, Jan; Hofkens, Johan

2012-02-01

Venus is a recently developed, fast maturating, yellow fluorescent protein that has been used as a probe for in vivo applications. In the present work the photophysical characteristics of Venus were analyzed spectroscopically at the bulk and single molecule level. Through time-resolved single molecule measurements we found that single molecules of Venus display pronounced fluctuations in fluorescence emission, with clear fluorescence on- and off-times. These fluorescence intermittencies were found to occupy a broad range of time scales, ranging from milliseconds to several seconds. Such long off-times can complicate the analysis of single molecule counting experiments or single-molecule FRET experiments. This journal is © The Royal Society of Chemistry and Owner Societies 2012

Single molecule data under scrutiny. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb & S.K. Sarkar

NASA Astrophysics Data System (ADS)

Wohland, Thorsten

2015-06-01

Single Molecule Detection and Spectroscopy have grown from their first beginnings into mainstream, mature research areas that are widely applied in the biological sciences. However, despite the advances in technology and the application of many single molecule techniques even in in vivo settings, the data analysis of single molecule experiments is complicated by noise, systematic errors, and complex underlying processes that are only incompletely understood. Colomb and Sarkar provide in this issue an overview of single molecule experiments and the accompanying problems in data analysis, which have to be overcome for a proper interpretation of the experiments [1].

Single Molecule Electronics and Devices

PubMed Central

Tsutsui, Makusu; Taniguchi, Masateru

2012-01-01

The manufacture of integrated circuits with single-molecule building blocks is a goal of molecular electronics. While research in the past has been limited to bulk experiments on self-assembled monolayers, advances in technology have now enabled us to fabricate single-molecule junctions. This has led to significant progress in understanding electron transport in molecular systems at the single-molecule level and the concomitant emergence of new device concepts. Here, we review recent developments in this field. We summarize the methods currently used to form metal-molecule-metal structures and some single-molecule techniques essential for characterizing molecular junctions such as inelastic electron tunnelling spectroscopy. We then highlight several important achievements, including demonstration of single-molecule diodes, transistors, and switches that make use of electrical, photo, and mechanical stimulation to control the electron transport. We also discuss intriguing issues to be addressed further in the future such as heat and thermoelectric transport in an individual molecule. PMID:22969345

Reversible gating of smart plasmonic molecular traps using thermoresponsive polymers for single-molecule detection

PubMed Central

Zheng, Yuanhui; Soeriyadi, Alexander H.; Rosa, Lorenzo; Ng, Soon Hock; Bach, Udo; Justin Gooding, J.

2015-01-01

Single-molecule surface-enhanced Raman spectroscopy (SERS) has attracted increasing interest for chemical and biochemical sensing. Many conventional substrates have a broad distribution of SERS enhancements, which compromise reproducibility and result in slow response times for single-molecule detection. Here we report a smart plasmonic sensor that can reversibly trap a single molecule at hotspots for rapid single-molecule detection. The sensor was fabricated through electrostatic self-assembly of gold nanoparticles onto a gold/silica-coated silicon substrate, producing a high yield of uniformly distributed hotspots on the surface. The hotspots were isolated with a monolayer of a thermoresponsive polymer (poly(N-isopropylacrylamide)), which act as gates for molecular trapping at the hotspots. The sensor shows not only a good SERS reproducibility but also a capability to repetitively trap and release molecules for single-molecular sensing. The single-molecule sensitivity is experimentally verified using SERS spectral blinking and bianalyte methods. PMID:26549539

Direct single-molecule dynamic detection of chemical reactions.

PubMed

Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N; Zhang, Deqing; Guo, Xuefeng

2018-02-01

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

Direct single-molecule dynamic detection of chemical reactions

PubMed Central

Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N.; Zhang, Deqing; Guo, Xuefeng

2018-01-01

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry. PMID:29487914

Experimental setup for investigation of nanoclusters at cryogenic temperatures by electron spin resonance and optical spectroscopies

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

Mao, S., E-mail: maoshunghost@tamu.edu; Meraki, A.; McColgan, P. T.

2014-07-15

We present the design and performance of an experimental setup for simultaneous electron spin resonance (ESR) and optical studies of nanoclusters with stabilized free radicals at cryogenic temperatures. A gas mixture of impurities and helium after passing through a RF discharge for dissociation of molecules is directed onto the surface of superfluid helium to form the nanoclusters of impurities. A specially designed ESR cavity operated in the TE{sub 011} mode allows optical access to the sample. The cavity is incorporated into a homemade insert which is placed inside a variable temperature insert of a Janis {sup 4}He cryostat. The temperaturemore » range for sample investigation is 1.25–300 K. A Bruker EPR 300E and Andor 500i optical spectrograph incorporated with a Newton EMCCD camera are used for ESR and optical registration, respectively. The current experimental system makes it possible to study the ESR and optical spectra of impurity-helium condensates simultaneously. The setup allows a broad range of research at low temperatures including optically detected magnetic resonance, studies of chemical processes of the active species produced by photolysis in solid matrices, and investigations of nanoclusters produced by laser ablation in superfluid helium.« less

Exact diagonalization library for quantum electron models

NASA Astrophysics Data System (ADS)

Iskakov, Sergei; Danilov, Michael

2018-04-01

We present an exact diagonalization C++ template library (EDLib) for solving quantum electron models, including the single-band finite Hubbard cluster and the multi-orbital impurity Anderson model. The observables that can be computed using EDLib are single particle Green's functions and spin-spin correlation functions. This code provides three different types of Hamiltonian matrix storage that can be chosen based on the model.

[Biophysics of single molecules].

PubMed

Serdiuk, I N; Deriusheva, E I

2011-01-01

The modern methods of research of biological molecules whose application led to the development of a new field of science, biophysics of single molecules, are reviewed. The measurement of the characteristics of single molecules enables one to reveal their individual features, and it is just for this reason that much more information can be obtained from one molecule than from the entire ensample of molecules. The high sensitivity of the methods considered in detail makes it possible to come close to the solution of the basic problem of practical importance, namely, the determination of the nucleotide sequence of a single DNA molecule.

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

Ngo, Anh T.; Kim, Eugene H.; Ulloa, Sergio E.

Single-atom gating, achieved by manipulation of adatoms on a surface, has been shown in experiments to allow precise control over superposition of electronic states in quantum corrals. Using a Green's function approach, we demonstrate theoretically that such atom gating can also be used to control the coupling between magnetic degrees of freedom in these systems. Atomic gating enables control not only on the direct interaction between magnetic adatoms, but also over superpositions of many-body states which can then control long distance interactions. We illustrate this effect by considering the competition between direct exchange between magnetic impurities and the Kondo screeningmore » mediated by the host electrons, and how this is affected by gating. These results suggest that both magnetic and nonmagnetic single-atom gating may be used to investigate magnetic impurity systems with tailored interactions, and may allow the control of entanglement of different spin states.« less

Hydrogen defects in α-Al2O3 and water weakening of sapphire and alumina ceramics between 600 and 1000°C: I. Infrared characterization of defects

USGS Publications Warehouse

Kronenberg, A.K.; Castaing, J.; Mitchell, T.E.; Kirby, S.H.

2000-01-01

Hydrogen impurities in materials influence their properties, including flow strength. α-Al2O3 single crystals and polycrystalline ceramics were annealed in supercritical water between 850 and 1025°C, under pressures in the range 1500–2000 MPa. A few specimens were further subjected to plastic deformation. Hydrogen penetration was examined using infrared absorption measurements of O–H bond vibrations, which revealed two kinds of hydrogen defects. In single crystals, defects are characterized by sharp O–H absorption bands assigned to interstitial protons. Hydrogen impurities of hydrothermally annealed ceramics and of all hydrothermally deformed specimens are characterized by broad O–H bands assigned to molecular water. The grain boundaries of hydrothermally annealed ceramics are severely damaged. The kinetics of hydrogen penetration is consistent with diffusion data.

Orbital effect of the magnetic field in dynamical mean-field theory

NASA Astrophysics Data System (ADS)

Acheche, S.; Arsenault, L.-F.; Tremblay, A.-M. S.

2017-12-01

The availability of large magnetic fields at international facilities and of simulated magnetic fields that can reach the flux-quantum-per-unit-area level in cold atoms calls for systematic studies of orbital effects of the magnetic field on the self-energy of interacting systems. Here we demonstrate theoretically that orbital effects of magnetic fields can be treated within single-site dynamical mean-field theory with a translationally invariant quantum impurity problem. As an example, we study the one-band Hubbard model on the square lattice using iterated perturbation theory as an impurity solver. We recover the expected quantum oscillations in the scattering rate, and we show that the magnetic fields allow the interaction-induced effective mass to be measured through the single-particle density of states accessible in tunneling experiments. The orbital effect of magnetic fields on scattering becomes particularly important in the Hofstadter butterfly regime.

2D- and 3D SIMS investigations on hot-pressed steel powder HS 6-5-3-8.

PubMed

Rosner, M; Pöckl, G; Danninger, H; Hutter, H

2002-10-01

Processing of steel with powder metallurgical methods such as sintering or hot-pressing have proven to be a powerful tool for the production of industrial parts and for components in the automotive industry. Series of steel-powders (HS 6-5-3-8) produced by gas atomization has been hot-pressed in a graphite tube at temperatures from 820 degrees C to 1050 degrees C. The samples have been characterized with a Secondary Electron Microscope (SEM) due to their porosity and then investigated with 2D- and 3D- SIMS. The spatial distribution of the non-metallic impurities and the covering oxide layer of the single particles has been traced dependent to the pressing temperature. Powders pressed at temperatures higher than 880 degrees C exhibited different precipitation behavior of the impurities and an excessive loss of the covering oxide layer of the single powder particles.

Potential productivity benefits of float-zone versus Czochralski crystal growth

NASA Technical Reports Server (NTRS)

Abe, T.

1985-01-01

Efficient mass production of single-crystal silicon is necessary for the efficient silicon solar arrays needed in the coming decade. However, it is anticipated that there will be difficulty growing such volumes of crystals using conventional Czochralski (Cz) methods. While the productivity of single crystals might increase with a crystal diameter increase, there are two obstacles to the mass production of large diameter Czochralski crystals, the long production cycle due to slow growth rate and the high heat requirements of the furnaces. Also counterproductive would be the large resistivity gradient along the growth direction of the crystals due to impurity concentration. Comparison between Float zone (FZ) and Cz crystal growth on the basis of a crystal 150 mm in diameter is on an order of two to four times in favor of the FZ method. This advantage results from high growth rates and steady-state growth while maintaining a dislocation-free condition and impurity segregation.

Characterization of PVT Grown ZnSe by Low Temperature Photoluminescence

NASA Technical Reports Server (NTRS)

Wang, Ling Jun

1998-01-01

ZnSe, a II-VI semiconductor with a large direct band gap of 2.7 eV at room temperature and 2.82 eV at 10 K, is considered a promising material for optoelectric applications in the blue-green region of the spectrum. Photoemitting devices and diode laser action has been demonstrated as a result of decades of research. A key issue in the development of II-VI semiconductors is the control of the concentration of the various impurities. The II-VI semiconductors seem to defy the effort of high level doping due to the well known self compensation of the donors and the acceptors. A good understanding of roles of the impurities and the behavior of the various intrinsic defects such as vacancies, interstitials and their complexes with impurities is necessary in the development and application of these materials. Persistent impurities such as Li and Cu have long played a central role in the photoelectronic properties of many II-VI compounds, particularly ZnSe. The shallow centers which may promote useful electrical conductivity are of particular interest. They contribute the richly structured near gap edge luminescence, containing weak to moderate phonon coupling and therefore very accessible information about the energy states of the different centers. Significance of those residual impurities which may contribute such centers in II-VI semiconductors must be fully appreciated before improved control of their electrical properties may be possible. Low temperature photoluminescence spectroscopy is an important source of information and a useful tool of characterization of II-VI semiconductors such as ZnSe. The low temperature photoluminescence spectrum of a ZnSe single crystal typically consists of a broad band emission peaking at 2.34 eV, known as the Cu-green band, and some very sharp lines near the band gap. These bands and lines are used to identify the impurity ingredients and the defects. The assessment of the quality of the crystal based on the photoluminescence analysis is then possible. In this report we present the characterization of a ZnSe single crystal as grown by the physical vapor transport method, with special intention paid to the possible effects of the gravitational field to the growth of the crystal.

Improvement of pesticide adsorption capacity of cellulose fibre by high-energy irradiation-initiated grafting of glycidyl methacrylate

NASA Astrophysics Data System (ADS)

Takács, Erzsébet; Wojnárovits, László; Koczog Horváth, Éva; Fekete, Tamás; Borsa, Judit

2012-09-01

Cellulose as a renewable raw material was used for preparation of adsorbent of organic impurities in wastewater treatment. Hydrophobic surface of cellulose substrate was developed by grafting glycidyl methacrylate in simultaneous grafting using gamma irradiation initiation. Water uptake of cellulose significantly decreased while adsorption of phenol and a pesticide molecule (2,4-dichlorophenoxyacetic acid: 2,4-D) increased upon grafting. Adsorption equilibrium data fitted the Freundlich isotherm for both solutes.

Accelerated aging: prediction of chemical stability of pharmaceuticals.

PubMed

Waterman, Kenneth C; Adami, Roger C

2005-04-11

Methods of rapidly and accurately assessing the chemical stability of pharmaceutical dosage forms are reviewed with respect to the major degradation mechanisms generally observed in pharmaceutical development. Methods are discussed, with the appropriate caveats, for accelerated aging of liquid and solid dosage forms, including small and large molecule active pharmaceutical ingredients. In particular, this review covers general thermal methods, as well as accelerated aging methods appropriate to oxidation, hydrolysis, reaction with reactive excipient impurities, photolysis and protein denaturation.

Experimental and theoretical investigation of Fe-catalysis phenomenon in hydrogen thermal desorption from hydrocarbon plasma-discharge films from T-10 tokama

NASA Astrophysics Data System (ADS)

Stankevich, Vladimir G.; Sukhanov, Leonid P.; Svechnikov, Nicolay Yu.; Lebedev, Alexey M.; Menshikov, Kostantin A.; Kolbasov, Boris N.

2017-10-01

Investigations of the effect of Fe impurities on D2 thermal desorption (TD) from homogeneous CDx films (x ˜ 0.5) formed in the D-plasma discharge of the T-10 tokamak were carried out. The experimental TD spectra of the films showed two groups of peaks at 650-850 K and 900-1000 K for two adsorption states. The main result of the iron catalysis effect consists in the shift of the high-temperature peak by -24 K and in the increase in the fraction of the weakly bonded adsorption states. To describe the effect of iron impurities on TD of hydrogen isotopes, a structural cluster model based on the interaction of the Fe+ ion with the 1,3-C6H8 molecule was proposed. The potential energy surfaces of chemical reactions with the H2 elimination were calculated using ab initio methods of quantum chemistry. It was established that the activation barrier of hydrogen TD is reduced by about 1 eV due to the interaction of the Fe+ ion with the π-subsystem of the 1,3-C6H8 molecule leading to a redistribution of the double bonds along the carbon system. Contribution to the topical issue "Plasma Sources and Plasma Processes (PSPP)"", edited by Luis Lemos Alves, Thierry Belmonte and Tiberiu Minea

The magnetodynamic filters in monitoring the contaminants from polluted water systems (abstract)

NASA Astrophysics Data System (ADS)

Swarup, R.; Singh, Bharat

1994-05-01

The magnetic interaction seems to influence the ``structural memory'' of water systems which is quenched in ideally pure water. The sedentary lifetime of each water molecule is extremely short (10-10 s) and its molecular structures may be influenced by some physical effect like magnetic field treatment, it's space time gradients, water velocity, pressure drop, etc. in the interpolar space, so as to yield a noticeable temporal magnetopotential development characterizing the properties of homogeneous and heterogeneous water systems. This principle is also extended to prevailing water systems which always contain various impurities, gas, molecules, ions, microscopic particles in random order. Still the existence of structural memory may be verified by reliable experimental data. The magnetopotential curves of different water systems depict the design and develop-software package for constructing the magnetodynamic-filters superior to the existing techniques on pollution studies like remote sensing, muon spin resonance, laser spectroscopy, nuclear techniques, the gamma ray peak efficiency method, trace elemental characterization due to NBS, neutron activation analysis, and graphite furnance atomic absorption spectrometer. The physiochemical characteristics of water calibrated in terms of magnetopotential curves change with the removal of dissolved gasses, impurities, thermal activation, etc. and the algae, bacteria, phosphates, etc. have been removed at a rapid rate. The magnetodynamic study of ganga water proves it to be an extremely pure and highly resourced fluid.

Impact of perturbative, non-axisymmetric impurity fueling on Alcator C-Mod H-modes

NASA Astrophysics Data System (ADS)

Reinke, M. L.; Lore, J. D.; Terry, J.; Brunner, D.; LaBombard, B.; Lipschultz, B.; Hubbard, A.; Hughes, J. W.; Mumgaard, R.; Pitts, R. A.

2017-12-01

Experiments on Alcator C-Mod have been performed to investigate the impact of toroidally localized impurity injection on H-mode exhaust scenarios. Results help to inform sub-divertor gas injector designs, in particular that of the ITER machine, for which this work was primarily undertaken. In repeated EDA H-modes, the amount of N2 injected into the private flux region was scanned up to levels which strongly impacted normalized energy confinement, H98, and led to an H/L back-transition. Repeated scans increased the toroidal peaking of the gas injection, reducing from five equally spaced locations to a single toroidal and poloidal injector. Results show the impact on the pedestal and core plasma is similar between all cases as long as the total gas injection rate is held constant. An influence on toroidally localized impurity spectroscopy is shown, demonstrating a complication in using such data in interpreting experiments and supporting boundary modeling in cases where there are localized extrinsic or intrinsic impurity sources. These results, along with prior work in this area on Alcator C-Mod, form a comprehensive set of L-mode and H-mode data to be used for validation of 3D boundary physics codes.

Studies of Impurities in the Pegasus Spherical Tokamak

NASA Astrophysics Data System (ADS)

Rodriguez Sanchez, C.; Bodner, G. M.; Bongard, M. W.; Burke, M. G.; Fonck, R. J.; Perry, J. M.; Reusch, J. A.; Weberski, J. D.

2017-10-01

Local Helicity Injection (LHI) is used to initiate ST plasmas without a solenoid. Testing predictive models for the evolution of Ip(t) during LHI requires measurement of the plasma resistivity to quantify the dissipation of helicity. To that end, three diagnostic systems are coupled with an impurity transport model to quantify plasma contaminants. These are: visible bremsstrahlung (VB) spectroscopy; bolometry; and VUV spectroscopy. A spectral survey has been performed to identify line-free regions for VB measurements in the visible. Initial VB measurements are obtained with a single sightline through the plasma, and will be expanded to an imaging array to provide spatial resolution. A SPRED multichannel VUV spectrometer is being upgraded to provide high-speed ( 0.2 ms) spectral surveys for ion species identification, with a high-resolution grating installed for metallic line identification. A 16-channel thinistor bolometer array is planned. Absolutely calibrated VB, bolometer measurements, and qualitative ion species identification from SPRED are used as constraints in an impurity transport code to estimate absolute impurity content. Earlier work using this general approach indicated Zeff < 3 , before the edge current sources were shielded to reduce plasma-injector interactions. Work supported by US DOE Grant DE-FG02-96ER54375.

Electronic, optical and photocatalytic behavior of Mn, N doped and co-doped TiO{sub 2}: Experiment and simulation

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

Zhao, Ya Fei; Li, Can, E-mail: canli1983@gmail.com; Lu, Song

2016-03-15

The crystal phase structure, surface morphology, chemical states and optical properties of Mn, N mono-doped and co-doped TiO{sub 2} nanoparticles were investigated by X-ray powder diffractometry, Raman spectra, scanning electron microscopy, X-ray photoelectron spectroscopy and UV–vis diffuse reflectance spectroscopy. Meanwhile, geometry structures, formation energies, electronic and optical properties of all systems have been also analyzed by density functional theory. The results showed that the band gap values and the carrier mobility in the valence band, conduction band and impurity levels have a synergetic influence on the visible-light absorption and photocatalytic activity of the doped TiO{sub 2}. The number and themore » carrier mobility of impurity level jointly influence the photocatalytic activity of catalyst under visible-light. Especially, the photocatalytic activity of Mn-2N co-doped TiO{sub 2} beyond three-fold than that of pure TiO{sub 2} under visible-light. - Graphical abstract: The ILs formed by N-2p orbital in N single doped specimen lie above the VB, while the ILs formed by Mn-3d orbital in Mn single doped specimen appear below the CB. However, a large amount of ILs formed by N-2p orbital and Mn-3d orbital in N and Mn codoped specimens. The band gap values and the carrier mobility in the valence band, conduction band and impurity levels have a synergetic influence on the visible-light absorption and photocatalytic activity of the doped TiO{sub 2}. The number and the carrier mobility of impurity level jointly influence the photocatalytic activity of catalyst under visible-light.« less

The Dynamical Mean Field Study of Competition between Ferromagnetism and Disorder in Ferromagnetic Semiconductors

NASA Astrophysics Data System (ADS)

Aryanpour, Karan

2003-03-01

We employ the Dynamical Mean Field Approximation (DMFA) to study the Janko-Zarand model [1] for the combination of large spin-orbit coupling and spatial disorder effects in GaAs doped with Mn. In this model the electronic dispersion and the spin-orbit coupling are simultaneously diagonalized and therefore, the Hamiltonian for the pure system takes a surprisingly simple form. The price for this simplicity is that the quantization axis for the spin must be rotated along the direction of momentum. This chiral basis greatly complicates the form of the hole-impurity interaction at a single site i. In the DMFA, since all the crossing Feynman diagrams for the hole-impurity interaction vanish, the problem simplifies to the local diagrams for the holes scattering off of a single Mn impurity site only. The diagrammatics for the self-energy reduces to the local Green functions and potentials in the non-chiral basis in which they have very simple forms. We first calculate the initial green function G(k) in the chiral basis and then rotate G(k) back into the non chiral basis and coarse grain it over all the k momenta. The hole-impurity interaction is greatly simplified in the non-chiral basis and can be averaged over all the spin configurations and orientations of the Mn atoms on the lattice.The self energy may be extracted from the averaged Green function, and used to recalculate the initial cluster Green function, etc. completing the DMFA self-consistent loop. We intend to calculate the spin and charge transport coefficients, and spectra such as the AC susceptibility and the ARPES which may be directly compared with experiment. [1] Phys. Rev. Lett.89,047201/1-4 (2002)

Development of Carbon Based optically Transparent Electrodes from Pyrolyzed Photoresist for the Investigation of Phenomena at Electrified Carbon-Solution Interfaces

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

Donner, Sebastian

2007-01-01

The work presented herein describes a fundamental investigations of carbon as electrode material by using the pyrolysis of photoresist to create an optically transparent material. The development of these carbon-based optically transparent electrodes (C-OTEs) enables investigations of molecular interactions within the electrical double layer, processes that are central to a wide range of important phenomena, including the impact of changes in the surface charge density on adsorption. The electrochemical importance of carbon cannot be understated, having relevance to separations and detection by providing a wide potential window and low background current in addition to being low cost and light weight.more » The interactions that govern the processes at the carbon electrode surface has been studied extensively. A variety of publications from the laboratories of McCreery and Kinoshita provide in depth summaries about carbon and its many applications in electrochemistry. These studies reveal that defects, impurities, oxidation, and a variety of functional groups create adsorption sites on carbon surfaces with different characteristics. The interest in C-OTEs was sparked by the desire to study and understand the behavior of individual molecules at electrified interfaces. It draws on the earlier development of Electrochemically Modulated Liquid Chromatography (EMLC), which uses carbon as the stationary phase. EMLC takes advantage of changing the applied potential to the carbon electrode to influence the retention behavior of analytes. However, perspectives gained from, for example, chromatographic measurements reflect the integrated response of a large ensemble of potentially diverse interactions between the adsorbates and the carbon electrode. Considering the chemically and physically heterogeneous surface of electrode materials such as glassy carbon, the integrated response provides little insight into the interactions at a single molecule level. To investigate individual processes, they have developed C-OTEs in order to couple electrochemistry with single molecule spectroscopy (SMS). Like EMLC, the novel merger of SMS with electrochemistry is a prime example of how a hybrid method can open new and intriguing avenues that are of both fundamental and technological importance. They show that by taking the benefits of total internal reflection fluorescence microscopy (TIRFM) and incorporating carbon as electrode material observations central to the interactions between single DNA molecules and an electrified carbon surface can be delineated. Using TIRFM while applying a positive potential to the electrode, individual molecules can be observed as they reversibly and irreversibly adsorb to the carbon surface. The positive potential attracts the negatively charged DNA molecules to the electrode surface. Dye labels on the DNA within the evanescent wave are excited and their fluorescence is captured by an intensified charge coupled device (ICCD) camera. Results are therefore presented regarding the interactions of λ-DNA, 48,502 base pairs (48.5 kbp), HPV-16, 7.9 kbp, and 1 kbp fraction of pBR322 DNA. In addition to the influence of molecular size on adsorption, the fabrication, characterization, and more conventional spectroelectrochemical applications of these novel C-OTEs are presented.« less

Single molecule photobleaching (SMPB) technology for counting of RNA, DNA, protein and other molecules in nanoparticles and biological complexes by TIRF instrumentation.

PubMed

Zhang, Hui; Guo, Peixuan

2014-05-15

Direct counting of biomolecules within biological complexes or nanomachines is demanding. Single molecule counting using optical microscopy is challenging due to the diffraction limit. The single molecule photobleaching (SMPB) technology for direct counting developed by our team (Shu et al., 2007 [18]; Zhang et al., 2007 [19]) offers a simple and straightforward method to determine the stoichiometry of molecules or subunits within biocomplexes or nanomachines at nanometer scales. Stoichiometry is determined by real-time observation of the number of descending steps resulted from the photobleaching of individual fluorophore. This technology has now been used extensively for single molecule counting of protein, RNA, and other macromolecules in a variety of complexes or nanostructures. Here, we elucidate the SMPB technology, using the counting of RNA molecules within a bacteriophage phi29 DNA-packaging biomotor as an example. The method described here can be applied to the single molecule counting of other molecules in other systems. The construction of a concise, simple and economical single molecule total internal reflection fluorescence (TIRF) microscope combining prism-type and objective-type TIRF is described. The imaging system contains a deep-cooled sensitive EMCCD camera with single fluorophore detection sensitivity, a laser combiner for simultaneous dual-color excitation, and a Dual-View™ imager to split the multiple outcome signals to different detector channels based on their wavelengths. Methodology of the single molecule photobleaching assay used to elucidate the stoichiometry of RNA on phi29 DNA packaging motor and the mechanism of protein/RNA interaction are described. Different methods for single fluorophore labeling of RNA molecules are reviewed. The process of statistical modeling to reveal the true copy number of the biomolecules based on binomial distribution is also described. Copyright © 2014 Elsevier Inc. All rights reserved.

Mutiple Czochralski growth of silicon crystals from a single crucible

NASA Technical Reports Server (NTRS)

Lane, R. L.; Kachare, A. H.

1980-01-01

An apparatus for the Czochralski growth of silicon crystals is presented which is capable of producing multiple ingots from a single crucible. The growth chamber features a refillable crucible with a water-cooled, vacuum-tight isolation valve located between the pull chamber and the growth furnace tank which allows the melt crucible to always be at vacuum or low argon pressure when retrieving crystal or introducing recharge polysilicon feed stock. The grower can thus be recharged to obtain 100 kg of silicon crystal ingots from one crucible, and may accommodate crucibles up to 35 cm in diameter. Evaluation of the impurity contents and I-V characteristics of solar cells fabricated from seven ingots grown from two crucibles reveals a small but consistent decrease in cell efficiency from 10.4% to 9.6% from the first to the fourth ingot made in a single run, which is explained by impurity build-up in the residual melt. The crystal grower thus may offer economic benefits through the extension of crucible lifetime and the reduction of furnace downtime.

Single-Wall Carbon Nanotube Production by the Arc Process: A Parametric Study

NASA Technical Reports Server (NTRS)

Scott, Carl D.; Gorelik, Olga; Proft, William J.

2000-01-01

Single wall carbon nanotubes are produced using the arc discharge process. Graphite anodes are filled with a mixture of nickel and yttrium metallic powders, then vaporized by creating a high current arc. By varying the current, gap distance, and ambient pressure it is shown that the best yield of single wall carbon nanotubes is obtained within a narrow range of conditions. The relative yield and purity of the product are indicated semi-quantitatively from scanning electric microscopy (SEM) and thermogravimetric analysis (TGA). Two types of anodes have been investigated. The first is hollow and filled with a powder mixture of graphite, nickel and yttrium. The second is filled with a paste made of a mixture of metal nitrates, graphite powder and carbon adhesive, then reduced in an argon atmosphere at high temperature. Product purity and yield will be compared for the two types of anodes. The graphite in the anodes may have hydrogen attached in the pores. To remove this impurity anodes have been baked up to 1400 - 1500 C. The effect of baking the anodes on impurities in the product will be given.

Microscopic observation of magnon bound states and their dynamics.

PubMed

Fukuhara, Takeshi; Schauß, Peter; Endres, Manuel; Hild, Sebastian; Cheneau, Marc; Bloch, Immanuel; Gross, Christian

2013-10-03

The existence of bound states of elementary spin waves (magnons) in one-dimensional quantum magnets was predicted almost 80 years ago. Identifying signatures of magnon bound states has so far remained the subject of intense theoretical research, and their detection has proved challenging for experiments. Ultracold atoms offer an ideal setting in which to find such bound states by tracking the spin dynamics with single-spin and single-site resolution following a local excitation. Here we use in situ correlation measurements to observe two-magnon bound states directly in a one-dimensional Heisenberg spin chain comprising ultracold bosonic atoms in an optical lattice. We observe the quantum dynamics of free and bound magnon states through time-resolved measurements of two spin impurities. The increased effective mass of the compound magnon state results in slower spin dynamics as compared to single-magnon excitations. We also determine the decay time of bound magnons, which is probably limited by scattering on thermal fluctuations in the system. Our results provide a new way of studying fundamental properties of quantum magnets and, more generally, properties of interacting impurities in quantum many-body systems.

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

Patsha, Avinash, E-mail: avinash.phy@gmail.com, E-mail: dhara@igcar.gov.in; Dhara, Sandip; Tyagi, A. K.

The localized effect of impurities in single GaN nanowires in the sub-diffraction limit is reported using the study of lattice vibrational modes in the evanescent field of Au nanoparticle assisted tip enhanced Raman spectroscopy (TERS). GaN nanowires with the O impurity and the Mg dopants were grown by the chemical vapor deposition technique in the catalyst assisted vapor-liquid-solid process. Symmetry allowed Raman modes of wurtzite GaN are observed for undoped and doped nanowires. Unusually very strong intensity of the non-zone center zone boundary mode is observed for the TERS studies of both the undoped and the Mg doped GaN singlemore » nanowires. Surface optical mode of A{sub 1} symmetry is also observed for both the undoped and the Mg doped GaN samples. A strong coupling of longitudinal optical (LO) phonons with free electrons, however, is reported only in the O rich single nanowires with the asymmetric A{sub 1}(LO) mode. Study of the local vibration mode shows the presence of Mg as dopant in the single GaN nanowires.« less

SNSMIL, a real-time single molecule identification and localization algorithm for super-resolution fluorescence microscopy

PubMed Central

Tang, Yunqing; Dai, Luru; Zhang, Xiaoming; Li, Junbai; Hendriks, Johnny; Fan, Xiaoming; Gruteser, Nadine; Meisenberg, Annika; Baumann, Arnd; Katranidis, Alexandros; Gensch, Thomas

2015-01-01

Single molecule localization based super-resolution fluorescence microscopy offers significantly higher spatial resolution than predicted by Abbe’s resolution limit for far field optical microscopy. Such super-resolution images are reconstructed from wide-field or total internal reflection single molecule fluorescence recordings. Discrimination between emission of single fluorescent molecules and background noise fluctuations remains a great challenge in current data analysis. Here we present a real-time, and robust single molecule identification and localization algorithm, SNSMIL (Shot Noise based Single Molecule Identification and Localization). This algorithm is based on the intrinsic nature of noise, i.e., its Poisson or shot noise characteristics and a new identification criterion, QSNSMIL, is defined. SNSMIL improves the identification accuracy of single fluorescent molecules in experimental or simulated datasets with high and inhomogeneous background. The implementation of SNSMIL relies on a graphics processing unit (GPU), making real-time analysis feasible as shown for real experimental and simulated datasets. PMID:26098742

Research Update: Molecular electronics: The single-molecule switch and transistor

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

Sotthewes, Kai; Heimbuch, René, E-mail: r.heimbuch@utwente.nl; Kumar, Avijit

2014-01-01

In order to design and realize single-molecule devices it is essential to have a good understanding of the properties of an individual molecule. For electronic applications, the most important property of a molecule is its conductance. Here we show how a single octanethiol molecule can be connected to macroscopic leads and how the transport properties of the molecule can be measured. Based on this knowledge we have realized two single-molecule devices: a molecular switch and a molecular transistor. The switch can be opened and closed at will by carefully adjusting the separation between the electrical contacts and the voltage dropmore » across the contacts. This single-molecular switch operates in a broad temperature range from cryogenic temperatures all the way up to room temperature. Via mechanical gating, i.e., compressing or stretching of the octanethiol molecule, by varying the contact's interspace, we are able to systematically adjust the conductance of the electrode-octanethiol-electrode junction. This two-terminal single-molecule transistor is very robust, but the amplification factor is rather limited.« less

Stability-indicating HPLC Method for Simultaneous Determination of Terbutaline Sulphate, Bromhexine Hydrochloride and Guaifenesin

PubMed Central

Porel, A.; Haty, Sanjukta; Kundu, A.

2011-01-01

The aim of the present study was the development and subsequent validation of a simple, precise and stability-indicating reversed phase HPLC method for the simultaneous determination of guaifenesin, terbutaline sulphate and bromhexine hydrochloride in the presence of their potential impurities in a single run. The photolytic as well as hydrolytic impurities were detected as 3,5-dihydroxybenzoic acid, 3,5-dihydroxybenzaldehyde, 1-(3,5-dihydroxyphenyl)-2-[(1,1-dimethylethyl) amino]-ethanone from terbutaline, 2-methoxyphenol and an unknown impurity identified as (2RS)-3-(2-hydroxyphenoxy)-propane-1,2-diol from guaifenesin. The chromatographic separation of all the three active components and their impurities was achieved on Wakosil II column, using phosphate buffer (pH 3.0) and acetonitrile as mobile phase which was delivered initially in the ratio of 80:20 (v/v) for 18 min, then changed to 60:40 (v/v) for next 12 min, and finally equilibrated back to 80:20 (v/v) for 10 min. Other HPLC parameters were: Flow rate at 1.0 ml/min, detection wavelengths 248 and 280 nm, injection volume 10 μl. The calibration graphs plotted with five concentrations of each component were linear with a regression coefficient R2 >0.9999. The limit of detection and limit of quantitation were estimated for all the five impurities. The established method was then validated for linearity, precision, accuracy, and specificity and demonstrated to be applicable to the determination of the active ingredients in commercial and model cough syrup. No interference from the formulation excipients was observed. These results suggest that this LC method can be used for the determination of multiple active ingredients and their impurities in a cough and cold syrup. PMID:22131621

Stability-indicating HPLC Method for Simultaneous Determination of Terbutaline Sulphate, Bromhexine Hydrochloride and Guaifenesin.

PubMed

Porel, A; Haty, Sanjukta; Kundu, A

2011-01-01

The aim of the present study was the development and subsequent validation of a simple, precise and stability-indicating reversed phase HPLC method for the simultaneous determination of guaifenesin, terbutaline sulphate and bromhexine hydrochloride in the presence of their potential impurities in a single run. The photolytic as well as hydrolytic impurities were detected as 3,5-dihydroxybenzoic acid, 3,5-dihydroxybenzaldehyde, 1-(3,5-dihydroxyphenyl)-2-[(1,1-dimethylethyl) amino]-ethanone from terbutaline, 2-methoxyphenol and an unknown impurity identified as (2RS)-3-(2-hydroxyphenoxy)-propane-1,2-diol from guaifenesin. The chromatographic separation of all the three active components and their impurities was achieved on Wakosil II column, using phosphate buffer (pH 3.0) and acetonitrile as mobile phase which was delivered initially in the ratio of 80:20 (v/v) for 18 min, then changed to 60:40 (v/v) for next 12 min, and finally equilibrated back to 80:20 (v/v) for 10 min. Other HPLC parameters were: Flow rate at 1.0 ml/min, detection wavelengths 248 and 280 nm, injection volume 10 μl. The calibration graphs plotted with five concentrations of each component were linear with a regression coefficient R(2) >0.9999. The limit of detection and limit of quantitation were estimated for all the five impurities. The established method was then validated for linearity, precision, accuracy, and specificity and demonstrated to be applicable to the determination of the active ingredients in commercial and model cough syrup. No interference from the formulation excipients was observed. These results suggest that this LC method can be used for the determination of multiple active ingredients and their impurities in a cough and cold syrup.

Selective gas adsorption and I-V response of monolayer boron phosphide introduced by dopants: A first-principle study

NASA Astrophysics Data System (ADS)

Cheng, Yongfa; Meng, Ruishen; Tan, Chunjian; Chen, Xianping; Xiao, Jing

2018-01-01

Two-dimensional (2D) materials have gained tremendous research interests for gas sensing applications because of their ultrahigh theoretical specific surface areas and unique electronic properties. Here, we investigate the adsorption of CO, SO2, NH3, O2, NO and NO2 gas molecules on pure and doped boron phosphide (BP) systems using first-principles calculations to exploit their potential in gas sensing. Our results predict that all six gas molecules show stronger adsorption interactions on impurities-doped BP over the pristine monolayer BP. Al-doped BP shows the highest sensitivity to all gas molecules, but N-doped BP is more suitable as a sensing material for SO2, NO and NO2 due to the feasibility of desorption. We further calculated the current-voltage (I-V) relation by mean of nonequilibrium Green's function (NEGF) formalism. The I-V curves indicate that the electronic properties of the doping systems change significantly with gas adsorption by studying the nonparamagnetic molecules NH3 and the paramagnetic molecules NO, which can be more likely to be measured experimentally compared to graphene and phosphorene. This work explores the possibility of BP as a superior sensor through introducing the appropriate dopants.

Room-temperature ultrafast nonlinear spectroscopy of a single molecule

NASA Astrophysics Data System (ADS)

Liebel, Matz; Toninelli, Costanza; van Hulst, Niek F.

2018-01-01

Single-molecule spectroscopy aims to unveil often hidden but potentially very important contributions of single entities to a system's ensemble response. Albeit contributing tremendously to our ever growing understanding of molecular processes, the fundamental question of temporal evolution, or change, has thus far been inaccessible, thus painting a static picture of a dynamic world. Here, we finally resolve this dilemma by performing ultrafast time-resolved transient spectroscopy on a single molecule. By tracing the femtosecond evolution of excited electronic state spectra of single molecules over hundreds of nanometres of bandwidth at room temperature, we reveal their nonlinear ultrafast response in an effective three-pulse scheme with fluorescence detection. A first excitation pulse is followed by a phase-locked de-excitation pulse pair, providing spectral encoding with 25 fs temporal resolution. This experimental realization of true single-molecule transient spectroscopy demonstrates that two-dimensional electronic spectroscopy of single molecules is experimentally within reach.

Single Molecule Enzymology via Nanoelectronic Circuits

NASA Astrophysics Data System (ADS)

Collins, Philip

Traditional single-molecule techniques rely on fluorescence or force transduction to monitor conformational changes and biochemical activity. Recent demonstrations of single-molecule monitoring with electronic transistors are poised to add to the single-molecule research toolkit. The transistor-based technique is sensitive to the motion of single charged side chain residues and can transduce those motions with microsecond resolution, opening the doors to single-molecule enzymology with unprecedented resolution. Furthermore, the solid-state platform provides opportunities for parallelization in arrays and long-duration monitoring of one molecule's activity or processivity, all without the limitations caused by photo-oxidation or mutagenic fluorophore incorporation. This presentation will review some of these advantages and their particular application to DNA polymerase I processing single-stranded DNA templates. This research was supported financially by the NIH NCI (R01 CA133592-01), the NIH NIGMS (1R01GM106957-01) and the NSF (DMR-1104629 and ECCS-1231910).

Finding a Single Molecule in a Haystack: Optical Detection and Spectroscopy of Single Absorbers in Solids

DTIC Science & Technology

1989-08-18

CODES 18 SUBJECT TERMS (Continue on reverse if necessary and identify by block number) FIELD GROUP SUB-GROUP Single Molecule Detection Pentacene in p...and 10 additional pentacene molecules. This may be accomplished by- a combination of laser FM spectroscopy and either Stark or ultrasonic double...6099 408-927-2426 ABSTRACT: Single-absorber optical spectroscopy in solids is described for the case of finding a single pentacene molecule in a

Exploration of bulk and interface behavior of gas molecules and 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid using equilibrium and nonequilibrium molecular dynamics simulation and quantum chemical calculation.

PubMed

Yang, Quan; Achenie, Luke E K

2018-04-18

Ionic liquids (ILs) show brilliant performance in separating gas impurities, but few researchers have performed an in-depth exploration of the bulk and interface behavior of penetrants and ILs thoroughly. In this research, we have performed a study on both molecular dynamics (MD) simulation and quantum chemical (QC) calculation to explore the transport of acetylene and ethylene in the bulk and interface regions of 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]-[BF4]). The diffusivity, solubility and permeability of gas molecules in the bulk were researched with MD simulation first. The subdiffusion behavior of gas molecules is induced by coupling between the motion of gas molecules and the ions, and the relaxation processes of the ions after the disturbance caused by gas molecules. Then, QC calculation was performed to explore the optical geometry of ions, ion pairs and complexes of ions and penetrants, and interaction potential for pairs and complexes. Finally, nonequilibrium MD simulation was performed to explore the interface structure and properties of the IL-gas system and gas molecule behavior in the interface region. The research results may be used in the design of IL separation media.

Correlation between impurity distribution and location of ferroelectric domain walls in Nd : Mg : LiNbO 3 single crystal

NASA Astrophysics Data System (ADS)

Naumova, I. I.; Evlanova, N. F.; Blokhin, S. A.; Lavrishchev, S. V.

1998-04-01

Using selective chemical etching, scanning electron microscope (SEM) and wave dispersive X-ray (WDX) microanalysis we showed that the ferroelectric domain walls coincide with the maxima and minima Nd-impurity modulation in a periodically poled Nd : Mg : LiNbO 3 crystal grown by the Czochralski method along the normal to the (0 1 1¯ 2) face. Asymmetric form of the Nd-modulation produces nonequal positive and negative domains for one period. Variations of instantaneous rate of growth were estimated for facet and nonfacet crystal region in the framework of Burton-Prim-Slichter theory.

Parity Anomaly and Spin Transmutation in Quantum Spin Hall Josephson Junctions.

PubMed

Peng, Yang; Vinkler-Aviv, Yuval; Brouwer, Piet W; Glazman, Leonid I; von Oppen, Felix

2016-12-23

We study the Josephson effect in a quantum spin Hall system coupled to a localized magnetic impurity. As a consequence of the fermion parity anomaly, the spin of the combined system of impurity and spin-Hall edge alternates between half-integer and integer values when the superconducting phase difference across the junction advances by 2π. This leads to characteristic differences in the splittings of the spin multiplets by exchange coupling and single-ion anisotropy at phase differences, for which time-reversal symmetry is preserved. We discuss the resulting 8π-periodic (or Z_{4}) fractional Josephson effect in the context of recent experiments.

Investigating single molecule adhesion by atomic force spectroscopy.

PubMed

Stetter, Frank W S; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

2015-02-27

Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment.

Investigating Single Molecule Adhesion by Atomic Force Spectroscopy

PubMed Central

Stetter, Frank W. S.; Kienle, Sandra; Krysiak, Stefanie; Hugel, Thorsten

2015-01-01

Atomic force spectroscopy is an ideal tool to study molecules at surfaces and interfaces. An experimental protocol to couple a large variety of single molecules covalently onto an AFM tip is presented. At the same time the AFM tip is passivated to prevent unspecific interactions between the tip and the substrate, which is a prerequisite to study single molecules attached to the AFM tip. Analyses to determine the adhesion force, the adhesion length, and the free energy of these molecules on solid surfaces and bio-interfaces are shortly presented and external references for further reading are provided. Example molecules are the poly(amino acid) polytyrosine, the graft polymer PI-g-PS and the phospholipid POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine). These molecules are desorbed from different surfaces like CH3-SAMs, hydrogen terminated diamond and supported lipid bilayers under various solvent conditions. Finally, the advantages of force spectroscopic single molecule experiments are discussed including means to decide if truly a single molecule has been studied in the experiment. PMID:25867282

Development and Validation of a Precise, Single HPLC Method for the Determination of Tolperisone Impurities in API and Pharmaceutical Dosage Forms.

PubMed

Raju, Thummala Veera Raghava; Seshadri, Raja Kumar; Arutla, Srinivas; Mohan, Tharlapu Satya Sankarsana Jagan; Rao, Ivaturi Mrutyunjaya; Nittala, Someswara Rao

2013-01-01

A novel, sensitive, stability-indicating HPLC method has been developed for the quantitative estimation of Tolperisone-related impurities in both bulk drugs and pharmaceutical dosage forms. Effective chromatographic separation was achieved on a C18 stationary phase with a simple mobile phase combination delivered in a simple gradient programme, and quantitation was by ultraviolet detection at 254 nm. The mobile phase consisted of a buffer and acetonitrile delivered at a flow rate 1.0 ml/min. The buffer consisted of 0.01 M potassium dihydrogen phosphate with the pH adjusted to 8.0 by using diethylamine. In the developed HPLC method, the resolution between Tolperisone and its four potential impurities was found to be greater than 2.0. Regression analysis showed an R value (correlation coefficient) of greater than 0.999 for the Tolperisone impurities. This method was capable of detecting all four impurities of Tolperisone at a level of 0.19 μg/mL with respect to the test concentration of 1000 μg/mL for a 10 µl injection volume. The tablets were subjected to the stress conditions of hydrolysis, oxidation, photolysis, and thermal degradation. Considerable degradation was found to occur in base hydrolysis, water hydrolysis, and oxidation. The stress samples were assayed against a qualified reference standard and the mass balance was found to be close to 100%. The established method was validated and found to be linear, accurate, precise, specific, robust, and rugged.

Development and validation of an ICP-MS method for the determination of elemental impurities in TP-6076 active pharmaceutical ingredient (API) according to USP 〈232〉/〈233〉.

PubMed

Chahrour, Osama; Malone, John; Collins, Mark; Salmon, Vrushali; Greenan, Catherine; Bombardier, Amy; Ma, Zhongze; Dunwoody, Nick

2017-10-25

The new guidelines of the United States pharmacopeia (USP), European pharmacopeia (EP) and international conference on harmonization (ICH) regulating elemental impurities limits in pharmaceuticals signify the end of unspecific analysis of metals as outlined in USP 〈231〉. The new guidelines specify both daily doses and concentration/limits of elemental impurities in pharmaceutical final products, active pharmaceutical ingredients (API) and excipients. In chapter USP 〈233〉 method implementation, validation and quality control during the analytical process are described. We herein report the use of a stabilising matrix that overcomes low spike recovery problem encountered with Os and allows the determination of all USP required elemental impurities (As, Cd, Hg, Pb, V, Cr, Ni, Mo, Cu, Pt, Pd, Ru, Rh, Os and Ir) in a single analysis. The matrix was used in the validation of a method to determine elemental impurities in TP-6076 active pharmaceutical ingredient (API) by ICP-MS according to the procedures defined in USP〈233〉 and to GMP requirements. This validation will support the regulatory submission of TP-6076 which is a novel tetracycline analogue effective against the most urgent multidrug-resistant gram-negative bacteria. Evaluation of TP-6076 in IND-enabling toxicology studies has led to the initiation of a phase 1 clinical trial. Copyright © 2017 Elsevier B.V. All rights reserved.

VACUUM TRAP

DOEpatents

Gordon, H.S.

1959-09-15

An improved adsorption vacuum trap for use in vacuum systems was designed. The distinguishing feature is the placement of a plurality of torsionally deformed metallic fins within a vacuum jacket extending from the walls to the central axis so that substantially all gas molecules pass through the jacket will impinge upon the fin surfaces. T fins are heated by direct metallic conduction, thereby ol taining a uniform temperature at the adeorbing surfaces so that essentially all of the condensible impurities from the evacuating gas are removed from the vacuum system.

Voltage-Driven Conformational Switching with Distinct Raman Signature in a Single-Molecule Junction.

PubMed

Bi, Hai; Palma, Carlos-Andres; Gong, Yuxiang; Hasch, Peter; Elbing, Mark; Mayor, Marcel; Reichert, Joachim; Barth, Johannes V

2018-04-11

Precisely controlling well-defined, stable single-molecule junctions represents a pillar of single-molecule electronics. Early attempts to establish computing with molecular switching arrays were partly challenged by limitations in the direct chemical characterization of metal-molecule-metal junctions. While cryogenic scanning probe studies have advanced the mechanistic understanding of current- and voltage-induced conformational switching, metal-molecule-metal conformations are still largely inferred from indirect evidence. Hence, the development of robust, chemically sensitive techniques is instrumental for advancement in the field. Here we probe the conformation of a two-state molecular switch with vibrational spectroscopy, while simultaneously operating it by means of the applied voltage. Our study emphasizes measurements of single-molecule Raman spectra in a room-temperature stable single-molecule switch presenting a signal modulation of nearly 2 orders of magnitude.

Analyzing Single-Molecule Time Series via Nonparametric Bayesian Inference

PubMed Central

Hines, Keegan E.; Bankston, John R.; Aldrich, Richard W.

2015-01-01

The ability to measure the properties of proteins at the single-molecule level offers an unparalleled glimpse into biological systems at the molecular scale. The interpretation of single-molecule time series has often been rooted in statistical mechanics and the theory of Markov processes. While existing analysis methods have been useful, they are not without significant limitations including problems of model selection and parameter nonidentifiability. To address these challenges, we introduce the use of nonparametric Bayesian inference for the analysis of single-molecule time series. These methods provide a flexible way to extract structure from data instead of assuming models beforehand. We demonstrate these methods with applications to several diverse settings in single-molecule biophysics. This approach provides a well-constrained and rigorously grounded method for determining the number of biophysical states underlying single-molecule data. PMID:25650922

Challenges for single molecule electronic devices with nanographene and organic molecules. Do single molecules offer potential as elements of electronic devices in the next generation?

NASA Astrophysics Data System (ADS)

Enoki, Toshiaki; Kiguchi, Manabu

2018-03-01

Interest in utilizing organic molecules to fabricate electronic materials has existed ever since organic (molecular) semiconductors were first discovered in the 1950s. Since then, scientists have devoted serious effort to the creation of various molecule-based electronic systems, such as molecular metals and molecular superconductors. Single-molecule electronics and the associated basic science have emerged over the past two decades and provided hope for the development of highly integrated molecule-based electronic devices in the future (after the Si-based technology era has ended). Here, nanographenes (nano-sized graphene) with atomically precise structures are among the most promising molecules that can be utilized for electronic/spintronic devices. To manipulate single small molecules for an electronic device, a single molecular junction has been developed. It is a powerful tool that allows even small molecules to be utilized. External electric, magnetic, chemical, and mechanical perturbations can change the physical and chemical properties of molecules in a way that is different from bulk materials. Therefore, the various functionalities of molecules, along with changes induced by external perturbations, allows us to create electronic devices that we cannot create using current top-down Si-based technology. Future challenges that involve the incorporation of condensed matter physics, quantum chemistry calculations, organic synthetic chemistry, and electronic device engineering are expected to open a new era in single-molecule device electronic technology.

Ultrasensitive Laser Spectroscopy in Solids: Statistical Fine Structure and Single-Molecule Detection

DTIC Science & Technology

1990-03-28

observation, detection of the optical absorption of a single pentacene molecule in a p-terphenyl crystal, opens the door to new studies of single local ...produce appreciable quadratic Stark shifting. Such effects would greatly perturb the local field around the pentacene molecule, making detection of the...of the local surroundings of pentacene molecules with single injected charge carriers nearby may become an interesting field; however, for the

Single-molecule electronics: Cooling individual vibrational modes by the tunneling current.

PubMed

Lykkebo, Jacob; Romano, Giuseppe; Gagliardi, Alessio; Pecchia, Alessandro; Solomon, Gemma C

2016-03-21

Electronic devices composed of single molecules constitute the ultimate limit in the continued downscaling of electronic components. A key challenge for single-molecule electronics is to control the temperature of these junctions. Controlling heating and cooling effects in individual vibrational modes can, in principle, be utilized to increase stability of single-molecule junctions under bias, to pump energy into particular vibrational modes to perform current-induced reactions, or to increase the resolution in inelastic electron tunneling spectroscopy by controlling the life-times of phonons in a molecule by suppressing absorption and external dissipation processes. Under bias the current and the molecule exchange energy, which typically results in heating of the molecule. However, the opposite process is also possible, where energy is extracted from the molecule by the tunneling current. Designing a molecular "heat sink" where a particular vibrational mode funnels heat out of the molecule and into the leads would be very desirable. It is even possible to imagine how the vibrational energy of the other vibrational modes could be funneled into the "cooling mode," given the right molecular design. Previous efforts to understand heating and cooling mechanisms in single molecule junctions have primarily been concerned with small models, where it is unclear which molecular systems they correspond to. In this paper, our focus is on suppressing heating and obtaining current-induced cooling in certain vibrational modes. Strategies for cooling vibrational modes in single-molecule junctions are presented, together with atomistic calculations based on those strategies. Cooling and reduced heating are observed for two different cooling schemes in calculations of atomistic single-molecule junctions.

Syntheses, Characterizations, and Applications of Molecular Metal Wires and Functional Nanomaterials

DTIC Science & Technology

2009-12-22

challenges Conductance of single molecules Concluding Remarks...values of single -molecule conductance for such pentaruthenium EMACs, other triruthenium and trirhodium EMACs (Dalton Trans. 2009, 2623) were obtained...a voltage-activated switch, or a single -molecule transistor. Among the molecules reported in this research field,1 EMACs2 are particularly

Optical-nanofiber-based interface for single molecules

NASA Astrophysics Data System (ADS)

Skoff, Sarah M.; Papencordt, David; Schauffert, Hardy; Bayer, Bernhard C.; Rauschenbeutel, Arno

2018-04-01

Optical interfaces for quantum emitters are a prerequisite for implementing quantum networks. Here, we couple single molecules to the guided modes of an optical nanofiber. The molecules are embedded within a crystal that provides photostability and, due to the inhomogeneous broadening, a means to spectrally address single molecules. Single molecules are excited and detected solely via the nanofiber interface without the requirement of additional optical access. In this way, we realize a fully fiber-integrated system that is scalable and may become a versatile constituent for quantum hybrid systems.

SISGR: Room Temperature Single-Molecule Detection and Imaging by Stimulated Emission Microscopy

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

Xie, Xiaoliang Sunney

Single-molecule spectroscopy has made considerable impact on many disciplines including chemistry, physics, and biology. To date, most single-molecule spectroscopy work is accomplished by detecting fluorescence. On the other hand, many naturally occurring chromophores, such as retinal, hemoglobin and cytochromes, do not have detectable fluorescence. There is an emerging need for single-molecule spectroscopy techniques that do not require fluorescence. In the last proposal period, we have successfully demonstrated stimulated emission microscopy, single molecule absorption, and stimulated Raman microscopy based on a high-frequency modulation transfer technique. These first-of-a- kind new spectroscopy/microscopy methods tremendously improved our ability to observe molecules that fluorescence weakly,more » even to the limit of single molecule detection for absorption measurement. All of these methods employ two laser beams: one (pump beam) excites a single molecule to a real or virtual excited state, and the other (probe beam) monitors the absorption/emission property of the single. We extract the intensity change of the probe beam with high sensitivity by implementing a high-frequency phase-sensitive detection scheme, which offers orders of magnitude improvement in detection sensitivity over direct absorption/emission measurement. However, single molecule detection based on fluorescence or absorption is fundamentally limited due to their broad spectral response. It is important to explore other avenues in single molecule detection and imaging which provides higher molecular specificity for studying a wide variety of heterogeneous chemical and biological systems. This proposal aimed to achieve single-molecule detection sensitivity with near resonance stimulated Raman scattering (SRS) microscopy. SRS microscopy was developed in our lab as a powerful technique for imaging heterogeneous samples based on their intrinsic vibrational contrasts, which provides much higher molecular specificity than absorption and fluorescence. Current sensitivity limit of SRS microscopy has not yet reached single molecule detection. We proposed to capitalize on our state-of-the-art SRS microscopy and develop near-resonance enhanced SRS for single molecule detection of carotenoids and heme proteins. The specific aims we pursued are: (1) building the next SRS generation microscope that utilizes near resonance enhancement to allow detection and imaging of single molecules with undetectable fluorescence, such as -carotene. (2) using near-resonance SRS as a contrast mechanism to study dye-sensitize semiconductor interface, elucidating the heterogeneous electron ejection kinetics with high spatial and temporal resolution. (3) studying the binding and unbinding of oxygen in single hemoglobin molecules in order to gain molecular level understanding of the long-standing issue of cooperativity. The new methods developed in the fund period of this grant have advanced the detection sensitivity in many aspects. Near-resonance SRS improved the signal by using shorter wavelengths for SRS microscopy. Frequency modulation and multi-color SRS target the reduction of background to improve the chemical specificity of SRS while maintaining the high imaging speed. Time-domain coherent Raman scattering microscopy targets to reduce the noise floor of coherent Raman microscopy. These methods have already demonstrated first-of-a-kind new applications in biology and medical research. However, we are still one order of magnitude away from single molecule limit. It is important to continue to improve the laser specification and develop new imaging methods to finally achieve label-free single molecule microscopy.« less

Accurate Quantification of microRNA via Single Strand Displacement Reaction on DNA Origami Motif

PubMed Central

Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can

2013-01-01

DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs. PMID:23990889

Single Molecule Spectral Diffusion in a Solid Detected Via Fluorescence Spectroscopy

DTIC Science & Technology

1991-10-15

other local fields) at the position of the molecule, the spectral jumps may occur because the class II pentacene molecules are coupled to an...and identify by block number) FIELD jGROUP SUB-GROUP_ Single molecule spectroscopy Precision detection Spectral diffusion, Pentacene in p-terphenyl 19...significant increases in detection sensitivity for single pentacene molecules in crystals of p-terphenyl at low temperatures. With the increased signal to

Formation of Methane Hydrate in the Presence of Natural and Synthetic Nanoparticles

PubMed Central

2018-01-01

Natural gas hydrates occur widely on the ocean-bed and in permafrost regions, and have potential as an untapped energy resource. Their formation and growth, however, poses major problems for the energy sector due to their tendency to block oil and gas pipelines, whereas their melting is viewed as a potential contributor to climate change. Although recent advances have been made in understanding bulk methane hydrate formation, the effect of impurity particles, which are always present under conditions relevant to industry and the environment, remains an open question. Here we present results from neutron scattering experiments and molecular dynamics simulations that show that the formation of methane hydrate is insensitive to the addition of a wide range of impurity particles. Our analysis shows that this is due to the different chemical natures of methane and water, with methane generally excluded from the volume surrounding the nanoparticles. This has important consequences for our understanding of the mechanism of hydrate nucleation and the design of new inhibitor molecules. PMID:29401390

Insight into unusual impurity absorbability of GeO(2) in GeO(2)∕Ge stacks.

PubMed

Ogawa, Shingo; Suda, Taichi; Yamamoto, Takashi; Kutsuki, Katsuhiro; Hideshima, Iori; Hosoi, Takuji; Shimura, Takayoshi; Watanabe, Heiji

2011-10-03

Adsorbed species and its diffusion behaviors in GeO(2)∕Ge stacks, which are future alternative metal-oxide-semiconductor (MOS) materials, have been investigated using various physical analyses. We clarified that GeO(2) rapidly absorbs moisture in air just after its exposure. After the absorbed moisture in GeO(2) reaches a certain limit, the GeO(2) starts to absorb some organic molecules, which is accompanied by a structural change in GeO(2) to form a partial carbonate or hydroxide. We also found that the hydrogen distribution in GeO(2) shows intrinsic characteristics, indicative of different diffusion behaviors at the surface and at the GeO(2)∕Ge interface. Because the impurity absorbability of GeO(2) has a great influence on the electrical properties in Ge-MOS devices, these results provide valuable information in realizing high quality GeO(2)∕Ge stacks for the actual use of Ge-MOS technologies.

Oxygen Impurities Link Bistability and Magnetoresistance in Organic Spin Valves.

PubMed

Bergenti, Ilaria; Borgatti, Francesco; Calbucci, Marco; Riminucci, Alberto; Cecchini, Raimondo; Graziosi, Patrizio; MacLaren, Donald A; Giglia, Angelo; Rueff, Jean Pascal; Céolin, Denis; Pasquali, Luca; Dediu, Valentin

2018-03-07

Vertical crossbar devices based on manganite and cobalt injecting electrodes and a metal-quinoline molecular transport layer are known to manifest both magnetoresistance (MR) and electrical bistability. The two effects are strongly interwoven, inspiring new device applications such as electrical control of the MR and magnetic modulation of bistability. To explain the device functionality, we identify the mechanism responsible for electrical switching by associating the electrical conductivity and the impedance behavior with the chemical states of buried layers obtained by in operando photoelectron spectroscopy. These measurements revealed that a significant fraction of oxygen ions migrate under voltage application, resulting in a modification of the electronic properties of the organic material and of the oxidation state of the interfacial layer with the ferromagnetic contacts. Variable oxygen doping of the organic molecules represents the key element for correlating bistability and MR, and our measurements provide the first experimental evidence in favor of the impurity-driven model describing the spin transport in organic semiconductors in similar devices.

Noncatalytic transformation of the crude lipid of ChlorellaI vulgaris into fatty acid methyl ester (FAME) with charcoal via a thermo-chemical process.

PubMed

Kwon, Eilhann E; Jeon, Young Jae; Yi, Haakrho

2013-02-01

The noncatalytic transformation of the crude lipid of Chlorella vulgaris (C. vulgaris) into fatty acid methyl ester (FAME) via a thermo-chemical process was mainly investigated in this work. The crude lipid of C. vulgaris was recovered by means of solvent extraction from C. vulgaris cultivated in a raceway pond. The conventional catalyzed transesterification of crude lipid of C. vulgaris is notably inhibited by the impurities contained in the crude lipid of C. vulgaris. These impurities are inevitably derived from the solvent extraction process for C. vulgaris. However, this work presents the noncatalytic transesterification of microalgal lipid into FAME, which could be an alternative option. For example, the noncatalytic transformation of microalgal lipid into FAME provides evidence that the esterification of free fatty acids (FFAs) and the transesterification of triglycerides can be combined into a single step less susceptible to the impurities and with a high conversion efficiency (∼97%). Copyright © 2012 Elsevier Ltd. All rights reserved.

Preparation of special purity Ge - S - I and Ge - Se - I glasses

NASA Astrophysics Data System (ADS)

Velmuzhov, A. P.; Sukhanov, M. V.; Shiryaev, V. S.; Kotereva, T. V.; Snopatin, G. E.; Churbanov, M. F.

2017-05-01

The paper considers the new approaches for the production of special pure Ge - S - I and Ge - Se - I glasses via the germanium(IV) iodide, germanium(II) sulfide, as well as the Ge2S3, Ge2S3I2 and Ge2Se3I2 glassy alloys. The glass samples containing 0.03-0.17 ppm(wt) hydrogen impurity in the form of SH-group, 0.04-0.15 ppm(wt) hydrogen impurity in the form of SeH-group, and 0.5-7.8 ppm(wt) oxygen impurity in the form of Ge-O were produced. Using a crucible technique, the single-index [GeSe4]95I5 glass fibers of 300-400 μm diameter were drawn. The minimum optical losses in the best fiber were 1.7 dB/m at a wavelength of 5.5 μm; the background optical losses were within 2-3 dB/m in the spectral range of 2.5-8 μm.

Kerr effect from diffractive skew scattering in chiral px +/- ipy superconductors

NASA Astrophysics Data System (ADS)

König, Elio; Levchenko, Alex

We calculate the temperature dependent anomalous ac Hall conductance σH (Ω , T) for a two-dimensional chiral p-wave superconductor. This quantity determines the polar Kerr effect, as it was observed in Sr2RuO4. We concentrate on a single band model with arbitrary isotropic dispersion relation subjected to rare, weak impurities treated in the Born approximation. As we explicitly show by detailed computation, previously omitted contributions to extrinsic part of an anomalous Hall response, physically originating from diffractive skew scattering on quantum impurity complexes, appear to the leading order in impurity concentration. By direct comparison with published results from the literature we demonstrate the relevance of our findings for the interpretation of the Kerr effect measurements in superconductors. This work was financially supported in part by NSF Grants No. DMR-1606517 and ECCS-1560732 and at U of Wisconsin by the Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation.

Molecular dynamics simulation of metallic impurity diffusion in liquid lead-bismuth eutectic (LBE)

NASA Astrophysics Data System (ADS)

Gao, Yun; Takahashi, Minoru; Cavallotti, Carlo; Raos, Guido

2018-04-01

Corrosion of stainless steels by lead-bismuth eutectic (LBE) is an important problem which depends, amongst other things, on the diffusion of the steel components inside this liquid alloy. Here we present the results of classical molecular dynamics simulations of the diffusion of Fe and Ni within LBE. The simulations complement experimental studies of impurity diffusion by our group and provide an atomic-level understanding of the relevant diffusion phenomena. They are based on the embedded atom method (EAM) to represent many-body interactions among atoms. The EAM potentials employed in our simulations have been validated against ab initio density functional calculations. We show that the experimental and simulation results for the temperature-dependent viscosity of LBE and the impurity diffusion coefficients can be reconciled by assuming that the Ni and Fe diffuse mainly as nanoscopic clusters below 1300 K. The average Fe and Ni cluster sizes decrease with increasing the temperature and there is essentially single-atom diffusion at higher temperatures.

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].

Spontaneous emission near the edge of a photonic band gap

NASA Astrophysics Data System (ADS)

John, Sajeev; Quang, Tran

1994-08-01

The spectral and dynamical features of spontaneous emission from two and three-level atoms in which one transition frequency lay near the edge of a photonic band gap (PBG) were derived. These features included temporal oscillations, fractionalized steady-state atomic population on the excited state, spectral splitting and subnatural bandwidth. The effect of N-1 unexcited atoms were also taken into account. The direct consequences of photon localization as embodied in the photon-atom bound state were observed. One feasible experimental accomplishment of these effects may ensue from laser-cooled atoms in the void regions of a PBG medium. Another option is the application of an organic impurity molecule such as pentacene. Such molecules were known to show extremely narrow linewidths when placed in fitting solid hosts.

Interpretation of the molecular fluxes measured at the periphery of a magnetically confined plasma

NASA Astrophysics Data System (ADS)

Liu-Hinz, C.; Terreault, B.; Martin, F.

1995-04-01

A new instrument ("Variable Geometry Sniffer Probe" or VGSP), allowing one to sample and mass analyse atoms, ions or molecules moving in different directions and at different locations at the periphery of a plasma, has been built and used in plasma edge studies in the TdeV tokamak. Three different regimes of particle sampling have been identified. First, the VGSP can measure the fluxes of hydrogen and impurity molecules issuing from the walls. Second, it has the capability of detecting low energy charge-exchange and Franck-Condon neutrals. Finally, there is a parallel ion flux sampling regime, for which it is shown that both the connection lengths to the divertor plates and the X × B plasma flows induced by edge electric fields play major roles.

Protein crystals and their growth

NASA Technical Reports Server (NTRS)

Chernov, Alexander A.

2003-01-01

Recent results on the associations between protein molecules in crystal lattices, crystal-solution surface energy, elastic properties, strength, and spontaneous crystal cracking are reviewed and discussed. In addition, some basic approaches to understanding the solubility of proteins are followed by an overview of crystal nucleation and growth. It is argued that variability of mixing in batch crystallization may be a source of the variation in the number of crystals ultimately appearing in the sample. The frequency at which new molecules join a crystal lattice is measured by the kinetic coefficient and is related to the observed crystal growth rate. Numerical criteria used to discriminate diffusion- and kinetic-limited growth are discussed on this basis. Finally, the creation of defects is discussed with an emphasis on the role of impurities and convection on macromolecular crystal perfection.

Single Molecule Raman Spectroscopy Under High Pressure

NASA Astrophysics Data System (ADS)

Fu, Yuanxi; Dlott, Dana

2014-06-01

Pressure effects on surface-enhanced Raman scattering spectra of Rhdoamine 6G adsorbed on silver nanoparticle surfaces was studied using a confocal Raman microscope. Colloidal silver nanoparticles were treated with Rhodamine 6G (R6G) and its isotopically substituted partner, R6G-d4. Mixed isotopomers let us identify single-molecule spectra, since multiple-molecule spectra would show vibrational transitions from both species. The nanoparticles were embedded into a poly vinyl alcohol film, and loaded into a diamond anvil cell for the high-pressure Raman scattering measurement. Argon was the pressure medium. Ambient pressure Raman scattering spectra showed few single-molecule spectra. At moderately high pressure ( 1GPa), a surprising effect was observed. The number of sites with observable spectra decreased dramatically, and most of the spectra that could be observed were due to single molecules. The effects of high pressure suppressed the multiple-molecule Raman sites, leaving only the single-molecule sites to be observed.

Computer systems for annotation of single molecule fragments

DOEpatents

Schwartz, David Charles; Severin, Jessica

2016-07-19

There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

Extracting Models in Single Molecule Experiments

NASA Astrophysics Data System (ADS)

Presse, Steve

2013-03-01

Single molecule experiments can now monitor the journey of a protein from its assembly near a ribosome to its proteolytic demise. Ideally all single molecule data should be self-explanatory. However data originating from single molecule experiments is particularly challenging to interpret on account of fluctuations and noise at such small scales. Realistically, basic understanding comes from models carefully extracted from the noisy data. Statistical mechanics, and maximum entropy in particular, provide a powerful framework for accomplishing this task in a principled fashion. Here I will discuss our work in extracting conformational memory from single molecule force spectroscopy experiments on large biomolecules. One clear advantage of this method is that we let the data tend towards the correct model, we do not fit the data. I will show that the dynamical model of the single molecule dynamics which emerges from this analysis is often more textured and complex than could otherwise come from fitting the data to a pre-conceived model.

Smart SERS Hot Spots: Single Molecules Can Be Positioned in a Plasmonic Nanojunction Using Host-Guest Chemistry.

PubMed

Kim, Nam Hoon; Hwang, Wooseup; Baek, Kangkyun; Rohman, Md Rumum; Kim, Jeehong; Kim, Hyun Woo; Mun, Jungho; Lee, So Young; Yun, Gyeongwon; Murray, James; Ha, Ji Won; Rho, Junsuk; Moskovits, Martin; Kim, Kimoon

2018-04-04

Single-molecule surface-enhanced Raman spectroscopy (SERS) offers new opportunities for exploring the complex chemical and biological processes that cannot be easily probed using ensemble techniques. However, the ability to place the single molecule of interest reliably within a hot spot, to enable its analysis at the single-molecule level, remains challenging. Here we describe a novel strategy for locating and securing a single target analyte in a SERS hot spot at a plasmonic nanojunction. The "smart" hot spot was generated by employing a thiol-functionalized cucurbit[6]uril (CB[6]) as a molecular spacer linking a silver nanoparticle to a metal substrate. This approach also permits one to study molecules chemically reluctant to enter the hot spot, by conjugating them to a moiety, such as spermine, that has a high affinity for CB[6]. The hot spot can accommodate at most a few, and often only a single, analyte molecule. Bianalyte experiments revealed that one can reproducibly treat the SERS substrate such that 96% of the hot spots contain a single analyte molecule. Furthermore, by utilizing a series of molecules each consisting of spermine bound to perylene bisimide, a bright SERS molecule, with polymethylene linkers of varying lengths, the SERS intensity as a function of distance from the center of the hot spot could be measured. The SERS enhancement was found to decrease as 1 over the square of the distance from the center of the hot spot, and the single-molecule SERS cross sections were found to increase with AgNP diameter.

Molecular simulation of the thermophysical properties and phase behaviour of impure CO2 relevant to CCS.

PubMed

Cresswell, Alexander J; Wheatley, Richard J; Wilkinson, Richard D; Graham, Richard S

2016-10-20

Impurities from the CCS chain can greatly influence the physical properties of CO 2 . This has important design, safety and cost implications for the compression, transport and storage of CO 2 . There is an urgent need to understand and predict the properties of impure CO 2 to assist with CCS implementation. However, CCS presents demanding modelling requirements. A suitable model must both accurately and robustly predict CO 2 phase behaviour over a wide range of temperatures and pressures, and maintain that predictive power for CO 2 mixtures with numerous, mutually interacting chemical species. A promising technique to address this task is molecular simulation. It offers a molecular approach, with foundations in firmly established physical principles, along with the potential to predict the wide range of physical properties required for CCS. The quality of predictions from molecular simulation depends on accurate force-fields to describe the interactions between CO 2 and other molecules. Unfortunately, there is currently no universally applicable method to obtain force-fields suitable for molecular simulation. In this paper we present two methods of obtaining force-fields: the first being semi-empirical and the second using ab initio quantum-chemical calculations. In the first approach we optimise the impurity force-field against measurements of the phase and pressure-volume behaviour of CO 2 binary mixtures with N 2 , O 2 , Ar and H 2 . A gradient-free optimiser allows us to use the simulation itself as the underlying model. This leads to accurate and robust predictions under conditions relevant to CCS. In the second approach we use quantum-chemical calculations to produce ab initio evaluations of the interactions between CO 2 and relevant impurities, taking N 2 as an exemplar. We use a modest number of these calculations to train a machine-learning algorithm, known as a Gaussian process, to describe these data. The resulting model is then able to accurately predict a much broader set of ab initio force-field calculations at comparatively low numerical cost. Although our method is not yet ready to be implemented in a molecular simulation, we outline the necessary steps here. Such simulations have the potential to deliver first-principles simulation of the thermodynamic properties of impure CO 2 , without fitting to experimental data.

Deposition and properties of cobalt- and ruthenium-based ultra-thin films

NASA Astrophysics Data System (ADS)

Henderson, Lucas Benjamin

Future copper interconnect systems will require replacement of the materials that currently comprise both the liner layer(s) and the capping layer. Ruthenium has previously been considered as a material that could function as a single material liner, however its poor ability to prevent copper diffusion makes it incompatible with liner requirements. A recently described chemical vapor deposition route to amorphous ruthenium-phosphorus alloy films could correct this problem by eliminating the grain boundaries found in pure ruthenium films. Bias-temperature stressing of capacitor structures using 5 nm ruthenium-phosphorus film as a barrier to copper diffusion and analysis of the times-to-failure at accelerated temperature and field conditions implies that ruthenium-phosphorus performs acceptably as a diffusion barrier for temperatures above 165°C. The future problems associated with the copper capping layer are primarily due to the poor adhesion between copper and the current Si-based capping layers. Cobalt, which adheres well to copper, has been widely proposed to replace the Si-based materials, but its ability to prevent copper diffusion must be improved if it is to be successfully implemented in the interconnect. Using a dual-source chemistry of dicobaltoctacarbonyl and trimethylphosphine at temperatures from 250-350°C, amorphous cobalt-phosphorus can be deposited by chemical vapor deposition. The films contain elemental cobalt and phosphorus, plus some carbon impurity, which is incorporated in the film as both graphitic and carbidic (bonded to cobalt) carbon. When deposited on copper, the adhesion between the two materials remains strong despite the presence of phosphorus and carbon at the interface, but the selectivity for growth on copper compared to silicon dioxide is poor and must be improved prior to consideration for application in interconnect systems. A single molecule precursor containing both cobalt and phosphorus atoms, tetrakis(trimethylphosphine)cobalt(0), yields cobalt-phosphorus films without any co-reactant. However, the molecule does not contain sufficient amounts of amorphizing agents to fully eliminate grain boundaries, and the resulting film is nanocrystalline.

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

PubMed

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

2017-04-01

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

Single molecule techniques in DNA repair: A primer

PubMed Central

Hughes, Craig D.; Simons, Michelle; Mackenzie, Cassidy E.; Van Houten, Bennett; Kad, Neil M.

2016-01-01

A powerful new approach has become much more widespread and offers insights into aspects of DNA repair unattainable with billions of molecules. Single molecule techniques can be used to image, manipulate or characterize the action of a single repair protein on a single strand of DNA. This allows search mechanisms to be probed, and the effects of force to be understood. These physical aspects can dominate a biochemical reaction, where at the ensemble level their nuances are obscured. In this paper we discuss some of the many technical advances that permit study at the single molecule level. We focus on DNA repair to which these techniques are actively being applied. DNA repair is also a process that encompasses so much of what single molecule studies benefit – searching for targets, complex formation, sequential biochemical reactions and substrate hand-off to name just a few. We discuss how single molecule biophysics is poised to transform our understanding of biological systems, in particular DNA repair. PMID:24819596

Electric dipole moments of nanosolvated acid molecules in water clusters.

PubMed

Guggemos, Nicholas; Slavíček, Petr; Kresin, Vitaly V

2015-01-30

The electric dipole moments of (H2O)nDCl (n=3-9) clusters have been measured by the beam-deflection method. Reflecting the (dynamical) charge distribution within the system, the dipole moment contributes information about the microscopic structure of nanoscale solvation. The addition of a DCl molecule to a water cluster results in a strongly enhanced susceptibility. There is evidence for a noticeable rise in the dipole moment occurring at n≈5-6. This size is consistent with predictions for the onset of ionic dissociation. Additionally, a molecular-dynamics model suggests that even with a nominally bound impurity an enhanced dipole moment can arise due to the thermal and zero-point motion of the proton and the water molecules. The experimental measurements and the calculations draw attention to the importance of fluctuations in defining the polarity of water-based nanoclusters and generally to the essential role played by motional effects in determining the response of fluxional nanoscale systems under realistic conditions.

Probe-type of superconductivity by impurity in materials with short coherence length: the s-wave and η-wave phases study

NASA Astrophysics Data System (ADS)

Ptok, Andrzej; Jerzy Kapcia, Konrad

2015-04-01

The effects of a single non-magnetic impurity on superconducting states in the Penson-Kolb-Hubbard model have been analyzed. The investigations have been performed within the Hartree-Fock mean field approximation in two steps: (i) the homogeneous system is analysed using the Bogoliubov transformation, whereas (ii) the inhomogeneous system is investigated by self-consistent Bogoliubov-de Gennes equations (with the exact diagonalization and the kernel polynomial method). We analysed both signs of the pair hopping, which correspond to s-wave and η-wave superconductivity. Our results show that an enhancement of the local superconducting gap at the impurity-site occurs for both cases. We obtained that Cooper pairs are scattered (at the impurity site) into the states which are from the neighborhoods of the states, which are commensurate ones with the crystal lattice. Additionally, in the η-phase there are peaks in the local-energy gap (in momentum space), which are connected with long-range oscillations in the spatial distribution of the energy gap, superconducting order parameter (SOP), as well as effective pairing potential. Our results can be contrasted with the experiment and predicts how to experimentally differentiate these two different symmetries of SOP by the scanning tunneling microscopy technique.

Clusters of Point Defects Near Dislocations as a Tool to Control CdZnTe Electrical Parameters by Ultrasound

NASA Astrophysics Data System (ADS)

Olikh, Ya. M.; Tymochko, M. D.; Olikh, O. Ya.; Shenderovsky, V. A.

2018-05-01

We studied the temperature dependence (77-300 K) of the electron concentration and mobility using the Hall method under ultrasound (the acoustic Hall method) to determine the mechanisms by which ultrasound influences the electrical activity of near-dislocation clusters in n-type low-ohmic Cd1-x Zn x Te single crystals (N Cl ≈ 1024 m-3; x = 0; 0.04) with different dislocation density (0.4-5.1) × 1010 m-2. Changes in electrophysical parameters were found to occur as a function of temperature and ultrasound intensity. To evaluate the relative contribution of different charge carrier scattering mechanisms (lattice scattering, ionized impurity scattering, neutral impurity scattering, and dislocation scattering) and their change under ultrasound, a differential evolution method was used. This method made it possible to analyze experimental mobility μ H(T) by its nonlinear approximation with characteristic temperature dependence for each mechanism. An increase in neutral impurity scattering and a decrease in ionized impurity and dislocation scattering components were observed under ultrasound. The character and the amount of these acoustically induced changes correlate with particular sample dislocation characteristics. It was concluded that the observed effects are related to the acoustically induced transformation of the point-defect structure, mainly in the near dislocation crystal regions.

Zero-phonon-line emission of single molecules for applications in quantum information processing

NASA Astrophysics Data System (ADS)

Kiraz, Alper; Ehrl, M.; Mustecaplioglu, O. E.; Hellerer, T.; Brauchle, C.; Zumbusch, A.

2005-07-01

A single photon source which generates transform limited single photons is highly desirable for applications in quantum optics. Transform limited emission guarantees the indistinguishability of the emitted single photons. This, in turn brings groundbreaking applications in linear optics quantum information processing within an experimental reach. Recently, self-assembled InAs quantum dots and trapped atoms have successfully been demonstrated as such sources for highly indistinguishable single photons. Here, we demonstrate that nearly transform limited zero-phonon-line (ZPL) emission from single molecules can be obtained by using vibronic excitation. Furthermore we report the results of coincidence detection experiments at the output of a Michelson-type interferometer. These experiments reveal Hong-Ou-Mandel correlations as a proof of the indistinguishability of the single photons emitted consecutively from a single molecule. Therefore, single molecules constitute an attractive alternative to single InAs quantum dots and trapped atoms for applications in linear optics quantum information processing. Experiments were performed with a home-built confocal microscope keeping the sample in a superfluid liquid Helium bath at 1.4K. We investigated terrylenediimide (TDI) molecules highly diluted in hexadecane (Shpol'skii matrix). A continuous wave single mode dye laser was used for excitation of vibronic transitions of individual molecules. From the integral fluorescence, the ZPL of single molecules was selected with a spectrally narrow interference filter. The ZPL emission was then sent to a scanning Fabry-Perot interferometer for linewidth measurements or a Michelson-type interferometer for coincidence detection.

Zero-mode waveguide nanophotonic structures for single molecule characterization

NASA Astrophysics Data System (ADS)

Crouch, Garrison M.; Han, Donghoon; Bohn, Paul W.

2018-05-01

Single-molecule characterization has become a crucial research tool in the chemical and life sciences, but limitations, such as limited concentration range, inability to control molecular distributions in space, and intrinsic phenomena, such as photobleaching, present significant challenges. Recent developments in non-classical optics and nanophotonics offer promising routes to mitigating these restrictions, such that even low affinity (K D ~ mM) biomolecular interactions can be studied. Here we introduce and review specific nanophotonic devices used to support single molecule studies. Optical nanostructures, such as zero-mode waveguides (ZMWs), are usually fabricated in thin gold or aluminum films and serve to confine the observation volume of optical microspectroscopy to attoliter to zeptoliter volumes. These simple nanostructures allow individual molecules to be isolated for optical and electrochemical analysis, even when the molecules of interest are present at high concentration (µM–mM) in bulk solution. Arrays of ZMWs may be combined with optical probes such as single molecule fluorescence, single molecule fluorescence resonance energy transfer, and fluorescence correlation spectroscopy for distributed analysis of large numbers of single-molecule reactions or binding events in parallel. Furthermore, ZMWs may be used as multifunctional devices, for example by combining optical and electrochemical functions in a single discrete architecture to achieve electrochemical ZMWs. In this review, we will describe the optical properties, fabrication, and applications of ZMWs for single-molecule studies, as well as the integration of ZMWs into systems for chemical and biochemical analysis.

Photophysical Behaviors of Single Fluorophores Localized on Zinc Oxide Nanostructures

PubMed Central

Fu, Yi; Zhang, Jian; Lakowicz, Joseph R.

2012-01-01

Single-molecule fluorescence spectroscopy has now been widely used to investigate complex dynamic processes which would normally be obscured in an ensemble-averaged measurement. In this report we studied photophysical behaviors of single fluorophores in proximity to zinc oxide nanostructures by single-molecule fluorescence spectroscopy and time-correlated single-photon counting (TCSPC). Single fluorophores on ZnO surfaces showed enhanced fluorescence brightness to various extents compared with those on glass; the single-molecule time trajectories also illustrated pronounced fluctuations of emission intensities, with time periods distributed from milliseconds to seconds. We attribute fluorescence fluctuations to the interfacial electron transfer (ET) events. The fluorescence fluctuation dynamics were found to be inhomogeneous from molecule to molecule and from time to time, showing significant static and dynamic disorders in the interfacial electron transfer reaction processes. PMID:23109903

Combining single-molecule manipulation and single-molecule detection.

PubMed

Cordova, Juan Carlos; Das, Dibyendu Kumar; Manning, Harris W; Lang, Matthew J

2014-10-01

Single molecule force manipulation combined with fluorescence techniques offers much promise in revealing mechanistic details of biomolecular machinery. Here, we review force-fluorescence microscopy, which combines the best features of manipulation and detection techniques. Three of the mainstay manipulation methods (optical traps, magnetic traps and atomic force microscopy) are discussed with respect to milestones in combination developments, in addition to highlight recent contributions to the field. An overview of additional strategies is discussed, including fluorescence based force sensors for force measurement in vivo. Armed with recent exciting demonstrations of this technology, the field of combined single-molecule manipulation and single-molecule detection is poised to provide unprecedented views of molecular machinery. Copyright © 2014 Elsevier Ltd. All rights reserved.

Single-Molecule Analysis of Pre-mRNA Splicing with Colocalization Single-Molecule Spectroscopy (CoSMoS).

PubMed

Braun, Joerg E; Serebrov, Victor

2017-01-01

Recent development of single-molecule techniques to study pre-mRNA splicing has provided insights into the dynamic nature of the spliceosome. Colocalization single-molecule spectroscopy (CoSMoS) allows following spliceosome assembly in real time at single-molecule resolution in the full complexity of cellular extracts. A detailed protocol of CoSMoS has been published previously (Anderson and Hoskins, Methods Mol Biol 1126:217-241, 2014). Here, we provide an update on the technical advances since the first CoSMoS studies including slide surface treatment, data processing, and representation. We describe various labeling strategies to generate RNA reporters with multiple dyes (or other moieties) at specific locations.

Manipulating, Reacting, and Constructing Single Molecules with a Scanning Tunneling Microscope Tip

NASA Astrophysics Data System (ADS)

Hla, S.-W.

The fascinating advances in atom and molecule manipulation with the scanning tunneling microscope (STM) tip allow scientists to fabricate artificial atomic scale structures, to study local quantum phenomena, or to probe physical and chemical properties of single atoms and molecules on surfaces. Recent achievements in individual synthesis of single molecules with the STM tip further open up an entirely new opportunities in nanoscience and technology. The STM manipulation techniques usef ul in the molecular construction are reviewed and prospects for future opportunities of single molecule chemical engineering and their possible implications to nano-scale science and technology are discussed.

Single-molecule conductance studies of photo-active and photochromic molecules

NASA Astrophysics Data System (ADS)

Tam, E. S.; Parks, J. J.; Santiago-Berrios, M. B.; Zhong, Y.-W.; Abruna, H. D.; Ralph, D. C.

2010-03-01

We perform statistical measurements of single molecule conductance in repeatedly-formed metal-molecule-metal junctions at room temperature. Our results on diaminoalkanes are consistent with those reported by the Venkataraman group. We focus on photo-active and photochromic molecules, including a series of transition-metal complexes with different metal centers and endgroups. We compare the trend in conductance across the family of complexes with that expected from electrochemical measurements. We will also report initial results on the voltage dependence of single-molecule conductances and the effects of optical excitations.

Toward the Space-Time Limit

NASA Astrophysics Data System (ADS)

Rios, Laura

A chemical reaction is fundamentally initiated by the restructuring of a chemical bond. Chemical reactions occur so quickly that their exact trajectory is unknown. To unlock the secret, first one would seek to know the inner working of a single molecule, and therein, a single chemical bond. However, the task is no small feat. Single molecule studies require exquisite spatial resolution afforded by relatively new technologies, and ultrafast laser techniques. The overarching theme of my dissertation will be the path towards achieving the space-time limit in chemistry: namely, the ability to record the structural changes of individual molecules during a reaction, one event at a time. A scanning tunneling microscope (STM) is used to image the molecules and manipulate their electronic environments. STM has the capacity to create topographical images of molecules with Angstrom ($10-10 m - the size of an atom) resolution, and can also probe the molecule electronically by use of a tunneling current (It). STM images reflect the changes in the potential energy surface (PES), and help us understand how molecules interact with surfaces and each other, thereby accessing the fundamental problem of catalysis and chemical reactions. In addition to seeing the molecule, we use Raman spectroscopy to track its molecular changes with chemical specificity. I combine these experimental tools to investigate tip-enhanced Raman spectra (TERS) of single molecules within the confines of a STM. These methods were used to report the conformational change of a single azobenzene-thiol derivative molecule. Although we were able to definitely isolate a single molecule signature, imaging the single molecule in real space and time proved elusive. Additionally, I report on a conductance switch based on the observable change of the topographic STM images of a radical anion mediated by the spin flip of a single electron on a single molecule. This is effectively the smallest achievable architecture of molecular electronics, negating the need for heat dissipation in small systems. A related work found how physisorption potentials of molecules to metals could be experimentally visually verified and modeled by STM, thus allowing us to use the STM tip as a driver for molecular motion on surfaces. Throughtout this work, we noted that a dominant feature of single molecule chemistry are intensity and spectral fluctuations that are difficult to characterize, as the molecule contorts wildly when it experiences distinct and powerful electromagnetic fields and field gradients. This much is evident in the last experiment, and chapter, of this thesis. Raman spectra associated with cobalt (II) tetraphenyl porphyrin (CoTPP) axially coordinated with bipyridyl ethylene (BPE) were captured with Raman mapping with nanometer resolution. However, the stochastic apperance of Raman lines and low resolution images made it difficult to ascertain which molecule we captured. The preliminary results as well as follow-up control experiments are discussed. While each experiment constitutes in and of itself an important, individual contribution, their sum establishes the principles of seeing single-molecule chemistry.

Manipulating quantum coherence of charge states in interacting double-dot Aharonov–Bohm interferometers

NASA Astrophysics Data System (ADS)

Jin, Jinshuang; Wang, Shikuan; Zhou, Jiahuan; Zhang, Wei-Min; Yan, YiJing

2018-04-01

We investigate the dynamics of charge-state coherence in a degenerate double-dot Aharonov–Bohm interferometer with finite inter-dot Coulomb interactions. The quantum coherence of the charge states is found to be sensitive to the transport setup configurations, involving both the single-electron impurity channels and the Coulomb-assisted ones. We numerically demonstrate the emergence of a complete coherence between the two charge states, with the relative phase being continuously controllable through the magnetic flux. Interestingly, a fully coherent charge qubit arises at the double-dots electron pair tunneling resonance condition, where the chemical potential of one electrode is tuned at the center between a single-electron impurity channel and the related Coulomb-assisted channel. This pure quantum state of charge qubit could be experimentally realized at the current–voltage characteristic turnover position, where differential conductance sign changes. We further elaborate the underlying mechanism for both the real-time and the stationary charge-states coherence in the double-dot systems of study.

Extended and Point Defects in Diamond Studied with the Aid of Various Forms of Microscopy.

PubMed

Steeds; Charles; Gilmore; Butler

2000-07-01

It is shown that star disclinations can be a significant source of stress in chemical vapor deposited (CVD) diamond. This purely geometrical origin contrasts with other sources of stress that have been proposed previously. The effectiveness is demonstrated of the use of electron irradiation using a transmission electron microscope (TEM) to displace atoms from their equilibrium sites to investigate intrinsic defects and impurities in CVD diamond. After irradiation, the samples are studied by low temperature photoluminescence microscopy using UV or blue laser illumination. Results are given that are interpreted as arising from isolated <100> split self-interstitials and positively charged single vacancies. Negatively charged single vacancies can also be revealed by this technique. Nitrogen and boron impurities may also be studied similarly. In addition, a newly developed liquid gallium source scanned ion beam mass spectrometry (SIMS) instrument has been used to map out the B distribution in B doped CVD diamond specimens. The results are supported by micro-Raman spectroscopy.

Improvement of minority carrier life time in N-type monocrystalline Si by the Czochralski method

NASA Astrophysics Data System (ADS)

Baik, Sungsun; Pang, Ilsun; Kim, Jaemin; Kim, Kwanghun

2016-07-01

The installation amount of solar power plants increases every year. Multi-crystalline Si solar cells comprise a large share of the market of solar power plants. Multi-crystalline and single-crystalline Si solar cells are competing against one another in the market. Many single-crystalline companies are trying to develop and produce n-type solar cells with higher cell efficiency than that of p-type. In n-type wafers with high cell efficiency, wafer quality has become increasingly important. In order to make ingots with higher MCLT, the effects of both poly types related to metal impurities and pull speeds related to vacancy concentration on minority carrier life time were studied. In the final part of ingots, poly types related to the metal impurities are a dominant factor on MCLT. In the initial part of ingots, pull speeds related to vacancy concentration are a dominant factor on MCLT. [Figure not available: see fulltext.

NASA-JSC Protocol for the Characterization of Single Wall Carbon Nanotube Material Quality

NASA Technical Reports Server (NTRS)

Arepalli, Sivaram; Nikolaev, Pasha; Gorelik, Olga; Hadjiev, Victor; Holmes, William; Devivar, Rodrigo; Files, Bradley; Yowell, Leonard

2010-01-01

It is well known that the raw as well as purified single wall carbon nanotube (SWCNT) material always contain certain amount of impurities of varying composition (mostly metal catalyst and non-tubular carbon). Particular purification method also creates defects and/or functional groups in the SWCNT material and therefore affects the its dispersability in solvents (important to subsequent application development). A number of analytical characterization tools have been used successfully in the past years to assess various properties of nanotube materials, but lack of standards makes it difficult to compare these measurements across the board. In this work we report the protocol developed at NASA-JSC which standardizes measurements using TEM, SEM, TGA, Raman and UV-Vis-NIR absorption techniques. Numerical measures are established for parameters such as metal content, homogeneity, thermal stability and dispersability, to allow easy comparison of SWCNT materials. We will also report on the recent progress in quantitative measurement of non-tubular carbon impurities and a possible purity standard for SWCNT materials.

Reusability of contaminated seed crystal for cast quasi-single crystalline silicon ingots

NASA Astrophysics Data System (ADS)

Li, Zaoyang; Liu, Lijun; Zhou, Genshu

2015-04-01

Reusing seed crystal is beneficial for reducing the production costs for cast quasi-single crystalline (QSC) silicon ingots. We numerically investigate the reusability of seed crystal in the casting processes with quartz crucible and silicon feedstock of different purities. The reused seed crystal is recycled from the standard QSC ingot and has been highly contaminated by iron impurity. Transient simulations of iron transport are carried out and special attention is paid to the diffusion and distribution characteristics of iron impurity at the ingot bottom. The heights of the bottom iron contaminated region are compared for silicon ingots grown from normal and recycled seed crystals. The results show that the purity of quartz crucible can influence the reusability of seed crystal more significantly than that of the feedstock. The recycled seed crystal with high iron concentration can be reused for casting processes with standard crucible, whereas it is not recommended for reusing for processes with pure crucible.

Zirconia ceramics for excess weapons plutonium waste

NASA Astrophysics Data System (ADS)

Gong, W. L.; Lutze, W.; Ewing, R. C.

2000-01-01

We synthesized a zirconia (ZrO 2)-based single-phase ceramic containing simulated excess weapons plutonium waste. ZrO 2 has large solubility for other metallic oxides. More than 20 binary systems A xO y-ZrO 2 have been reported in the literature, including PuO 2, rare-earth oxides, and oxides of metals contained in weapons plutonium wastes. We show that significant amounts of gadolinium (neutron absorber) and yttrium (additional stabilizer of the cubic modification) can be dissolved in ZrO 2, together with plutonium (simulated by Ce 4+, U 4+ or Th 4+) and impurities (e.g., Ca, Mg, Fe, Si). Sol-gel and powder methods were applied to make homogeneous, single-phase zirconia solid solutions. Pu waste impurities were completely dissolved in the solid solutions. In contrast to other phases, e.g., zirconolite and pyrochlore, zirconia is extremely radiation resistant and does not undergo amorphization. Baddeleyite (ZrO 2) is suggested as the natural analogue to study long-term radiation resistance and chemical durability of zirconia-based waste forms.

Oxygen diffusion in alpha-Al2O3. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Cawley, J. D.; Halloran, J. W.; Cooper, A. R.

1984-01-01

Oxygen self diffusion coefficients were determined in single crystal alpha-Al2O3 using the gas exchange technique. The samples were semi-infinite slabs cut from five different boules with varying background impurities. The diffusion direction was parallel to the c-axis. The tracer profiles were determined by two techniques, single spectrum proton activation and secondary ion mass spectrometry. The SIMS proved to be a more useful tool. The determined diffusion coefficients, which were insensitive to impurity levels and oxygen partial pressure, could be described by D = .00151 exp (-572kJ/RT) sq m/s. The insensitivities are discussed in terms of point defect clustering. Two independent models are consistent with the findings, the first considers the clusters as immobile point defect traps which buffer changes in the defect chemistry. The second considers clusters to be mobile and oxygen diffusion to be intrinsic behavior, the mechanism for oxygen transport involving neutral clusters of Schottky quintuplets.

One-by-one single-molecule detection of mutated nucleobases by monitoring tunneling current using a DNA tip.

PubMed

Bui, Phuc Tan; Nishino, Tomoaki; Shiigi, Hiroshi; Nagaoka, Tsutomu

2015-01-31

A DNA molecule was utilized as a probe tip to achieve single-molecule genetic diagnoses. Hybridization of the probe and target DNAs resulted in electron tunneling along the emergent double-stranded DNA. Simple stationary monitoring of the tunneling current leads to single-molecule DNA detection and discovery of base mismatches and methylation.

Extracting physics of life at the molecular level: A review of single-molecule data analyses.

PubMed

Colomb, Warren; Sarkar, Susanta K

2015-06-01

Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

Inferring diffusion in single live cells at the single-molecule level

PubMed Central

Robson, Alex; Burrage, Kevin; Leake, Mark C.

2013-01-01

The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single-molecule and single-cell level can add significant insight into understanding molecular architectures of diffusing molecules and the nanoscale environment in which the molecules diffuse. The tool of choice for monitoring dynamic molecular localization in live cells is fluorescence microscopy, especially so combining total internal reflection fluorescence with the use of fluorescent protein (FP) reporters in offering exceptional imaging contrast for dynamic processes in the cell membrane under relatively physiological conditions compared with competing single-molecule techniques. There exist several different complex modes of diffusion, and discriminating these from each other is challenging at the molecular level owing to underlying stochastic behaviour. Analysis is traditionally performed using mean square displacements of tracked particles; however, this generally requires more data points than is typical for single FP tracks owing to photophysical instability. Presented here is a novel approach allowing robust Bayesian ranking of diffusion processes to discriminate multiple complex modes probabilistically. It is a computational approach that biologists can use to understand single-molecule features in live cells. PMID:23267182

Temperature dependence of the electrical resistivity of LaxLu1-xAs

NASA Astrophysics Data System (ADS)

Rahimi, S.; Krivoy, E. M.; Lee, J.; Michael, M. E.; Bank, S. R.; Akinwande, D.

2013-08-01

We investigate the temperature-dependent resistivity of single-crystalline films of LaxLu1-xAs over the 5-300 K range. The resistivity was separated into lattice, carrier and impurity scattering regions. The effect of impurity scattering is significant below 20 K, while carrier scattering dominates at 20-80 K and lattice scattering dominates above 80 K. All scattering regions show strong dependence on the La content of the films. While the resistivity of 600 nm LuAs films agree well with the reported bulk resistivity values, 3 nm films possessed significantly higher resistivity, suggesting that interfacial roughness significantly impacts the scattering of carriers at the nanoscale limit.

Electromagnetically Induced Transparency Experiments for the Advanced Undergraduate Laboratory: Suppression of Polarization Impurity and Stray Magnetic Fields

NASA Astrophysics Data System (ADS)

Campbell, Kaleb; Jackson, Richard; van Vleet, Matthew; Kuhnash, Kodi; Worth, Bradley; Day, Amanda; Bali, Samir

2014-05-01

We investigate electromagnetically induced transparency (EIT) and electromagnetically induced absorption (EIA) in rubidium vapor using a single laser beam and a scanning magnetic field co-aligned with the laser propagation direction. We show that polarization impurity, stray magnetic fields and imperfect optical alignments cause broadening of the EIT/EIA signal and other spurious effects. We describe a systematic approach to minimizing these undesired effects, which produces EIT/EIA signals nearly two orders of magnitude narrower than the natural linewidth. We gratefully acknowledge funding from the American Chemical Society Petroleum Research Fund and Miami University. We also acknowledge the Miami University Instrumentation Laboratory for their invaluable contributions.

Porous materials with pre-designed single-molecule traps for CO2 selective adsorption

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

Li, JR; Yu, JM; Lu, WG

2013-02-26

Despite tremendous efforts, precise control in the synthesis of porous materials with pre-designed pore properties for desired applications remains challenging. Newly emerged porous metal-organic materials, such as metal-organic polyhedra and metal-organic frameworks, are amenable to design and property tuning, enabling precise control of functionality by accurate design of structures at the molecular level. Here we propose and validate, both experimentally and computationally, a precisely designed cavity, termed a 'single-molecule trap', with the desired size and properties suitable for trapping target CO2 molecules. Such a single-molecule trap can strengthen CO2-host interactions without evoking chemical bonding, thus showing potential for CO2 capture.more » Molecular single-molecule traps in the form of metal-organic polyhedra are designed, synthesised and tested for selective adsorption of CO2 over N-2 and CH4, demonstrating the trapping effect. Building these pre-designed single-molecule traps into extended frameworks yields metal-organic frameworks with efficient mass transfer, whereas the CO2 selective adsorption nature of single-molecule traps is preserved.« less

Quantitative Aspects of Single Molecule Microscopy

PubMed Central

Ober, Raimund J.; Tahmasbi, Amir; Ram, Sripad; Lin, Zhiping; Ward, E. Sally

2015-01-01

Single molecule microscopy is a relatively new optical microscopy technique that allows the detection of individual molecules such as proteins in a cellular context. This technique has generated significant interest among biologists, biophysicists and biochemists, as it holds the promise to provide novel insights into subcellular processes and structures that otherwise cannot be gained through traditional experimental approaches. Single molecule experiments place stringent demands on experimental and algorithmic tools due to the low signal levels and the presence of significant extraneous noise sources. Consequently, this has necessitated the use of advanced statistical signal and image processing techniques for the design and analysis of single molecule experiments. In this tutorial paper, we provide an overview of single molecule microscopy from early works to current applications and challenges. Specific emphasis will be on the quantitative aspects of this imaging modality, in particular single molecule localization and resolvability, which will be discussed from an information theoretic perspective. We review the stochastic framework for image formation, different types of estimation techniques and expressions for the Fisher information matrix. We also discuss several open problems in the field that demand highly non-trivial signal processing algorithms. PMID:26167102

Vacancy-impurity centers in diamond: prospects for synthesis and applications

NASA Astrophysics Data System (ADS)

Ekimov, E. A.; Kondrin, M. V.

2017-06-01

The bright luminescence of impurity-vacancy complexes, combined with high chemical and radiation resistance, makes diamond an attractive platform for the production of single-photon emitters and luminescent biomarkers for applications in nanoelectronics and medicine. Two representatives of this kind of defects in diamond, silicon-vacancy (SiV) and germanium-vacancy (GeV) centers, are discussed in this review; their similarities and differences are demonstrated in terms of the more thoroughly studied nitrogen-vacancy (NV) complexes. The recent discovery of GeV luminescent centers opens a unique opportunity for the controlled synthesis of single-photon emitters in nanodiamonds. We demonstrate prospects for the high-pressure high-temperature (HPHT) technique to create single-photon emitters, not only as an auxiliary to chemical vapor deposition (CVD) and ion-implantation methods but also as a primary synthesis tool for producing color centers in nanodiamonds. Besides practical applications, comparative studies of these two complexes, which belong to the same structural class of defects, have a fundamental importance for deeper understanding of shelving levels, the electronic structure, and optical properties of these centers. In conclusion, we discuss several open problems regarding the structure, charge state, and practical application of these centers, which still require a solution.

Photoionization cross section and binding energy of single dopant in hollow cylindrical core/shell quantum dot

NASA Astrophysics Data System (ADS)

Feddi, E.; El-Yadri, M.; Dujardin, F.; Restrepo, R. L.; Duque, C. A.

2017-02-01

In this study, we have investigated the confined donor impurity in a hollow cylindrical-shell quantum dot. The charges are assumed to be completely confined to the interior of the shell with rigid walls. Within the framework of the effective-mass approximation and by using a simple variational approach, we have computed the donor binding energy as a function of the shell sizes in order to study the behavior of the electron-impurity attraction for a very small thickness. Our results show that the binding energy of a donor impurity placed at the center of cylindrical core/shell dots depends strongly on the shell size. The binding energy increases when the shell-wideness becomes smaller and shows the same behavior as in a simple cylindrical quantum dot. A special case has been studied, which corresponds to the ratio between the inner and outer radii near to one (a/b → 1) for which our model gives a non-significant behavior of the impurity binding energy. This fact implies the existence of a critical value (a/b) for which the binding energy of the donor impurity tends to the limit value of 4 effective Rydbergs as in a 2D quantum well. We also analyse the photoionization cross section considering only the in-plane incident radiation polarization. We determine its behavior as a function of photon energy, shell size, and donor position. The measurement of photoionization in such systems would be of great interest to understand the optical properties of carriers in quantum dots.

Repurposing a Benchtop Centrifuge for High-Throughput Single-Molecule Force Spectroscopy.

PubMed

Yang, Darren; Wong, Wesley P

2018-01-01

We present high-throughput single-molecule manipulation using a benchtop centrifuge, overcoming limitations common in other single-molecule approaches such as high cost, low throughput, technical difficulty, and strict infrastructure requirements. An inexpensive and compact Centrifuge Force Microscope (CFM) adapted to a commercial centrifuge enables use by nonspecialists, and integration with DNA nanoswitches facilitates both reliable measurements and repeated molecular interrogation. Here, we provide detailed protocols for constructing the CFM, creating DNA nanoswitch samples, and carrying out single-molecule force measurements.

Single molecule detection, thermal fluctuation and life

PubMed Central

YANAGIDA, Toshio; ISHII, Yoshiharu

2017-01-01

Single molecule detection has contributed to our understanding of the unique mechanisms of life. Unlike artificial man-made machines, biological molecular machines integrate thermal noises rather than avoid them. For example, single molecule detection has demonstrated that myosin motors undergo biased Brownian motion for stepwise movement and that single protein molecules spontaneously change their conformation, for switching to interactions with other proteins, in response to thermal fluctuation. Thus, molecular machines have flexibility and efficiency not seen in artificial machines. PMID:28190869

Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data.

PubMed

Greenfeld, Max; van de Meent, Jan-Willem; Pavlichin, Dmitri S; Mabuchi, Hideo; Wiggins, Chris H; Gonzalez, Ruben L; Herschlag, Daniel

2015-01-16

Single-molecule techniques have emerged as incisive approaches for addressing a wide range of questions arising in contemporary biological research [Trends Biochem Sci 38:30-37, 2013; Nat Rev Genet 14:9-22, 2013; Curr Opin Struct Biol 2014, 28C:112-121; Annu Rev Biophys 43:19-39, 2014]. The analysis and interpretation of raw single-molecule data benefits greatly from the ongoing development of sophisticated statistical analysis tools that enable accurate inference at the low signal-to-noise ratios frequently associated with these measurements. While a number of groups have released analysis toolkits as open source software [J Phys Chem B 114:5386-5403, 2010; Biophys J 79:1915-1927, 2000; Biophys J 91:1941-1951, 2006; Biophys J 79:1928-1944, 2000; Biophys J 86:4015-4029, 2004; Biophys J 97:3196-3205, 2009; PLoS One 7:e30024, 2012; BMC Bioinformatics 288 11(8):S2, 2010; Biophys J 106:1327-1337, 2014; Proc Int Conf Mach Learn 28:361-369, 2013], it remains difficult to compare analysis for experiments performed in different labs due to a lack of standardization. Here we propose a standardized single-molecule dataset (SMD) file format. SMD is designed to accommodate a wide variety of computer programming languages, single-molecule techniques, and analysis strategies. To facilitate adoption of this format we have made two existing data analysis packages that are used for single-molecule analysis compatible with this format. Adoption of a common, standard data file format for sharing raw single-molecule data and analysis outcomes is a critical step for the emerging and powerful single-molecule field, which will benefit both sophisticated users and non-specialists by allowing standardized, transparent, and reproducible analysis practices.

Extending Single-Molecule Microscopy Using Optical Fourier Processing

PubMed Central

2015-01-01

This article surveys the recent application of optical Fourier processing to the long-established but still expanding field of single-molecule imaging and microscopy. A variety of single-molecule studies can benefit from the additional image information that can be obtained by modulating the Fourier, or pupil, plane of a widefield microscope. After briefly reviewing several current applications, we present a comprehensive and computationally efficient theoretical model for simulating single-molecule fluorescence as it propagates through an imaging system. Furthermore, we describe how phase/amplitude-modulating optics inserted in the imaging pathway may be modeled, especially at the Fourier plane. Finally, we discuss selected recent applications of Fourier processing methods to measure the orientation, depth, and rotational mobility of single fluorescent molecules. PMID:24745862

Extending single-molecule microscopy using optical Fourier processing.

PubMed

Backer, Adam S; Moerner, W E

2014-07-17

This article surveys the recent application of optical Fourier processing to the long-established but still expanding field of single-molecule imaging and microscopy. A variety of single-molecule studies can benefit from the additional image information that can be obtained by modulating the Fourier, or pupil, plane of a widefield microscope. After briefly reviewing several current applications, we present a comprehensive and computationally efficient theoretical model for simulating single-molecule fluorescence as it propagates through an imaging system. Furthermore, we describe how phase/amplitude-modulating optics inserted in the imaging pathway may be modeled, especially at the Fourier plane. Finally, we discuss selected recent applications of Fourier processing methods to measure the orientation, depth, and rotational mobility of single fluorescent molecules.

Meeting report: SMART timing--principles of single molecule techniques course at the University of Michigan 2014.

PubMed

Bartke, Rebecca M; Cameron, Elizabeth L; Cristie-David, Ajitha S; Custer, Thomas C; Denies, Maxwell S; Daher, May; Dhakal, Soma; Ghosh, Soumi; Heinicke, Laurie A; Hoff, J Damon; Hou, Qian; Kahlscheuer, Matthew L; Karslake, Joshua; Krieger, Adam G; Li, Jieming; Li, Xiang; Lund, Paul E; Vo, Nguyen N; Park, Jun; Pitchiaya, Sethuramasundaram; Rai, Victoria; Smith, David J; Suddala, Krishna C; Wang, Jiarui; Widom, Julia R; Walter, Nils G

2015-05-01

Four days after the announcement of the 2014 Nobel Prize in Chemistry for "the development of super-resolved fluorescence microscopy" based on single molecule detection, the Single Molecule Analysis in Real-Time (SMART) Center at the University of Michigan hosted a "Principles of Single Molecule Techniques 2014" course. Through a combination of plenary lectures and an Open House at the SMART Center, the course took a snapshot of a technology with an especially broad and rapidly expanding range of applications in the biomedical and materials sciences. Highlighting the continued rapid emergence of technical and scientific advances, the course underscored just how brightly the future of the single molecule field shines. © 2014 Wiley Periodicals, Inc.

Single Molecules as Optical Probes for Structure and Dynamics

NASA Astrophysics Data System (ADS)

Orrit, Michel

Single molecules and single nanoparticles are convenient links between the nanoscale world and the laboratory. We discuss the limits for their optical detection by three different methods: fluorescence, direct absorption, and photothermal detection. We briefly review some recent illustrations of qualitatively new information gathered from single-molecule signals: intermittency of the fluorescence intensity, acoustic vibrations of nanoparticles (1-100 GHz) or of extended defects in molecular crystals (0.1-1 MHz), and dynamical heterogeneity in glass-forming molecular liquids. We conclude with an outlook of future uses of single-molecule methods in physical chemistry, soft matter, and material science.

Single-Molecule Electronics: Chemical and Analytical Perspectives.

PubMed

Nichols, Richard J; Higgins, Simon J

2015-01-01

It is now possible to measure the electrical properties of single molecules using a variety of techniques including scanning probe microcopies and mechanically controlled break junctions. Such measurements can be made across a wide range of environments including ambient conditions, organic liquids, ionic liquids, aqueous solutions, electrolytes, and ultra high vacuum. This has given new insights into charge transport across molecule electrical junctions, and these experimental methods have been complemented with increasingly sophisticated theory. This article reviews progress in single-molecule electronics from a chemical perspective and discusses topics such as the molecule-surface coupling in electrical junctions, chemical control, and supramolecular interactions in junctions and gating charge transport. The article concludes with an outlook regarding chemical analysis based on single-molecule conductance.

Quantitative analysis of single-molecule superresolution images

PubMed Central

Coltharp, Carla; Yang, Xinxing; Xiao, Jie

2014-01-01

This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ability to quantify the number, clustering, and colocalization of molecules with 10 – 50 nm resolution. Here we describe typical workflows and precautions for quantitative analysis of single-molecule superresolution images. These guidelines include potential pitfalls and essential control experiments, allowing critical assessment and interpretation of superresolution images. PMID:25179006

Single-Molecule Imaging of an in Vitro-Evolved RNA Aptamer Reveals Homogeneous Ligand Binding Kinetics

PubMed Central

2009-01-01

Many studies of RNA folding and catalysis have revealed conformational heterogeneity, metastable folding intermediates, and long-lived states with distinct catalytic activities. We have developed a single-molecule imaging approach for investigating the functional heterogeneity of in vitro-evolved RNA aptamers. Monitoring the association of fluorescently labeled ligands with individual RNA aptamer molecules has allowed us to record binding events over the course of multiple days, thus providing sufficient statistics to quantitatively define the kinetic properties at the single-molecule level. The ligand binding kinetics of the highly optimized RNA aptamer studied here displays a remarkable degree of uniformity and lack of memory. Such homogeneous behavior is quite different from the heterogeneity seen in previous single-molecule studies of naturally derived RNA and protein enzymes. The single-molecule methods we describe may be of use in analyzing the distribution of functional molecules in heterogeneous evolving populations or even in unselected samples of random sequences. PMID:19572753

Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

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

Fischer, Sean A.; Aprà, Edoardo; Govind, Niranjan

2017-02-03

Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting withmore » a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.« less

Controlling single-molecule junction conductance by molecular interactions

NASA Astrophysics Data System (ADS)

Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

2015-07-01

For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment.

Probe-based measurement of lateral single-electron transfer between individual molecules

PubMed Central

Steurer, Wolfram; Fatayer, Shadi; Gross, Leo; Meyer, Gerhard

2015-01-01

The field of molecular electronics aims at using single molecules as functional building blocks for electronics components, such as switches, rectifiers or transistors. A key challenge is to perform measurements with atomistic control over the alignment of the molecule and its contacting electrodes. Here we use atomic force microscopy to examine charge transfer between weakly coupled pentacene molecules on insulating films with single-electron sensitivity and control over the atomistic details. We show that, in addition to the imaging capability, the probe tip can be used to control the charge state of individual molecules and to detect charge transfers to/from the tip, as well as between individual molecules. Our approach represents a novel route for molecular charge transfer studies with a host of opportunities, especially in combination with single atom/molecule manipulation and nanopatterning techniques. PMID:26387533

Probing molecular choreography through single-molecule biochemistry.

PubMed

van Oijen, Antoine M; Dixon, Nicholas E

2015-12-01

Single-molecule approaches are having a dramatic impact on views of how proteins work. The ability to observe molecular properties at the single-molecule level allows characterization of subpopulations and acquisition of detailed kinetic information that would otherwise be hidden in the averaging over an ensemble of molecules. In this Perspective, we discuss how such approaches have successfully been applied to in vitro-reconstituted systems of increasing complexity.

Single molecule image formation, reconstruction and processing: introduction.

PubMed

Ashok, Amit; Piestun, Rafael; Stallinga, Sjoerd

2016-07-01

The ability to image at the single molecule scale has revolutionized research in molecular biology. This feature issue presents a collection of articles that provides new insights into the fundamental limits of single molecule imaging and reports novel techniques for image formation and analysis.

Interaction of different poisons with MgCl2/TiCl4 based Ziegler-Natta catalysts

NASA Astrophysics Data System (ADS)

Bahri-Laleh, Naeimeh

2016-08-01

Adsorption of different poison molecules on activated MgCl2 is investigated within DFT using a cluster model of the MgCl2 surface with (MgCl2)16 formula containing four 4-coordinated and eight 5-coordinated Mg atoms as (110) and (104) surfaces, respectively. Studied poison molecules are chosen as possible impurities in hydrocarbon solvents and monomer feeds and contain water, hydrogensulfide, carbondioxide, molecular oxygen and methanol. First, adsorption of 1-4 molecules of different poisons to the (104) and (110) lateral cuts of MgCl2, as well as their adsorption on [MgCl2]/TiCl2Et active center and AlEt3 cocatalyst is considered. Results reveal that poisons strongly stabilize both crystal surfaces, mostly Ti active center relative to the unpoisoned solid. Second, energy barrier (ETS) for ethylene insertion in the presence of different poisons located on the first and second Mg atom relative to the active Ti is calculated. While poison molecule located on the second Mg does not change ETS, coordination of it into the first Mg atom increases ETS by 0.9-1.2 kcal mol-1. In the last part of this manuscript, the stereoselective behavior of active Ti species, with and without poison molecules and external electron donor, is fully explored.

Single-particle dynamics of the Anderson model: a local moment approach

NASA Astrophysics Data System (ADS)

Glossop, Matthew T.; Logan, David E.

2002-07-01

A non-perturbative local moment approach to single-particle dynamics of the general asymmetric Anderson impurity model is developed. The approach encompasses all energy scales and interaction strengths. It captures thereby strong coupling Kondo behaviour, including the resultant universal scaling behaviour of the single-particle spectrum; as well as the mixed valence and essentially perturbative empty orbital regimes. The underlying approach is physically transparent and innately simple, and as such is capable of practical extension to lattice-based models within the framework of dynamical mean-field theory.

Diffusion doping in quantum dots: bond strength and diffusivity.

PubMed

Saha, Avijit; Makkar, Mahima; Shetty, Amitha; Gahlot, Kushagra; A R, Pavan; Viswanatha, Ranjani

2017-02-23

Semiconducting materials uniformly doped with optical or magnetic impurities have been useful in a number of potential applications. However, clustering or phase separation during synthesis has made this job challenging. Recently the "inside out" diffusion doping was proposed to be successful in obtaining large sized quantum dots (QDs) uniformly doped with a dilute percentage of dopant atoms. Herein, we demonstrate the use of basic physical chemistry of diffusion to control the size and concentration of the dopants within the QDs for a given transition metal ion. We have studied three parameters; the bond strength of the core molecules and the diffusion coefficient of the diffusing metal ion are found to be important while the ease of cation exchange was not highly influential in the control of size and concentration of the single domain dilute magnetic semiconductor quantum dots (DMSQDs) with diverse dopant ions M 2+ (Fe 2+ , Ni 2+ , Co 2+ , Mn 2+ ). Steady state optical emission spectra reveal that the dopants are incorporated inside the semiconducting CdS and the emission can be tuned during shell growth. We have shown that this method enables control over doping percentage and the QDs show a superior ferromagnetic response at room temperature as compared to previously reported systems.

Fundamentals, achievements and challenges in the electrochemical sensing of pathogens.

PubMed

Monzó, Javier; Insua, Ignacio; Fernandez-Trillo, Francisco; Rodriguez, Paramaconi

2015-11-07

Electrochemical sensors are powerful tools widely used in industrial, environmental and medical applications. The versatility of electrochemical methods allows for the investigation of chemical composition in real time and in situ. Electrochemical detection of specific biological molecules is a powerful means for detecting disease-related markers. In the last 10 years, highly-sensitive and specific methods have been developed to detect waterborne and foodborne pathogens. In this review, we classify the different electrochemical techniques used for the qualitative and quantitative detection of pathogens. The robustness of electrochemical methods allows for accurate detection even in heterogeneous and impure samples. We present a fundamental description of the three major electrochemical sensing methods used in the detection of pathogens and the advantages and disadvantages of each of these methods. In each section, we highlight recent breakthroughs, including the utilisation of microfluidics, immunomagnetic separation and multiplexing for the detection of multiple pathogens in a single device. We also include recent studies describing new strategies for the design of future immunosensing systems and protocols. The high sensitivity and selectivity, together with the portability and the cost-effectiveness of the instrumentation, enhances the demand for further development in the electrochemical detection of microbes.

Single Molecule and Collective Dynamics of Motor Protein Coupled with Mechano-Sensitive Chemical Reaction

NASA Astrophysics Data System (ADS)

Iwaki, Mitsuhiro; Marcucci, Lorenzo; Togashi, Yuichi; Yanagida, Toshio

2013-12-01

Motor proteins such as myosin and kinesin hydrolyze ATP into ADP and Pi to convert chemical energy into mechanical work. This resultsin various motile processes like muscle contraction, vesicle transport and cell division. Recent single molecule experiments have revealed that external load applied to these motor proteins perturb not only the mechanical motion, but the ATP hydrolysis cycle as well, making these molecules mechano-enzymes. Here, we describe our single molecule detection techniques to reveal the mechano-enzymatic properties of myosin and introduce recent progress from both experimental and theoretical approaches at the single- and multiple-molecule level.

Beyond experimental noise: Analyzing single-molecule data of heterogeneous systems. 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)

Meroz, Yasmine

2015-06-01

In the 1980s the world witnessed the advent of single-molecule experiments. The first atomic resolution characterization of a surface was reported by scanning tunneling microscope (STM) in 1982 [1], followed by atomic force microscope (AFM) in 1986 [2]. The first optical detection and spectroscopy of a single molecule in a solid took place in 1989 [3,4], in a time where essentially all chemical experiments were made on bulk, i.e. averaging over millions of copies of the same molecule.

NMR and mass spectrometric characterization of vinblastine, vincristine and some new related impurities - part I.

PubMed

Dubrovay, Zsófia; Háda, Viktor; Béni, Zoltán; Szántay, Csaba

2013-10-01

In the course of exploring the possibilities of developing a new, improved process at Gedeon Richter for the production of the "bisindole" alkaloids vinblastine (VLB) and vincristine (VCR), some novel VLB/VCR-related trace impurities were detected by analytical HPLC. Following isolation by preparative HPLC, a combination of 1D and 2D ultra high-field NMR and high-resolution (HR) (LC-)MS/MS studies allowed the structural identification and complete spectral characterization of several hitherto unpublished VLB/VCR-analogue impurities. Since the impurities could not be isolated in entirely pure forms and were available only in minute, mass-limited quantities, accessing the spectral information needed for their ab initio structure determination was met with various practical difficulties. Successful structure determination therefore relied heavily on the availability and use of detailed and definitive spectral data for both VLB and VCR. In particular, the utilization of detailed (1)H, (13)C, and (15)N NMR assignments as well as (1)H-(1)H, (1)H-(13)C and (1)H-(15)N spin-spin connectivities pertaining to different solvents for VLB/VCR base and sulphate salt was required. Although NMR studies on VLB base and other bisindoles were reported earlier in the literature, an NMR characterization of VLB and VCR under the above-mentioned circumstances and using ultra-high field instrumentation is either scarcely available or entirely lacking, therefore the necessary data had to be obtained in-house. Likewise, a modern tandem HR-ESI-MS/MS(n) fragmentation study of VLB and VCR has not been published yet. In the present paper we therefore give a thorough NMR and MS characterization of VLB and VCR specifically with a view to filling this void and to provide sufficiently extensive and solid reference data for the structural investigation of the aforementioned VLB/VCR impurities. Besides being scientifically relevant in its own right, the disclosed data should be useful for anyone interested in VLB/VCR-related molecules at a structural level. Copyright © 2012 Elsevier B.V. All rights reserved.

Processing α-mercuric iodide by zone refining

NASA Astrophysics Data System (ADS)

Burger, A.; Morgan, S. H.; Henderson, D. O.; Biao, Y.; Zhang, K.; Silberman, E.; Nason, D.; van den Berg, L.; Ortale-Baccash, C.; Cross, E.

1993-03-01

An investigation is being conducted on zone refining α-mercuric iodide. Analytical studies using differential scanning calorimetry and anion chromatography indicate that impurities are accumulated mainly at the end where zone travel terminates. Early results indicate that single crystals can be readily grown from zone-refined material.

Hybrid materials and methods for producing the same

DOEpatents

Luzzi, David E [Wallingford, PA; Smith, Brian W [Schelton, CT

2003-04-08

A hybrid material is provided which comprises a first single-walled nanotube having a lumen, and a fill molecule contained within the lumen of the single-walled nanotube. A method for producing the hybrid material is also provided wherein a single-walled nanotube is contacted with a fill molecule to cause the fill molecule to enter the lumen of the single-walled nanotube.

Hybrid materials and methods for producing the same

DOEpatents

Luzzi, David E [Wallingford, PA; Smith, Brian W [Philadelphia, PA

2008-02-19

A hybrid material is provided which comprises a first single-walled nanotube having a lumen, and a fill molecule contained within the lumen of the single-walled nanotube. A method for producing the hybrid material is also provided wherein a single-walled nanotube is contacted with a fill molecule to cause the fill molecule to enter the lumen of the single-walled nanotube.

Techniques for 3D tracking of single molecules with nanometer accuracy in living cells

NASA Astrophysics Data System (ADS)

Gardini, Lucia; Capitanio, Marco; Pavone, Francesco S.

2013-06-01

We describe a microscopy technique that, combining wide-field single molecule microscopy, bifocal imaging and Highly Inclined and Laminated Optical sheet (HILO) microscopy, allows a 3D tracking with nanometer accuracy of single fluorescent molecules in vitro and in living cells.

Single-molecule electrocatalysis by single-walled carbon nanotubes.

PubMed

Xu, Weilin; Shen, Hao; Kim, Yoon Ji; Zhou, Xiaochun; Liu, Guokun; Park, Jiwoong; Chen, Peng

2009-12-01

We report a single-molecule fluorescence study of electrocatalysis by single-walled carbon nanotubes (SWNTs) at single-reaction resolution. Applying super-resolution optical imaging, we find that the electrocatalysis occurs at discrete, nanometer-dimension sites on SWNTs. Single-molecule kinetic analysis leads to an electrocatalytic mechanism, allowing quantification of the reactivity and heterogeneity of individual reactive sites. Combined with conductivity measurements, this approach will be powerful to interrogate how the electronic structure of SWNTs affects the electrocatalytic interfacial charge transfer, a process fundamental to photoelectrochemical cells.

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

Lykkebo, Jacob; Solomon, Gemma C., E-mail: gsolomon@nano.ku.dk; Romano, Giuseppe

Electronic devices composed of single molecules constitute the ultimate limit in the continued downscaling of electronic components. A key challenge for single-molecule electronics is to control the temperature of these junctions. Controlling heating and cooling effects in individual vibrational modes can, in principle, be utilized to increase stability of single-molecule junctions under bias, to pump energy into particular vibrational modes to perform current-induced reactions, or to increase the resolution in inelastic electron tunneling spectroscopy by controlling the life-times of phonons in a molecule by suppressing absorption and external dissipation processes. Under bias the current and the molecule exchange energy, whichmore » typically results in heating of the molecule. However, the opposite process is also possible, where energy is extracted from the molecule by the tunneling current. Designing a molecular “heat sink” where a particular vibrational mode funnels heat out of the molecule and into the leads would be very desirable. It is even possible to imagine how the vibrational energy of the other vibrational modes could be funneled into the “cooling mode,” given the right molecular design. Previous efforts to understand heating and cooling mechanisms in single molecule junctions have primarily been concerned with small models, where it is unclear which molecular systems they correspond to. In this paper, our focus is on suppressing heating and obtaining current-induced cooling in certain vibrational modes. Strategies for cooling vibrational modes in single-molecule junctions are presented, together with atomistic calculations based on those strategies. Cooling and reduced heating are observed for two different cooling schemes in calculations of atomistic single-molecule junctions.« less

On the Chemistry and Physical Properties of Flux and Floating Zone Grown SmB6 Single Crystals

PubMed Central

Phelan, W. A.; Koohpayeh, S. M.; Cottingham, P.; Tutmaher, J. A.; Leiner, J. C.; Lumsden, M. D.; Lavelle, C. M.; Wang, X. P.; Hoffmann, C.; Siegler, M. A.; Haldolaarachchige, N.; Young, D. P.; McQueen, T. M.

2016-01-01

Recent theoretical and experimental findings suggest the long-known but not well understood low temperature resistance plateau of SmB6 may originate from protected surface states arising from a topologically non-trivial bulk band structure having strong Kondo hybridization. Yet others have ascribed this feature to impurities, vacancies, and surface reconstructions. Given the typical methods used to prepare SmB6 single crystals, flux and floating-zone procedures, such ascriptions should not be taken lightly. We demonstrate how compositional variations and/or observable amounts of impurities in SmB6 crystals grown using both procedures affect the physical properties. From X-ray diffraction, neutron diffraction, and X-ray computed tomography experiments we observe that natural isotope containing (SmB6) and doubly isotope enriched (154Sm11B6) crystals prepared using aluminum flux contain co-crystallized, epitaxial aluminum. Further, a large, nearly stoichiometric crystal of SmB6 was successfully grown using the float-zone technique; upon continuing the zone melting, samarium vacancies were introduced. These samarium vacancies drastically alter the resistance and plateauing magnitude of the low temperature resistance compared to stoichiometric SmB6. These results highlight that impurities and compositional variations, even at low concentrations, must be considered when collecting/analyzing physical property data of SmB6. Finally, a more accurate samarium-154 coherent neutron scattering length, 8.9(1) fm, is reported. PMID:26892648

On the Chemistry and Physical Properties of Flux and Floating Zone Grown SmB 6 Single Crystals

DOE PAGES

Phelan, W. A.; Koohpayeh, S. M.; Cottingham, P.; ...

2016-02-19

Recent theoretical and experimental findings suggest the long-known but not well understood low temperature resistance plateau of SmB 6 may originate from protected surface states arising from a topologically non-trivial bulk band structure having strong Kondo hybridization. Yet others have ascribed this feature to impurities, vacancies, and surface reconstructions. Given the typical methods used to prepare SmB 6 single crystals, flux and floating-zone procedures, such ascriptions should not be taken lightly. We demonstrate how compositional variations and/or observable amounts of impurities in SmB 6 crystals grown using both procedures affect the physical properties. From X-ray diffraction, neutron diffraction, and X-raymore » computed tomography experiments we observe that natural isotope containing (SmB 6) and doubly isotope enriched ( 154Sm 11B 6) crystals prepared using aluminum flux contain co-crystallized, epitaxial aluminum. Further, a large, nearly stoichiometric crystal of SmB 6 was successfully grown using the float-zone technique; upon continuing the zone melting, samarium vacancies were introduced. These samarium vacancies drastically alter the resistance and plateauing magnitude of the low temperature resistance compared to stoichiometric SmB 6. Finally, these results highlight that impurities and compositional variations, even at low concentrations, must be considered when collecting/analyzing physical property data of SmB 6. Finally, a more accurate samarium-154 coherent neutron scattering length, 8.9(1) fm, is reported.« less

Protein Crystals and their Growth

NASA Technical Reports Server (NTRS)

Chernov, A. A.

2004-01-01

Recent results on binding between protein molecules in crystal lattice, crystal-solution surface energy, elastic properties and strength and spontaneous crystal cracking are reviewed and discussed in the first half of this paper (Sea 2-4). In the second par&, some basic approaches to solubility of proteins are followed by overview on crystal nucleation and growth (Sec 5). It is argued that variability of mixing in batch crystallization may be a source for scattering of crystal number ultimately appearing in the batch. Frequency at which new molecules join crystal lattice is measured by kinetic coefficient and related to the observable crystal growth rate. Numerical criteria to discriminate diffusion and kinetic limited growth are discussed on this basis in Sec 7. In Sec 8, creation of defects is discussed with the emphasis on the role of impurities and convection on macromolecular crystal I;erfection.

DNA origami as biocompatible surface to match single-molecule and ensemble experiments

PubMed Central

Gietl, Andreas; Holzmeister, Phil; Grohmann, Dina; Tinnefeld, Philip

2012-01-01

Single-molecule experiments on immobilized molecules allow unique insights into the dynamics of molecular machines and enzymes as well as their interactions. The immobilization, however, can invoke perturbation to the activity of biomolecules causing incongruities between single molecule and ensemble measurements. Here we introduce the recently developed DNA origami as a platform to transfer ensemble assays to the immobilized single molecule level without changing the nano-environment of the biomolecules. The idea is a stepwise transfer of common functional assays first to the surface of a DNA origami, which can be checked at the ensemble level, and then to the microscope glass slide for single-molecule inquiry using the DNA origami as a transfer platform. We studied the structural flexibility of a DNA Holliday junction and the TATA-binding protein (TBP)-induced bending of DNA both on freely diffusing molecules and attached to the origami structure by fluorescence resonance energy transfer. This resulted in highly congruent data sets demonstrating that the DNA origami does not influence the functionality of the biomolecule. Single-molecule data collected from surface-immobilized biomolecule-loaded DNA origami are in very good agreement with data from solution measurements supporting the fact that the DNA origami can be used as biocompatible surface in many fluorescence-based measurements. PMID:22523083

Simple method of DNA stretching on glass substrate for fluorescence image and spectroscopy

NASA Astrophysics Data System (ADS)

Neupane, Guru P.; Dhakal, Krishna P.; Lee, Hyunsoo; Guthold, Martin; Joseph, Vincent S.; Hong, Jong-Dal; Kim, Jeongyong

2013-05-01

Study of biological molecule DNA has contributed to developing many breaking thoughts and wide applications in multidisciplinary fields, such as genomic, medical, sensing and forensic fields. Stretching of DNA molecules is an important supportive tool for AFM or spectroscopic studies of DNA in a single molecular level. In this article, we established a simple method of DNA stretching (to its full length) that occurred on a rotating negatively-charged surface of glass substrate. The isolation of a single DNA molecule was attained by the two competitive forces on DNA molecules, that is, the electrostatic attraction developed between the positively charged YOYO-1 stained DNA and the negatively charged substrate, and the centrifugal force of the rotating substrate, which separates the DNA aggregates into the single molecule. Density of stretched DNA molecules was controlled by selecting the specific parameters such as spinning time and rates, loading volume of DNA-dye complex solution etc. The atomic force microscopy image exhibited a single DNA molecule on the negatively-charged substrate in an isolated state. Further, the photoluminescence spectra of a single DNA molecule stained with YOYO-1 were achieved using the method developed in the present study, which is strongly believed to effectively support the spectroscopic analysis of DNA in a single molecular level.

Ab-initio study of C and O impurities in uranium nitride

NASA Astrophysics Data System (ADS)

Lopes, Denise Adorno; Claisse, Antoine; Olsson, Pär

2016-09-01

Uranium nitride (UN) has been considered a potential fuel for Generation IV (GEN-IV) nuclear reactors as well as a possible new fuel for Light Water Reactors (LWR), which would permit an extension of the fuel residence time in the reactor. Carbon and oxygen impurities play a key role in the UN microstructure, influencing important parameters such as creep, swelling, gas release under irradiation, compatibility with structural steel and coolants, and thermal stability. In this work, a systematic study of the electronic structure of UN containing C and O impurities using first-principles calculations by the Density Functional Theory (DFT) method is presented. In order to describe accurately the localized U 5f electrons, the DFT + U formalism was adopted. Moreover, to avoid convergence toward metastable states, the Occupation Matrix Control (OMC) methodology was applied. The incorporation of C and O in the N-vacancy is found to be energetically favorable. In addition, only for O, the incorporation in the interstitial position is energetically possible, showing some degree of solubility for this element in this site. The binding energies show that the pairs (Csbnd Nvac) and (Osbnd Nvac) interact much further than the other defects, which indicate the possible occurrence of vacancy drag phenomena and clustering of these impurities in grain boundaries, dislocations and free surfaces. The migration energy of an impurity by single N-vacancy show that C and O employ different paths during diffusion. Oxygen migration requires significantly lower energy than carbon. This fact is due to flexibility in the Usbnd O chemical bonds, which bend during the diffusion forming a pseudo UO2 coordination. On the other hand, C and N have a directional and inflexible chemical bond with uranium; always requiring the octahedral coordination. These findings provide detailed insight into how these impurities behave in the UN matrix, and can be of great interest for assisting the development of this new nuclear fuel for next-generation reactors.

Apparatus and method for the preparation of dioxygen difluoride

DOEpatents

Beattie, W.H.

1985-01-30

Dioxygen difluoride, O/sub 2/F/sub 2/, is prepared in high yield by microwave discharge of a flowing gas mixture of F/sub 2/ with or without a carrier gas such as argon or helium with the subsequent reaction of the discharge products with molecular gaseous oxygen downstream from and outside of the region of discharge. The O/sub 2/F/sub 2/ product is collected by cryogenic trapping, and is free of oxygen difluoride impurity and ozone since the oxygen molecules are not dissociated before they react with the microwave discharge products.

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

Berdichevskii, M.G.; Marusin, V.V.

The possible contributions of several processes to the experimentally observed heating of nitrogen plasmas in an electarodeless rf capacitive discharge at pressures of p=2.7-67 kPa are discussed. These processes are electron-rotational, vibrational--translational (V--T), and nonresonance vibrational--vibrational (V--V) energy exchange and effects due to O/sub 2/, H/sub 2/O, and NO impurities in the gas. It is shown that as the pressure is decreased the heating mechanism changes from quasiequilibrium to nonequilibrium V--T heating caused by overpopulation of high vibrational levels in the ground state of the nitrogen molecule.

Biopharmaceutical production: Applications of surface plasmon resonance biosensors.

PubMed

Thillaivinayagalingam, Pranavan; Gommeaux, Julien; McLoughlin, Michael; Collins, David; Newcombe, Anthony R

2010-01-15

Surface plasmon resonance (SPR) permits the quantitative analysis of therapeutic antibody concentrations and impurities including bacteria, Protein A, Protein G and small molecule ligands leached from chromatography media. The use of surface plasmon resonance has gained popularity within the biopharmaceutical industry due to the automated, label free, real time interaction that may be exploited when using this method. The application areas to assess protein interactions and develop analytical methods for biopharmaceutical downstream process development, quality control, and in-process monitoring are reviewed. 2009 Elsevier B.V. All rights reserved.

Electrostatic placement of single ferritin molecules

NASA Astrophysics Data System (ADS)

Kumagai, Shinya; Yoshii, Shigeo; Yamada, Kiyohito; Matsukawa, Nozomu; Fujiwara, Isamu; Iwahori, Kenji; Yamashita, Ichiro

2006-04-01

We electrostatically placed a single ferritin molecule on a nanometric 3-aminopropyltriethoxysilane (APTES) pattern that was on an oxidized Si substrate. The numerical analysis of the total interaction free energy for ferritin predicted that a quadrilateral array of 15nm diameter APTES nanodisks placed at intervals of 100nm would accommodate a single molecule of ferritin in each disk under a Debye length of 14nm. The experiments we conducted conformed to theoretical predictions and we successfully placed a single ferritin molecule on each ATPES disk without ferritin adsorbing on the SiO2 substrate surface.

SINGLE MOLECULE APPROACHES TO BIOLOGY, 2010 GORDON RESEARCH CONFERENCE, JUNE 27-JULY 2, 2010, ITALY

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

Professor William Moerner

2010-07-09

The 2010 Gordon Conference on Single-Molecule Approaches to Biology focuses on cutting-edge research in single-molecule science. Tremendous technical developments have made it possible to detect, identify, track, and manipulate single biomolecules in an ambient environment or even in a live cell. Single-molecule approaches have changed the way many biological problems are addressed, and new knowledge derived from these approaches continues to emerge. The ability of single-molecule approaches to avoid ensemble averaging and to capture transient intermediates and heterogeneous behavior renders them particularly powerful in elucidating mechanisms of biomolecular machines: what they do, how they work individually, how they work together,more » and finally, how they work inside live cells. The burgeoning use of single-molecule methods to elucidate biological problems is a highly multidisciplinary pursuit, involving both force- and fluorescence-based methods, the most up-to-date advances in microscopy, innovative biological and chemical approaches, and nanotechnology tools. This conference seeks to bring together top experts in molecular and cell biology with innovators in the measurement and manipulation of single molecules, and will provide opportunities for junior scientists and graduate students to present their work in poster format and to exchange ideas with leaders in the field. A number of excellent poster presenters will be selected for short oral talks. Topics as diverse as single-molecule sequencing, DNA/RNA/protein interactions, folding machines, cellular biophysics, synthetic biology and bioengineering, force spectroscopy, new method developments, superresolution imaging in cells, and novel probes for single-molecule imaging will be on the program. Additionally, the collegial atmosphere of this Conference, with programmed discussion sessions as well as opportunities for informal gatherings in the afternoons and evenings in the beauty of the Il Ciocco site in Tuscany, provides an avenue for scientists from different disciplines to interact and brainstorm and promotes cross-disciplinary collaborations directed toward compelling biological problems.« less

Raman spectroscopy: Watching a molecule breathe

NASA Astrophysics Data System (ADS)

Piatkowski, Lukasz; Hugall, James T.; van Hulst, Niek F.

2014-08-01

Marrying the single-molecule detection ability of surface-enhanced Raman scattering with the extreme time resolution of ultrafast coherent spectroscopy enables the vibrations of a single molecule to be observed.

Single-Molecule Probing the Energy Landscape of Enzymatic Reaction and Non-Covalent Interactions

NASA Astrophysics Data System (ADS)

Lu, H. Peter; Hu, Dehong; Chen, Yu; Vorpagel, Erich R.

2002-03-01

We have applied single-molecule spectroscopy under physiological conditions to study the mechanisms and dynamics of T4 lysozyme enzymatic reactions, characterizing mode-specific protein conformational dynamics. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time. The overall reaction rates were found to vary widely from molecule-to-molecule, and the initial non-specific binding of the enzyme to the substrate was seen to dominate this inhomogeneity. The reaction steps subsequent to the initial binding were found to have homogeneous rates. Molecular dynamics simulation has been applied to elucidate the mechanism and intermediate states of the single-molecule enzymatic reaction. Combining the analysis of single-molecule experimental trajectories, MD simulation trajectories, and statistical modeling, we have revealed the nature of multiple intermediate states involved in the active enzyme-substrate complex formation and the associated conformational change mechanism and dynamics.

A quantum spin-probe molecular microscope

NASA Astrophysics Data System (ADS)

Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L. C. L.

2016-10-01

Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy.

Single-molecule detection of proteins with antigen-antibody interaction using resistive-pulse sensing of submicron latex particles

NASA Astrophysics Data System (ADS)

Takakura, T.; Yanagi, I.; Goto, Y.; Ishige, Y.; Kohara, Y.

2016-03-01

We developed a resistive-pulse sensor with a solid-state pore and measured the latex agglutination of submicron particles induced by antigen-antibody interaction for single-molecule detection of proteins. We fabricated the pore based on numerical simulation to clearly distinguish between monomer and dimer latex particles. By measuring single dimers agglutinated in the single-molecule regime, we detected single human alpha-fetoprotein molecules. Adjusting the initial particle concentration improves the limit of detection (LOD) to 95 fmol/l. We established a theoretical model of the LOD by combining the reaction kinetics and the counting statistics to explain the effect of initial particle concentration on the LOD. The theoretical model shows how to improve the LOD quantitatively. The single-molecule detection studied here indicates the feasibility of implementing a highly sensitive immunoassay by a simple measurement method using resistive-pulse sensing.

Peering into Cells One Molecule at a Time: Single-molecule and plasmon-enhanced fluorescence super-resolution imaging

NASA Astrophysics Data System (ADS)

Biteen, Julie

2013-03-01

Single-molecule fluorescence brings the resolution of optical microscopy down to the nanometer scale, allowing us to unlock the mysteries of how biomolecules work together to achieve the complexity that is a cell. This high-resolution, non-destructive method for examining subcellular events has opened up an exciting new frontier: the study of macromolecular localization and dynamics in living cells. We have developed methods for single-molecule investigations of live bacterial cells, and have used these techniques to investigate thee important prokaryotic systems: membrane-bound transcription activation in Vibrio cholerae, carbohydrate catabolism in Bacteroides thetaiotaomicron, and DNA mismatch repair in Bacillus subtilis. Each system presents unique challenges, and we will discuss the important methods developed for each system. Furthermore, we use the plasmon modes of bio-compatible metal nanoparticles to enhance the emissivity of single-molecule fluorophores. The resolution of single-molecule imaging in cells is generally limited to 20-40 nm, far worse than the 1.5-nm localization accuracies which have been attained in vitro. We use plasmonics to improve the brightness and stability of single-molecule probes, and in particular fluorescent proteins, which are widely used for bio-imaging. We find that gold-coupled fluorophores demonstrate brighter, longer-lived emission, yielding an overall enhancement in total photons detected. Ultimately, this results in increased localization accuracy for single-molecule imaging. Furthermore, since fluorescence intensity is proportional to local electromagnetic field intensity, these changes in decay intensity and rate serve as a nm-scale read-out of the field intensity. Our work indicates that plasmonic substrates are uniquely advantageous for super-resolution imaging, and that plasmon-enhanced imaging is a promising technique for improving live cell single-molecule microscopy.

Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes

NASA Astrophysics Data System (ADS)

Pirrotta, Alessandro; De Vico, Luca; Solomon, Gemma C.; Franco, Ignacio

2017-03-01

The emerging ability to study physical properties at the single-molecule limit highlights the disparity between what is observable in an ensemble of molecules and the heterogeneous contributions of its constituent parts. A particularly convenient platform for single-molecule studies are molecular junctions where forces and voltages can be applied to individual molecules, giving access to a series of electromechanical observables that can form the basis of highly discriminating multidimensional single-molecule spectroscopies. Here, we computationally examine the ability of force and conductance to inform about molecular recognition events at the single-molecule limit. For this, we consider the force-conductance characteristics of a prototypical class of hydrogen bonded bimolecular complexes sandwiched between gold electrodes. The complexes consist of derivatives of a barbituric acid and a Hamilton receptor that can form up to six simultaneous hydrogen bonds. The simulations combine classical molecular dynamics of the mechanical deformation of the junction with non-equilibrium Green's function computations of the electronic transport. As shown, in these complexes hydrogen bonds mediate transport either by directly participating as a possible transport pathway or by stabilizing molecular conformations with enhanced conductance properties. Further, we observe that force-conductance correlations can be very sensitive to small changes in the chemical structure of the complexes and provide detailed information about the behavior of single molecules that cannot be gleaned from either measurement alone. In fact, there are regions during the elongation that are only mechanically active, others that are only conductance active, and regions where both force and conductance changes as the complex is mechanically manipulated. The implication is that force and conductance provide complementary information about the evolution of molecules in junctions that can be used to interrogate basic structure-transport relations at the single-molecule limit.

The Scope of Direct Alkylation of Gold Surface with Solutions of C1-C4 n-Alkylstannanes.

PubMed

Kaletová, Eva; Kohutová, Anna; Hajduch, Jan; Kaleta, Jiří; Bastl, Zdeněk; Pospíšil, Lubomír; Stibor, Ivan; Magnera, Thomas F; Michl, Josef

2015-09-23

Treatment of cleaned gold surfaces with dilute tetrahydrofuran or chloroform solutions of tetraalkylstannanes (alkyl = methyl, ethyl, n-propyl, n-butyl) or di-n-butylmethylstannyl tosylate under ambient conditions causes a self-limited growth of disordered monolayers consisting of alkyls and tin oxide. Extensive use of deuterium labeling showed that the alkyls originate from the stannane and not from ambient impurities, and that trialkylstannyl groups are absent in the monolayers, contrary to previous proposals. Methyl groups attached to the Sn atom are not transferred to the surface. Ethyl groups are transferred slowly, and propyl and butyl rapidly. In all cases, tin oxide is codeposited in submonolayer amounts. The monolayers were characterized by ellipsometry, contact angle goniometry, polarization modulated IR reflection absorption spectroscopy, X-ray photoelectron spectroscopy, and electrochemical impedance spectroscopy with ferrocyanide/ferricyanide, which revealed a very low charge-transfer resistance. The thermal stability of the monolayers and their resistance to solvents are comparable with those of an n-octadecanethiol monolayer. A preliminary examination of the kinetics of monolayer deposition from a THF solution of tetra-n-butylstannane revealed an approximately half-order dependence on the bulk solution concentration of the stannane, hinting that more than one alkyl can be transferred from a single stannane molecule. A detailed structure of the attachment of the alkyl groups is not known, and it is proposed that it involves direct single or multiple bonding of one or more C atoms to one or more Au atoms.

Single-Cell and Single-Molecule Analysis of Gene Expression Regulation.

PubMed

Vera, Maria; Biswas, Jeetayu; Senecal, Adrien; Singer, Robert H; Park, Hye Yoon

2016-11-23

Recent advancements in single-cell and single-molecule imaging technologies have resolved biological processes in time and space that are fundamental to understanding the regulation of gene expression. Observations of single-molecule events in their cellular context have revealed highly dynamic aspects of transcriptional and post-transcriptional control in eukaryotic cells. This approach can relate transcription with mRNA abundance and lifetimes. Another key aspect of single-cell analysis is the cell-to-cell variability among populations of cells. Definition of heterogeneity has revealed stochastic processes, determined characteristics of under-represented cell types or transitional states, and integrated cellular behaviors in the context of multicellular organisms. In this review, we discuss novel aspects of gene expression of eukaryotic cells and multicellular organisms revealed by the latest advances in single-cell and single-molecule imaging technology.

40 CFR 92.112 - Analytical gases.

Code of Federal Regulations, 2010 CFR

2010-07-01

... hydrocarbons plus impurities or by dynamic blending. Nitrogen shall be the predominant diluent with the balance... grade nitrogen as the diluent. (b) Gases for the hydrocarbon analyzer shall be single blends of propane... with a maximum NO2 concentration of 5 percent of the nominal value using zero grade nitrogen as the...

40 CFR 92.112 - Analytical gases.

Code of Federal Regulations, 2013 CFR

2013-07-01

... hydrocarbons plus impurities or by dynamic blending. Nitrogen shall be the predominant diluent with the balance... grade nitrogen as the diluent. (b) Gases for the hydrocarbon analyzer shall be single blends of propane... with a maximum NO2 concentration of 5 percent of the nominal value using zero grade nitrogen as the...

40 CFR 92.112 - Analytical gases.

Code of Federal Regulations, 2012 CFR

2012-07-01

... hydrocarbons plus impurities or by dynamic blending. Nitrogen shall be the predominant diluent with the balance... grade nitrogen as the diluent. (b) Gases for the hydrocarbon analyzer shall be single blends of propane... with a maximum NO2 concentration of 5 percent of the nominal value using zero grade nitrogen as the...

40 CFR 92.112 - Analytical gases.

Code of Federal Regulations, 2011 CFR

2011-07-01

... hydrocarbons plus impurities or by dynamic blending. Nitrogen shall be the predominant diluent with the balance... grade nitrogen as the diluent. (b) Gases for the hydrocarbon analyzer shall be single blends of propane... with a maximum NO2 concentration of 5 percent of the nominal value using zero grade nitrogen as the...

Molecular electronics with single molecules in solid-state devices.

PubMed

Moth-Poulsen, Kasper; Bjørnholm, Thomas

2009-09-01

The ultimate aim of molecular electronics is to understand and master single-molecule devices. Based on the latest results on electron transport in single molecules in solid-state devices, we focus here on new insights into the influence of metal electrodes on the energy spectrum of the molecule, and on how the electron transport properties of the molecule depend on the strength of the electronic coupling between it and the electrodes. A variety of phenomena are observed depending on whether this coupling is weak, intermediate or strong.

Single molecule views of Nature's nano-machines

NASA Astrophysics Data System (ADS)

Ha, Taekjip

2006-03-01

We are interested in the perturbational analysis of biological molecules to better understand their mechanisms. Our readout is the fluorescence signal from individual biomolecules, mainly in the form of single molecule fluorescence resonance energy transfer (FRET). We are pioneering approaches to perturb and control biomolecular conformations using external force (combination of single molecule FRET and optical trap) or other biological motifs (DNA hybridization, G-quadruplex, aptamers,.). In this talk, I will present our latest results on mapping the conformational energy landscape of the Holliday junction through simultaneous fluorescence and force measurements. In addition, a new nanomechanical device called single molecule nano-metronome will be discussed with an outlook toward controlling protein conformations using nucleic acids motifs.

Giant light-harvesting nanoantenna for single-molecule detection in ambient light

PubMed Central

Trofymchuk, Kateryna; Reisch, Andreas; Didier, Pascal; Fras, François; Gilliot, Pierre; Mely, Yves; Klymchenko, Andrey S.

2017-01-01

Here, we explore the enhancement of single molecule emission by polymeric nano-antenna that can harvest energy from thousands of donor dyes to a single acceptor. In this nano-antenna, the cationic dyes are brought together in very close proximity using bulky counterions, thus enabling ultrafast diffusion of excitation energy (≤30 fs) with minimal losses. Our 60-nm nanoparticles containing >10,000 rhodamine-based donor dyes can efficiently transfer energy to 1-2 acceptors resulting in an antenna effect of ~1,000. Therefore, single Cy5-based acceptors become 25-fold brighter than quantum dots QD655. This unprecedented amplification of the acceptor dye emission enables observation of single molecules at illumination powers (1-10 mW cm-2) that are >10,000-fold lower than typically required in single-molecule measurements. Finally, using a basic setup, which includes a 20X air objective and a sCMOS camera, we could detect single Cy5 molecules by simply shining divergent light on the sample at powers equivalent to sunlight. PMID:28983324

Fully Converting Graphite into Graphene Oxide Hydrogels by Preoxidation with Impure Manganese Dioxide.

PubMed

Sun, Jiaojiao; Yang, Ningxin; Sun, Zhe; Zeng, Mengqi; Fu, Lei; Hu, Chengguo; Hu, Shengshui

2015-09-30

Potassium permanganate (KMnO4) has been proved to be an efficient oxidant for converting graphite into graphite oxide, but its slow diffusion in the interlayer of graphite seriously restricts the production of graphene oxide (GO). Here, we demonstrate that the preoxidation of graphite by impure manganese dioxide (MnO2) in a mixture of concentrated sulfuric acid (H2SO4) and phosphorus pentoxide (P2O5) can efficiently improve the synthesis of GO when KMnO4 is employed as the oxidant. The prepared honey-like GO hydrogels possess a high yield of single-layer sheets, large sizes (average lateral size up to 20 μm), wide ranges of stable dispersion concentrations (from dilute solutions, viscous hydrogels, to dry films), and good conductivity after reduction (~2.9 × 10(4) S/m). The mechanism for the improved synthesis of GO by impure MnO2 was explored. The enhanced exfoliation and oxidation of graphite by oxidative Mn ions (mainly Mn(3+)), which are synergistically produced by the reaction of impure MnO2 with H2SO4 and P2O5, are found to be responsible for the improved synthesis of such GO hydrogels. Particularly, preoxidized graphite (POG) can be partially dispersed in water with sonication, which allows the facile construction of flexible and highly conductive graphene nanosheet film electrodes with excellent electrochemical sensing properties.

A study of crystal growth by solution technique. [triglycine sulfate single crystals

NASA Technical Reports Server (NTRS)

Lal, R. B.

1979-01-01

The advantages and mechanisms of crystal growth from solution are discussed as well as the effects of impurity adsorption on the kinetics of crystal growth. Uncertainities regarding crystal growth in a low gravity environment are examined. Single crystals of triglycine sulfate were grown using a low temperature solution technique. Small components were assembled and fabricated for future space flights. A space processing experiment proposal accepted by NASA for the Spacelab-3 mission is included.

SINGLE STRAND-CONTAINING REPLICATING MOLECULES OF CIRCULAR MITOCHONDRIAL DNA

PubMed Central

Wolstenholme, David R.; Koike, Katsuro; Cochran-Fouts, Patricia

1973-01-01

Mitochondrial DNAs (mtDNAs) from Chang rat solid hepatomas and Novikoff rat ascites hepatomas were examined in the electron microscope after preparation by the aqueous and by the formamide protein monolayer techniques. MtDNAs from both tumors were found to include double-forked circular molecules with a form and size suggesting they were replicative intermediates. These molecules were of two classes. In molecules of one class, all three segments were apparently totally double stranded. Molecules of the second class were distinguished by the fact that one of the segments spanning the region between the forks in which replication had occurred (the daughter segments) was either totally single stranded, or contained a single-stranded region associated with one of the forks. Daughter segments of both totally double-stranded and single strand-containing replicating molecules varied in length from about 3 to about 80% of the circular contour length of the molecule. Similar classes of replicating molecules were found in mtDNA from regenerating rat liver and chick embryos, indicating them to be normal intermediates in the replication of mtDNA All of the mtDNAs examined included partially single-stranded simple (nonforked) circular molecules. A possible scheme for the replication of mtDNA is presented, based on the different molecular forms observed PMID:4345165

Single-Molecule Electronic Measurements with Metal Electrodes

ERIC Educational Resources Information Center

Lindsay, Stuart

2005-01-01

A review of concepts like tunneling through a metal-molecule-metal-junction, contrast with electrochemical and optical-charge injection, strong-coupling limit, calculations of tunnel transport, electron transfer through Redox-active molecules is presented. This is followed by a discussion of experimental approaches for single-molecule measurements.

Three-dimensional single-molecule localization with nanometer accuracy using Metal-Induced Energy Transfer (MIET) imaging

NASA Astrophysics Data System (ADS)

Karedla, Narain; Chizhik, Anna M.; Stein, Simon C.; Ruhlandt, Daja; Gregor, Ingo; Chizhik, Alexey I.; Enderlein, Jörg

2018-05-01

Our paper presents the first theoretical and experimental study using single-molecule Metal-Induced Energy Transfer (smMIET) for localizing single fluorescent molecules in three dimensions. Metal-Induced Energy Transfer describes the resonant energy transfer from the excited state of a fluorescent emitter to surface plasmons in a metal nanostructure. This energy transfer is strongly distance-dependent and can be used to localize an emitter along one dimension. We have used Metal-Induced Energy Transfer in the past for localizing fluorescent emitters with nanometer accuracy along the optical axis of a microscope. The combination of smMIET with single-molecule localization based super-resolution microscopy that provides nanometer lateral localization accuracy offers the prospect of achieving isotropic nanometer localization accuracy in all three spatial dimensions. We give a thorough theoretical explanation and analysis of smMIET, describe its experimental requirements, also in its combination with lateral single-molecule localization techniques, and present first proof-of-principle experiments using dye molecules immobilized on top of a silica spacer, and of dye molecules embedded in thin polymer films.

Watching cellular machinery in action, one molecule at a time.

PubMed

Monachino, Enrico; Spenkelink, Lisanne M; van Oijen, Antoine M

2017-01-02

Single-molecule manipulation and imaging techniques have become important elements of the biologist's toolkit to gain mechanistic insights into cellular processes. By removing ensemble averaging, single-molecule methods provide unique access to the dynamic behavior of biomolecules. Recently, the use of these approaches has expanded to the study of complex multiprotein systems and has enabled detailed characterization of the behavior of individual molecules inside living cells. In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with applications both in vitro and in vivo, highlighting these advances by describing their applications in studies on cytoskeletal motors and DNA replication. We also discuss how single-molecule approaches have increased our understanding of the dynamic behavior of complex multiprotein systems. These methods have shown that the behavior of multicomponent protein complexes is highly stochastic and less linear and deterministic than previously thought. Further development of single-molecule tools will help to elucidate the molecular dynamics of these complex systems both inside the cell and in solutions with purified components. © 2017 Monachino et al.

Detailed analysis of complex single molecule FRET data with the software MASH

NASA Astrophysics Data System (ADS)

Hadzic, Mélodie C. A. S.; Kowerko, Danny; Börner, Richard; Zelger-Paulus, Susann; Sigel, Roland K. O.

2016-04-01

The processing and analysis of surface-immobilized single molecule FRET (Förster resonance energy transfer) data follows systematic steps (e.g. single molecule localization, clearance of different sources of noise, selection of the conformational and kinetic model, etc.) that require a solid knowledge in optics, photophysics, signal processing and statistics. The present proceeding aims at standardizing and facilitating procedures for single molecule detection by guiding the reader through an optimization protocol for a particular experimental data set. Relevant features were determined from single molecule movies (SMM) imaging Cy3- and Cy5-labeled Sc.ai5γ group II intron molecules synthetically recreated, to test the performances of four different detection algorithms. Up to 120 different parameterizations per method were routinely evaluated to finally establish an optimum detection procedure. The present protocol is adaptable to any movie displaying surface-immobilized molecules, and can be easily reproduced with our home-written software MASH (multifunctional analysis software for heterogeneous data) and script routines (both available in the download section of www.chem.uzh.ch/rna).

Superconducting YBa2Cu3O7 Powder: Reduction of Carbon, Moisture, and Impurity Phase Concentrations in Commercial Powders and the Reactivity with Moisture and Carbon Dioxide

NASA Technical Reports Server (NTRS)

Stecura, Stephan

1994-01-01

The purpose of this study was to determine the experimental parameters under which commercially pure YBa2Cu3O7 (1237) powders would be converted into a single phase (1237) powder only. Carbon (present as carbonate) and impurity phase concentrations in the (1237) powder are very dependent upon the firing temperatures, heat-treating temperatures and times, and atmosphere, while the moisture concentration is not. YBa2Cu3O7 powder with about 0.03 wt/%, carbon, 0.03 wt% moisture, and low impurity phase concentrations was obtained. Moisture and carbon concentrations in heat-treated powders did not increase significantly after 48 and 72 h of exposure to air, respectively, and after 144 h of exposure they were less than 0.26 and 0.08 wt/%, respectively. The (1237) powder first reacts with moisture and then hydroxide reacts with CO2. Firing the as received powders in air led to the decomposition of the superconducting (1237) phase.

Transverse mode selection in vertical-cavity surface-emitting lasers via deep impurity-induced disordering

NASA Astrophysics Data System (ADS)

O'Brien, Thomas R.; Kesler, Benjamin; Dallesasse, John M.

2017-02-01

Top emission 850-nm vertical-cavity surface-emitting lasers (VCSELs) demonstrating transverse mode selection via impurity-induced disordering (IID) are presented. The IID apertures are fabricated via closed ampoule zinc diffusion. A simple 1-D plane wave model based on the intermixing of Group III atoms during IID is presented to optimize the mirror loss of higher-order modes as a function of IID strength and depth. In addition, the impact of impurity diffusion into the cap layer of the lasers is shown to improve contact resistance. Further investigation of the mode-dependent characteristics of the device imply an increase in the thermal impedance associated with the fraction of IID contained within the oxide aperture. The optimization of the ratio of the IID aperture to oxide aperture is experimentally determined. Single fundamental mode output of 1.6 mW with 30 dBm side mode suppression ratio is achieved by a 3.0 μm oxide-confined device with an IID aperture of 1.3 μm indicating an optimal IID aperture size of 43% of the oxide aperture.

Many-body interferometry of magnetic polaron dynamics

NASA Astrophysics Data System (ADS)

Ashida, Yuto; Schmidt, Richard; Tarruell, Leticia; Demler, Eugene

2018-02-01

The physics of quantum impurities coupled to a many-body environment is among the most important paradigms of condensed-matter physics. In particular, the formation of polarons, quasiparticles dressed by the polarization cloud, is key to the understanding of transport, optical response, and induced interactions in a variety of materials. Despite recent remarkable developments in ultracold atoms and solid-state materials, the direct measurement of their ultimate building block, the polaron cloud, has remained a fundamental challenge. We propose and analyze a platform to probe time-resolved dynamics of polaron-cloud formation with an interferometric protocol. We consider an impurity atom immersed in a two-component Bose-Einstein condensate where the impurity generates spin-wave excitations that can be directly measured by the Ramsey interference of surrounding atoms. The dressing by spin waves leads to the formation of magnetic polarons and reveals a unique interplay between few- and many-body physics that is signified by single- and multi-frequency oscillatory dynamics corresponding to the formation of many-body bound states. Finally, we discuss concrete experimental implementations in ultracold atoms.

Site-occupation embedding theory using Bethe ansatz local density approximations

NASA Astrophysics Data System (ADS)

Senjean, Bruno; Nakatani, Naoki; Tsuchiizu, Masahisa; Fromager, Emmanuel

2018-06-01

Site-occupation embedding theory (SOET) is an alternative formulation of density functional theory (DFT) for model Hamiltonians where the fully interacting Hubbard problem is mapped, in principle exactly, onto an impurity-interacting (rather than a noninteracting) one. It provides a rigorous framework for combining wave-function (or Green function)-based methods with DFT. In this work, exact expressions for the per-site energy and double occupation of the uniform Hubbard model are derived in the context of SOET. As readily seen from these derivations, the so-called bath contribution to the per-site correlation energy is, in addition to the latter, the key density functional quantity to model in SOET. Various approximations based on Bethe ansatz and perturbative solutions to the Hubbard and single-impurity Anderson models are constructed and tested on a one-dimensional ring. The self-consistent calculation of the embedded impurity wave function has been performed with the density-matrix renormalization group method. It has been shown that promising results are obtained in specific regimes of correlation and density. Possible further developments have been proposed in order to provide reliable embedding functionals and potentials.

High efficiency crystalline silicon solar cells

NASA Technical Reports Server (NTRS)

Sah, C. Tang

1986-01-01

A review of the entire research program since its inception ten years ago is given. The initial effort focused on the effects of impurities on the efficiency of silicon solar cells to provide figures of maximum allowable impurity density for efficiencies up to about 16 to 17%. Highly accurate experimental techniques were extended to characterize the recombination properties of the residual imputities in the silicon solar cell. A numerical simulator of the solar cell was also developed, using the Circuit Technique for Semiconductor Analysis. Recent effort focused on the delineation of the material and device parameters which limited the silicon efficiency to below 20% and on an investigation of cell designs to break the 20% barrier. Designs of the cell device structure and geometry can further reduce recombination losses as well as the sensitivity and criticalness of the fabrication technology required to exceed 20%. Further research is needed on the fundamental characterization of the carrier recombination properties at the chemical impurity and physical defect centers. It is shown that only single crystalline silicon cell technology can be successful in attaining efficiencies greater than 20%.

Effect of charged impurities and morphology on oxidation reactivity of graphene

NASA Astrophysics Data System (ADS)

Yamamoto, Mahito; Cullen, William; Einstein, Theodore; Fuhrer, Michael

2012-02-01

Chemical reactivity of single layer graphene supported on a substrate is observed to be enhanced over thicker graphene. Possible mechanisms for the enhancement are Fermi level fluctuations due to ionized impurities on the substrate, and structural deformation of graphene induced by coupling to the substrate geometry. Here, we study the substrate-dependent oxidation reactivity of graphene, employing various substrates such as SiO2, mica, SiO2 nanoparticle thin film, and hexagonal boron nitride, which exhibit different charged impurity concentrations and surface roughness. Graphene is prepared on each substrate via mechanical exfoliation and oxidized in Ar/O2 mixture at temperatures from 400-600 ^oC. After oxidation, the Raman spectrum of graphene is measured, and the Raman D to G peak ratio is used to quantify the density of point defects introduced by oxidation. We will discuss the correlations among the defect density in oxidized graphene, substrate charge inhomogeneity, substrate corrugations, and graphene layer thickness. This work has been supported by the University of Maryland NSF-MRSEC under Grant No. DMR 05-20471 with supplemental funding from NRI, and NSF-DMR 08-04976.

Impurity precipitation in atomized particles evidenced by nano x-ray diffraction computed tomography

NASA Astrophysics Data System (ADS)

Bonnin, Anne; Wright, Jonathan P.; Tucoulou, Rémi; Palancher, Hervé

2014-08-01

Performances and physical properties of high technology materials are influenced or even determined by their initial microstructure and by the behavior of impurity phases. Characterizing these impurities and their relations with the surrounding matrix is therefore of primary importance but it unfortunately often requires a destructive approach, with the risk of misinterpreting the observations. The improvement we have done in high resolution X-ray diffraction computed tomography combined with the use of an X-ray nanoprobe allows non-destructive crystallographic description of materials with microscopic heterogeneous microstructure (with a grain size between 10 nm and 10 μm). In this study, the grain localization in a 2D slice of a 20 μm solidified atomized γU-Mo particle is shown and a minority U(C,O) phase (1 wt. %) with sub-micrometer sized grains was characterized inside. Evidence is presented showing that the onset of U(C,O) grain crystallization can be described by a precipitation mechanism since one single U-Mo grain has direct orientation relationship with more than one surrounding U(C,O) grains.

Monitoring Single-Molecule Protein Dynamics with a Carbon Nanotube Transistor

NASA Astrophysics Data System (ADS)

Collins, Philip G.

2014-03-01

Nanoscale electronic devices like field-effect transistors have long promised to provide sensitive, label-free detection of biomolecules. Single-walled carbon nanotubes press this concept further by not just detecting molecules but also monitoring their dynamics in real time. Recent measurements have demonstrated this premise by monitoring the single-molecule processivity of three different enzymes: lysozyme, protein Kinase A, and the Klenow fragment of DNA polymerase I. With all three enzymes, single molecules tethered to nanotube transistors were electronically monitored for 10 or more minutes, allowing us to directly observe a range of activity including rare transitions to chemically inactive and hyperactive conformations. The high bandwidth of the nanotube transistors further allow every individual chemical event to be clearly resolved, providing excellent statistics from tens of thousands of turnovers by a single enzyme. Initial success with three different enzymes indicates the generality and attractiveness of the nanotube devices as a new tool to complement other single-molecule techniques. Research on transduction mechanisms provides the design rules necessary to further generalize this architecture and apply it to other proteins. The purposeful incorporation of just one amino acid is sufficient to fabricate effective, single molecule sensors from a wide range of enzymes or proteins.

Single-molecule pull-down (SiMPull) for new-age biochemistry: methodology and biochemical applications of single-molecule pull-down (SiMPull) for probing biomolecular interactions in crude cell extracts.

PubMed

Aggarwal, Vasudha; Ha, Taekjip

2014-11-01

Macromolecular interactions play a central role in many biological processes. Protein-protein interactions have mostly been studied by co-immunoprecipitation, which cannot provide quantitative information on all possible molecular connections present in the complex. We will review a new approach that allows cellular proteins and biomolecular complexes to be studied in real-time at the single-molecule level. This technique is called single-molecule pull-down (SiMPull), because it integrates principles of conventional immunoprecipitation with the powerful single-molecule fluorescence microscopy. SiMPull is used to count how many of each protein is present in the physiological complexes found in cytosol and membranes. Concurrently, it serves as a single-molecule biochemical tool to perform functional studies on the pulled-down proteins. In this review, we will focus on the detailed methodology of SiMPull, its salient features and a wide range of biological applications in comparison with other biosensing tools. © 2014 WILEY Periodicals, Inc.

A reversible single-molecule switch based on activated antiaromaticity

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

Yin, Xiaodong; Zang, Yaping; Zhu, Liangliang

Single-molecule electronic devices provide researchers with an unprecedented ability to relate novel physical phenomena to molecular chemical structures. Typically, conjugated aromatic molecular backbones are relied upon to create electronic devices, where the aromaticity of the building blocks is used to enhance conductivity. We capitalize on the classical physical organic chemistry concept of Hückel antiaromaticity by demonstrating a single-molecule switch that exhibits low conductance in the neutral state and, upon electrochemical oxidation, reversibly switches to an antiaromatic high-conducting structure. We form single-molecule devices using the scanning tunneling microscope–based break-junction technique and observe an on/off ratio of ~70 for a thiophenylidene derivativemore » that switches to an antiaromatic state with 6-4-6-p electrons. Through supporting nuclear magnetic resonance measurements, we show that the doubly oxidized core has antiaromatic character and we use density functional theory calculations to rationalize the origin of the high-conductance state for the oxidized single-molecule junction. Together, our work demonstrates how the concept of antiaromaticity can be exploited to create single-molecule devices that are highly conducting.« less

A reversible single-molecule switch based on activated antiaromaticity

DOE PAGES

Yin, Xiaodong; Zang, Yaping; Zhu, Liangliang; ...

2017-10-27

Single-molecule electronic devices provide researchers with an unprecedented ability to relate novel physical phenomena to molecular chemical structures. Typically, conjugated aromatic molecular backbones are relied upon to create electronic devices, where the aromaticity of the building blocks is used to enhance conductivity. We capitalize on the classical physical organic chemistry concept of Hückel antiaromaticity by demonstrating a single-molecule switch that exhibits low conductance in the neutral state and, upon electrochemical oxidation, reversibly switches to an antiaromatic high-conducting structure. We form single-molecule devices using the scanning tunneling microscope–based break-junction technique and observe an on/off ratio of ~70 for a thiophenylidene derivativemore » that switches to an antiaromatic state with 6-4-6-p electrons. Through supporting nuclear magnetic resonance measurements, we show that the doubly oxidized core has antiaromatic character and we use density functional theory calculations to rationalize the origin of the high-conductance state for the oxidized single-molecule junction. Together, our work demonstrates how the concept of antiaromaticity can be exploited to create single-molecule devices that are highly conducting.« less

Validity criteria for Fermi's golden rule scattering rates applied to metallic nanowires.

PubMed

Moors, Kristof; Sorée, Bart; Magnus, Wim

2016-09-14

Fermi's golden rule underpins the investigation of mobile carriers propagating through various solids, being a standard tool to calculate their scattering rates. As such, it provides a perturbative estimate under the implicit assumption that the effect of the interaction Hamiltonian which causes the scattering events is sufficiently small. To check the validity of this assumption, we present a general framework to derive simple validity criteria in order to assess whether the scattering rates can be trusted for the system under consideration, given its statistical properties such as average size, electron density, impurity density et cetera. We derive concrete validity criteria for metallic nanowires with conduction electrons populating a single parabolic band subjected to different elastic scattering mechanisms: impurities, grain boundaries and surface roughness.

High purity low dislocation GaAs single crystals

NASA Technical Reports Server (NTRS)

Chen, R. T.; Holmes, D. E.; Kirkpatrick, C. G.

1982-01-01

Recent advances in GaAs bulk crystal growth using the LEC (liquid encapsulated Czochralski) technique are described. The dependence of the background impurity concentration and the dislocation density distribution on the materials synthesis and growth conditions were investigated. Background impurity concentrations as low as 4 x 10 to the 15th power were observed in undoped LEC GaAs. The dislocation density in selected regions of individual ingots was very low, below the 3000 cm .3000/sq cm threshold. The average dislocation density over a large annular ring on the wafers fell below the 10000/sq cm level for 3 inch diameter ingots. The diameter control during the program advanced to a diameter variation along a 3 inch ingot less than 2 mm.

Bold-line Monte Carlo and the nonequilibrium physics of strongly correlated many-body systems

NASA Astrophysics Data System (ADS)

Cohen, Guy

2015-03-01

This talk summarizes real time bold-line diagrammatic Monte-Carlo approaches to quantum impurity models, which make significant headway against the sign problem by summing over corrections to self-consistent diagrammatic expansions rather than a bare diagrammatic series. When the bold-line method is combined with reduced dynamics techniques both local single-time properties and two time correlators such as Green functions can be computed at very long timescales, enabling studies of nonequilibrium steady state behavior of quantum impurity models and creating new solvers for nonequilibrium dynamical mean field theory. This work is supported by NSF DMR 1006282, NSF CHE-1213247, DOE ER 46932, TG-DMR120085 and TG-DMR130036, and the Yad Hanadiv-Rothschild Foundation.

Procedure for normalization of cDNA libraries

DOEpatents

Bonaldo, Maria DeFatima; Soares, Marcelo Bento

1997-01-01

This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library.

A systematic evaluation of contemporary impurity correction methods in ITS-90 aluminium fixed point cells

NASA Astrophysics Data System (ADS)

da Silva, Rodrigo; Pearce, Jonathan V.; Machin, Graham

2017-06-01

The fixed points of the International Temperature Scale of 1990 (ITS-90) are the basis of the calibration of standard platinum resistance thermometers (SPRTs). Impurities in the fixed point material at the level of parts per million can give rise to an elevation or depression of the fixed point temperature of order of millikelvins, which often represents the most significant contribution to the uncertainty of SPRT calibrations. A number of methods for correcting for the effect of impurities have been advocated, but it is becoming increasingly evident that no single method can be used in isolation. In this investigation, a suite of five aluminium fixed point cells (defined ITS-90 freezing temperature 660.323 °C) have been constructed, each cell using metal sourced from a different supplier. The five cells have very different levels and types of impurities. For each cell, chemical assays based on the glow discharge mass spectroscopy (GDMS) technique have been obtained from three separate laboratories. In addition a series of high quality, long duration freezing curves have been obtained for each cell, using three different high quality SPRTs, all measured under nominally identical conditions. The set of GDMS analyses and freezing curves were then used to compare the different proposed impurity correction methods. It was found that the most consistent corrections were obtained with a hybrid correction method based on the sum of individual estimates (SIE) and overall maximum estimate (OME), namely the SIE/Modified-OME method. Also highly consistent was the correction technique based on fitting a Scheil solidification model to the measured freezing curves, provided certain well defined constraints are applied. Importantly, the most consistent methods are those which do not depend significantly on the chemical assay.

Physical properties of antiferromagnetic Mn doped ZnO samples: Role of impurity phase

NASA Astrophysics Data System (ADS)

Neogi, S. K.; Karmakar, R.; Misra, A. K.; Banerjee, A.; Das, D.; Bandyopadhyay, S.

2013-11-01

Structural, morphological, optical, and magnetic properties of nanocrystalline Zn1-xMnxO samples (x=0.01, 0.02, 0.04, 0.06, 0.08 and 0.10) prepared by the sol-gel route are studied by X-ray diffraction (XRD), Scanning electron microscopy (SEM), UV-visible absorption spectroscopy, Superconducting quantum interference device (SQUID) magnetometry and positron annihilation lifetime spectroscopy (PALS). XRD confirms formation of wurzite structure in all the Mn-substituted samples. A systematic increase in lattice constants and decrease in grain size have been observed with increase in manganese doping concentration up to 6 at% in the ZnO structure. An impurity phase (ZnMnO3) has been detected when percentage of Mn concentration is 6 at% or higher. The optical band gap of the Mn-substituted ZnO samples decrease with increase in doping concentration of manganese whereas the width of the localized states increases. The antiferromagnetic exchange interaction is strong in the samples for 2 and 4 at% of Mn doping but it reduces when the doping level increases from 6 at% and further. Positron life time components τ1 and τ2 are found to decrease when concentration of the dopant exceeds 6 at%. The changes in magnetic properties as well as positron annihilation parameters at higher manganese concentration have been assigned as due to the formation of impurity phase. Single phase structure has been observed up to 6 at% of Mn doping. Impurity phase has been developed above 6 at% of Mn doping. Antiferromagnetic and paramagnetic interactions are present in the samples. Defect parameters show sharp fall as Mn concentration above 6 at%. The magnetic and defect properties are modified by the formation of impurity phase.

Magnetic disorder and gap symmetry in the optimally electron-doped Sr(Fe ,Co ) 2As2 superconductor

NASA Astrophysics Data System (ADS)

Harnagea, Luminita; Mani, Giri; Kumar, Rohit; Singh, Surjeet

2018-02-01

We study magnetic pair breaking due to Mn impurities in the optimally electron-doped superconductor Sr (Fe0.88Co0.12)2As2 . We found that the as-grown Sr (Fe0.88-yCo0.12Mny) 2As2 single crystals exhibit a Tc suppression rate of ˜30 mK/μ Ω cm . This rate is slow but in good agreement with the previous reports on various magnetic/nonmagnetic impurities doped in other structurally analogous iron-based superconductors. The slow Tc suppression rate for magnetic impurities is often cited as an evidence for the nonvalidity of the s++-wave symmetry, which should have suppressed Tc in accordance with the Abrikosov-Gor'kov theory. Here, we show that the crystallographic defects are the main source of pair breaking in the as-grown crystals. Once these defects are healed by a low-temperature annealing, the true Tc suppression rate due to Mn impurities is revealed. We thus estimate the actual Tc suppression rate due to Mn alone to be ≥325 mK / μ Ω cm , and that due to the nonmagnetic crystallographic defects to be nearly 35 mK/μ Ω cm . These findings can be reconciled with the fully gapped s+--wave symmetry provided the interband scattering is rather weak. On the other hand, the s++-wave symmetry, which is resilient to the nonmagnetic defects and fragile against the magnetic impurities, can be a possible pairing symmetry in the optimally electron-doped SrFe2As2 . The crucial information that we provide here is that the magnetic pair breaking in these superconductors is not as weak as is generally believed.

Counting and behavior of an individual fluorescent molecule without hydrodynamic flow, immobilization, or photon count statistics.

PubMed

Földes-Papp, Zeno; Baumann, Gerd; Demel, Ulrike; Tilz, Gernot P

2004-04-01

Many theoretical models of molecular interactions, biochemical and chemical reactions are described on the single-molecule level, although our knowledge about the biochemical/chemical structure and dynamics primarily originates from the investigation of many-molecule systems. At present, there are four experimental platforms to observe the movement and the behavior of single fluorescent molecules: wide-field epi-illumination, near-field optical scanning, and laser scanning confocal and multiphoton microscopy. The platforms are combined with analytical methods such as fluorescence resonance energy transfer (FRET), fluorescence auto-or two-color cross-correlation spectroscopy (FCS), fluorescence polarizing anisotropy, fluorescence quenching and fluorescence lifetime measurements. The original contribution focuses on counting and characterization of freely diffusing single molecules in a single-phase like a solution or a membrane without hydrodynamic flow, immobilization or burst size analysis of intensity traces. This can be achieved, for example, by Fluorescence auto- or two-color cross-Correlation Spectroscopy as demonstrated in this original article. Three criteria (Földes-Papp (2002) Pteridines, 13, 73-82; Földes-Papp et al. (2004a) J. Immunol. Meth., 286, 1-11; Földes-Papp et al. (2004b) J. Immunol. Meth., 286, 13-20) are discussed for performing continuous measurements with one and the same single (individual) molecule, freely diffusing in a solution or a membrane, from sub-milliseconds up to severals hours. The 'algorithms' developed for single-molecule fluorescence detection are called the 'selfsame single-fluorescent-molecule regime'. An interesting application of the results found is in the field of immunology. The application of the theory to experimental results shows that the theory is consistent with the experiments. The exposition of the novel ideas on Single (Solution)-Phase Single-Molecule Fluorescence auto- or two-color cross-Correlation Spectroscopy (SPSM-FCS) are comprehensively presented. As technology continues to improve, the limits of what FCS/FCCS is being asked to do are concomitantly pushed.

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

Bai, Rui; Yi, Shaoqiong; Zhang, Xuejie

Highlights: • We evaluated both single molecule binding ability and expression level of 4 ICAM-1 mutations. • AFM was used to measure single-molecule binding ability on living cells. • The SNP of ICAM-1 may induce changes in expressions rather than single-molecule binding ability. - Abstract: Atherosclerosis (As) is characterized by chronic inflammation and is a major cause of human mortality. ICAM-1-mediated adhesion of leukocytes in vessel walls plays an important role in the pathogenesis of atherosclerosis. Two single nucleotide polymorphisms (SNPs) of human intercellular adhesion molecule-1 (ICAM-1), G241R and K469E, are associated with a number of inflammatory diseases. SNP inducedmore » changes in ICAM-1 function rely not only on the expression level but also on the single-molecule binding ability which may be affected by single molecule conformation variations such as protein splicing and folding. Previous studies have shown associations between G241R/K469E polymorphisms and ICAM-1 gene expression. Nevertheless, few studies have been done that focus on the single-molecule forces of the above SNPs and their ligands. In the current study, we evaluated both single molecule binding ability and expression level of 4 ICAM-1 mutations – GK (G241/K469), GE (G241/E469), RK (R241/K469) and RE (R241/E469). No difference in adhesion ability was observed via cell adhesion assay or atomic force microscopy (AFM) measurement when comparing the GK, GE, RK, or RE genotypes of ICAM-1 to each other. On the other hand, flow cytometry suggested that there was significantly higher expression of GE genotype of ICAM-1 on transfected CHO cells. Thus, we concluded that genetic susceptibility to diseases related to ICAM-1 polymorphisms, G241R or K469E, might be due to the different expressions of ICAM-1 variants rather than to the single-molecule binding ability of ICAM-1.« less

Improved Dye Stability in Single-Molecule Fluorescence Experiments

NASA Astrophysics Data System (ADS)

EcheverrÍa Aitken, Colin; Marshall, R. Andrew; Pugi, Joseph D.

Complex biological systems challenge existing single-molecule methods. In particular, dye stability limits observation time in singlemolecule fluorescence applications. Current approaches to improving dye performance involve the addition of enzymatic oxygen scavenging systems and small molecule additives. We present an enzymatic oxygen scavenging system that improves dye stability in single-molecule experiments. Compared to the currently-employed glucose-oxidase/catalase system, the protocatechuate-3,4-dioxygenase system achieves lower dissolved oxygen concentration and stabilizes single Cy3, Cy5, and Alexa488 fluorophores. Moreover, this system possesses none of the limitations associated with the glucose oxidase/catalase system. We also tested the effects of small molecule additives in this system. Biological reducing agents significantly destabilize the Cy5 fluorophore as a function of reducing potential. In contrast, anti-oxidants stabilize the Cy3 and Alexa488 fluorophores. We recommend use of the protocatechuate-3,4,-dioxygenase system with antioxidant additives, and in the absence of biological reducing agents. This system should have wide application to single-molecule fluorescence experiments.

Rapid and efficient detection of single chromophore molecules in aqueous solution

NASA Astrophysics Data System (ADS)

Li, Li-Qiang; Davis, Lloyd M.

1995-06-01

The first experiments on the detection of single fluorescent molecules in a flowing stream of an aqueous solution with high total efficiency are reported. A capillary injection system for sample delivery causes all the dye molecules to pass in a diffusion-broadened stream within a fast-moving sheath flow, through the center of the tightly focused laser excitation beam. Single-molecule detection with a transit time of approximately 1 ms is accomplished with a high-quantum-efficiency single-photon avalanche diode and a low dead-time time-gating circuit for discrimination of Raman-scattered light from the solvent.

Axial Colocalization of Single Molecules with Nanometer Accuracy Using Metal-Induced Energy Transfer.

PubMed

Isbaner, Sebastian; Karedla, Narain; Kaminska, Izabela; Ruhlandt, Daja; Raab, Mario; Bohlen, Johann; Chizhik, Alexey; Gregor, Ingo; Tinnefeld, Philip; Enderlein, Jörg; Tsukanov, Roman

2018-04-11

Single-molecule localization based super-resolution microscopy has revolutionized optical microscopy and routinely allows for resolving structural details down to a few nanometers. However, there exists a rather large discrepancy between lateral and axial localization accuracy, the latter typically three to five times worse than the former. Here, we use single-molecule metal-induced energy transfer (smMIET) to localize single molecules along the optical axis, and to measure their axial distance with an accuracy of 5 nm. smMIET relies only on fluorescence lifetime measurements and does not require additional complex optical setups.

Theoretical Investigation of Single-Molecule Sensing Using Nanotube-Enhanced Circular Dichroism.

PubMed

Silva, Jaime; Milne, Bruce F; Nogueira, Fernando

2018-06-19

First-principles calculations have been used to investigate the potential use of circular dichroism (CD) spectroscopy in single-molecule sensing. Using a real-space implementation of time-dependent density functional theory (TDDFT), several systems involving single-walled carbon nanotubes (SWCNT) and small molecules have been studied to evaluate their CD response. Large induced CD (ICD) effects, differing for each test molecule, were observed in all SWCNT-molecule complexes. As the SWCNT used in this study shows no intrinsic CD response, the ICD spectra are the result of interaction with the small molecules. This finding is general and independent of the (a)chiral nature of the adsorbed molecule. Our results indicate that it is possible to design a system that uses SWCNT for detection of molecules using the change in CD spectrum of the system induced by adsorption of the molecule onto the SWCNT surface.

Assembly and diploid architecture of an individual human genome via single-molecule technologies

PubMed Central

Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali

2015-01-01

We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality. PMID:26121404

Assembly and diploid architecture of an individual human genome via single-molecule technologies.

PubMed

Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali

2015-08-01

We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.

Detection of kinetic change points in piece-wise linear single molecule motion

NASA Astrophysics Data System (ADS)

Hill, Flynn R.; van Oijen, Antoine M.; Duderstadt, Karl E.

2018-03-01

Single-molecule approaches present a powerful way to obtain detailed kinetic information at the molecular level. However, the identification of small rate changes is often hindered by the considerable noise present in such single-molecule kinetic data. We present a general method to detect such kinetic change points in trajectories of motion of processive single molecules having Gaussian noise, with a minimum number of parameters and without the need of an assumed kinetic model beyond piece-wise linearity of motion. Kinetic change points are detected using a likelihood ratio test in which the probability of no change is compared to the probability of a change occurring, given the experimental noise. A predetermined confidence interval minimizes the occurrence of false detections. Applying the method recursively to all sub-regions of a single molecule trajectory ensures that all kinetic change points are located. The algorithm presented allows rigorous and quantitative determination of kinetic change points in noisy single molecule observations without the need for filtering or binning, which reduce temporal resolution and obscure dynamics. The statistical framework for the approach and implementation details are discussed. The detection power of the algorithm is assessed using simulations with both single kinetic changes and multiple kinetic changes that typically arise in observations of single-molecule DNA-replication reactions. Implementations of the algorithm are provided in ImageJ plugin format written in Java and in the Julia language for numeric computing, with accompanying Jupyter Notebooks to allow reproduction of the analysis presented here.

Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy

PubMed Central

Jiang, Shenghang; Park, Seongjin; Challapalli, Sai Divya; Fei, Jingyi; Wang, Yong

2017-01-01

We report a robust nonparametric descriptor, J′(r), for quantifying the density of clustering molecules in single-molecule localization microscopy. J′(r), based on nearest neighbor distribution functions, does not require any parameter as an input for analyzing point patterns. We show that J′(r) displays a valley shape in the presence of clusters of molecules, and the characteristics of the valley reliably report the clustering features in the data. Most importantly, the position of the J′(r) valley (rJm′) depends exclusively on the density of clustering molecules (ρc). Therefore, it is ideal for direct estimation of the clustering density of molecules in single-molecule localization microscopy. As an example, this descriptor was applied to estimate the clustering density of ptsG mRNA in E. coli bacteria. PMID:28636661

Space charge characteristics of fluorinated polyethylene: Different effects of fluorine and oxygen

NASA Astrophysics Data System (ADS)

Zhao, Ni; Nie, Yongjie; Li, Shengtao

2018-04-01

Direct fluorination are proved having obvious effect on space charge characteristics of polyethylene. It is believed that fluorine has a positive effect on suppressing space charge injection while oxygen impurity has a negative effect. However, the mechanism for the opposite effect of fluorine and oxygen is still not clear. In this paper, the different effects of fluorine and oxygen on space charge characteristics of fluorinated low density polyethylene (LDPE) are investigated on the basis of dielectric property, chemical constitutes and trap performance of surface fluorinated layers. The results show that direct fluorination has obvious effect on chemical constitutes and dielectric properties of surface fluorinated layer. Introduced fluorine is the main factor for suppressing charge injection from the electrodes, because it seriously changes the chemical constitutes and further the trap properties of the surface fluorinated layer. While introduction of oxygen results in heterocharges and makes space charge distribution complex, due to the ionization of generated small groups like C=O containing groups. Moreover, direct fluorination will result in cleavage of some LDPE molecules whatever there is oxygen impurity or not.

Simulation of Carbon Production from Material Surfaces in Fusion Devices

NASA Astrophysics Data System (ADS)

Marian, J.; Verboncoeur, J.

2005-10-01

Impurity production at carbon surfaces by plasma bombardment is a key issue for fusion devices as modest amounts can lead to excessive radiative power loss and/or hydrogenic D-T fuel dilution. Here results of molecular dynamics (MD) simulations of physical and chemical sputtering of hydrocarbons are presented for models of graphite and amorphous carbon, the latter formed by continuous D-T impingement in conditions that mimic fusion devices. The results represent more extensive simulations than we reported last year, including incident energies in the 30-300 eV range for a variety of incident angles that yield a number of different hydrocarbon molecules. The calculated low-energy yields clarify the uncertainty in the complex chemical sputtering rate since chemical bonding and hard-core repulsion are both included in the interatomic potential. Also modeled is hydrocarbon break-up by electron-impact collisions and transport near the surface. Finally, edge transport simulations illustrate the sensitivity of the edge plasma properties arising from moderate changes in the carbon content. The models will provide the impurity background for the TEMPEST kinetic edge code.

Exploring the chemical enhancement for surface-enhanced Raman scattering with Au bowtie nanoantennas

PubMed Central

Fromm, David P.; Kinkhabwala, Anika; Schuck, P. James; Moerner, W. E.; Sundaramurthy, Arvind; Kino, Gordon S.

2006-01-01

Single metallic bowtie nanoantennas provide a controllable environment for surface-enhanced Raman scattering (SERS) of adsorbed molecules. Bowties have experimentally measured electromagnetic enhancements, enabling estimation of chemical enhancement for both the bulk and the few-molecule regime. Strong fluctuations of selected Raman lines imply that a small number of p-mercaptoaniline molecules on a single bowtie show chemical enhancement >107, much larger than previously believed, likely due to charge transfer between the Au surface and the molecule. This chemical sensitivity of SERS has significant implications for ultra-sensitive detection of single molecules. PMID:16483189

Unraveling helicase mechanisms one molecule at a time

PubMed Central

Rasnik, Ivan; Myong, Sua; Ha, Taekjip

2006-01-01

Recent years have seen an increasing number of biological applications of single molecule techniques, evolving from a proof of principle type to the more sophisticated studies. Here we compare the capabilities and limitations of different single molecule techniques in studying the activities of helicases. Helicases share a common catalytic activity but present a high variability in kinetic and phenomenological behavior, making their studies ideal in exemplifying the use of the new single molecule techniques to answer biological questions. Unexpected phenomena have also been observed from individual molecules suggesting extended or alternative functionality of helicases in vivo. PMID:16935883

The symmetry of single-molecule conduction.

PubMed

Solomon, Gemma C; Gagliardi, Alessio; Pecchia, Alessandro; Frauenheim, Thomas; Di Carlo, Aldo; Reimers, Jeffrey R; Hush, Noel S

2006-11-14

We introduce the conductance point group which defines the symmetry of single-molecule conduction within the nonequilibrium Green's function formalism. It is shown, either rigorously or to within a very good approximation, to correspond to a molecular-conductance point group defined purely in terms of the properties of the conducting molecule. This enables single-molecule conductivity to be described in terms of key qualitative chemical descriptors that are independent of the nature of the molecule-conductor interfaces. We apply this to demonstrate how symmetry controls the conduction through 1,4-benzenedithiol chemisorbed to gold electrodes as an example system, listing also the molecular-conductance point groups for a range of molecules commonly used in molecular electronics research.

Single molecules can operate as primitive biological sensors, switches and oscillators.

PubMed

Hernansaiz-Ballesteros, Rosa D; Cardelli, Luca; Csikász-Nagy, Attila

2018-06-18

Switch-like and oscillatory dynamical systems are widely observed in biology. We investigate the simplest biological switch that is composed of a single molecule that can be autocatalytically converted between two opposing activity forms. We test how this simple network can keep its switching behaviour under perturbations in the system. We show that this molecule can work as a robust bistable system, even for alterations in the reactions that drive the switching between various conformations. We propose that this single molecule system could work as a primitive biological sensor and show by steady state analysis of a mathematical model of the system that it could switch between possible states for changes in environmental signals. Particularly, we show that a single molecule phosphorylation-dephosphorylation switch could work as a nucleotide or energy sensor. We also notice that a given set of reductions in the reaction network can lead to the emergence of oscillatory behaviour. We propose that evolution could have converted this switch into a single molecule oscillator, which could have been used as a primitive timekeeper. We discuss how the structure of the simplest known circadian clock regulatory system, found in cyanobacteria, resembles the proposed single molecule oscillator. Besides, we speculate if such minimal systems could have existed in an RNA world.

Far-field photostable optical nanoscopy (PHOTON) for real-time super-resolution single-molecular imaging of signaling pathways of single live cells

NASA Astrophysics Data System (ADS)

Huang, Tao; Browning, Lauren M.; Xu, Xiao-Hong Nancy

2012-04-01

Cellular signaling pathways play crucial roles in cellular functions and design of effective therapies. Unfortunately, study of cellular signaling pathways remains formidably challenging because sophisticated cascades are involved, and a few molecules are sufficient to trigger signaling responses of a single cell. Here we report the development of far-field photostable-optical-nanoscopy (PHOTON) with photostable single-molecule-nanoparticle-optical-biosensors (SMNOBS) for mapping dynamic cascades of apoptotic signaling pathways of single live cells in real-time at single-molecule (SM) and nanometer (nm) resolutions. We have quantitatively imaged single ligand molecules (tumor necrosis factor α, TNFα) and their binding kinetics with their receptors (TNFR1) on single live cells; tracked formation and internalization of their clusters and their initiation of intracellular signaling pathways in real-time; and studied apoptotic signaling dynamics and mechanisms of single live cells with sufficient temporal and spatial resolutions. This study provides new insights into complex real-time dynamic cascades and molecular mechanisms of apoptotic signaling pathways of single live cells. PHOTON provides superior imaging and sensing capabilities and SMNOBS offer unrivaled biocompatibility and photostability, which enable probing of signaling pathways of single live cells in real-time at SM and nm resolutions.Cellular signaling pathways play crucial roles in cellular functions and design of effective therapies. Unfortunately, study of cellular signaling pathways remains formidably challenging because sophisticated cascades are involved, and a few molecules are sufficient to trigger signaling responses of a single cell. Here we report the development of far-field photostable-optical-nanoscopy (PHOTON) with photostable single-molecule-nanoparticle-optical-biosensors (SMNOBS) for mapping dynamic cascades of apoptotic signaling pathways of single live cells in real-time at single-molecule (SM) and nanometer (nm) resolutions. We have quantitatively imaged single ligand molecules (tumor necrosis factor α, TNFα) and their binding kinetics with their receptors (TNFR1) on single live cells; tracked formation and internalization of their clusters and their initiation of intracellular signaling pathways in real-time; and studied apoptotic signaling dynamics and mechanisms of single live cells with sufficient temporal and spatial resolutions. This study provides new insights into complex real-time dynamic cascades and molecular mechanisms of apoptotic signaling pathways of single live cells. PHOTON provides superior imaging and sensing capabilities and SMNOBS offer unrivaled biocompatibility and photostability, which enable probing of signaling pathways of single live cells in real-time at SM and nm resolutions. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr11739h

Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

PubMed Central

Serag, Maged F.; Abadi, Maram; Habuchi, Satoshi

2014-01-01

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields. PMID:25283876

A single molecule perspective on the functional diversity of in vitro evolved β-glucuronidase.

PubMed

Liebherr, Raphaela B; Renner, Max; Gorris, Hans H

2014-04-23

The mechanisms that drive the evolution of new enzyme activity have been investigated by comparing the kinetics of wild-type and in vitro evolved β-glucuronidase (GUS) at the single molecule level. Several hundred single GUS molecules were separated in large arrays of 62,500 ultrasmall reaction chambers etched into the surface of a fused silica slide to observe their individual substrate turnover rates in parallel by fluorescence microscopy. Individual GUS molecules feature long-lived but divergent activity states, and their mean activity is consistent with classic Michaelis-Menten kinetics. The large number of single molecule substrate turnover rates is representative of the activity distribution within an entire enzyme population. Partially evolved GUS displays a much broader activity distribution among individual enzyme molecules than wild-type GUS. The broader activity distribution indicates a functional division of work between individual molecules in a population of partially evolved enzymes that-as so-called generalists-are characterized by their promiscuous activity with many different substrates.

Characterization of directionally solidified lead chloride

NASA Technical Reports Server (NTRS)

Singh, Narsingh Bahadur; Duval, W. M. B.; Rosenthal, B. N.

1988-01-01

A directionally solidified PbCl2 material was prepared and analyzed and subsequently used to grow single crystals. It was found that silicon, halogens, sulfur, magnesium, and phosphorus were the hardest impurities to remove by the single-pass directional freezing. Single crystals grown from the purified material displayed good scattering beam quality and showed no absorption peaks between 0.30 to 20 microns. Direct photographic observations of the solid-liquid interface at several G/V (denoting the temperature gradient and the translation velocity, respectively) ratio values showed that, as the G/V ratio decreased, the interface varied from a smooth convex surface to dendritic.

Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy

PubMed Central

Li, Mi; Dang, Dan; Liu, Lianqing; Xi, Ning; Wang, Yuechao

2017-01-01

The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed. PMID:28117741

Electrostatic melting in a single-molecule field-effect transistor with applications in genomic identification

PubMed Central

Vernick, Sefi; Trocchia, Scott M.; Warren, Steven B.; Young, Erik F.; Bouilly, Delphine; Gonzalez, Ruben L.; Nuckolls, Colin; Shepard, Kenneth L.

2017-01-01

The study of biomolecular interactions at the single-molecule level holds great potential for both basic science and biotechnology applications. Single-molecule studies often rely on fluorescence-based reporting, with signal levels limited by photon emission from single optical reporters. The point-functionalized carbon nanotube transistor, known as the single-molecule field-effect transistor, is a bioelectronics alternative based on intrinsic molecular charge that offers significantly higher signal levels for detection. Such devices are effective for characterizing DNA hybridization kinetics and thermodynamics and enabling emerging applications in genomic identification. In this work, we show that hybridization kinetics can be directly controlled by electrostatic bias applied between the device and the surrounding electrolyte. We perform the first single-molecule experiments demonstrating the use of electrostatics to control molecular binding. Using bias as a proxy for temperature, we demonstrate the feasibility of detecting various concentrations of 20-nt target sequences from the Ebolavirus nucleoprotein gene in a constant-temperature environment. PMID:28516911

Asymmetric Top Rotors in Superfluid Para-Hydrogen Nano-Clusters

NASA Astrophysics Data System (ADS)

Zeng, Tao; Li, Hui; Roy, Pierre-Nicholas

2012-06-01

We present the first simulation study of bosonic clusters doped with an asymmetric top molecule. A variation of the path-integral Monte Carlo method is developed to study a para-water (pH_2O) impurity in para-hydrogen (pH_2) clusters. The growth pattern of the doped clusters is similar in nature to that of the pure clusters. The pH_2O molecule appears to rotate freely in the cluster due to its large rotational constants and the lack of adiabatic following. The presence of pH_2O substantially quenches the superfluid response of pH_2 with respect to the space fixed frame. We also study the behaviour of a sulphur dioxide (32S16O_2) dopant in the pH_2 clusters. For such a heavy rotor, the adiabatic following of the pH_2 molecules is established and the superfluid renormalization of the rotational constants is observed. The rotational structure of the SO_2-p(H_2)_N clusters' ro-vibrational spectra is predicted. The connection between the superfluid response respect to the external boundary rotation and the dopant rotation is discussed.

Anchoring transition metal elements on graphene-like ZnO monolayer by CO molecule to obtain spin gapless semiconductor

NASA Astrophysics Data System (ADS)

Lei, Jie; Xu, Ming-Chun; Hu, Shu-Jun

2017-09-01

Graphene-like zinc oxide monolayer (g-ZnO) is a newfound two-dimensional material. Here we utilize the transition metal (TM) elements (Cr, Mn, Fe, Co, Ni, and Cu) to functionalize the g-ZnO with the aim of designing novel spintronics materials by using first-principles calculations. Our results show that although the adsorption of TM atoms can endow g-ZnO with magnetization and impurity states in the bandgap, the interaction between TM elements and g-ZnO is weak. We found that the attachment of CO molecule on TM is able to stabilize the TM elements on g-ZnO based on the 'donation and back-donation' mechanism. As a result, the adsorption energy of the CO-TM complex on g-ZnO is as high as 1.41-2.11 eV. Furthermore, the incorporation of CO molecule modulates the magnetic and electronic properties of the TM-decorated g-ZnO. In particular, the CO-Mn-g-ZnO is predicted to be a spin gapless semiconductor.

Arrhenius plot for a reaction catalyzed by a single molecule of β-galactosidase.

PubMed

Craig, Douglas B; Chase, Linden N

2012-02-21

The activity of a single enzyme molecule of Escherichia coli β-galactosidase was measured using a capillary electrophoresis continuous flow assay. As the enzyme molecule traversed the capillary the incubation temperature was increased from 27 to 37 °C, providing a continuous record of the change in rate with temperature. This data was used to develop a single enzyme molecule Arrhenius plot, from which the activation energy of the reaction was determined to be 31 kJ mol(-1).

Lucky Imaging: Improved Localization Accuracy for Single Molecule Imaging

PubMed Central

Cronin, Bríd; de Wet, Ben; Wallace, Mark I.

2009-01-01

We apply the astronomical data-analysis technique, Lucky imaging, to improve resolution in single molecule fluorescence microscopy. We show that by selectively discarding data points from individual single-molecule trajectories, imaging resolution can be improved by a factor of 1.6 for individual fluorophores and up to 5.6 for more complex images. The method is illustrated using images of fluorescent dye molecules and quantum dots, and the in vivo imaging of fluorescently labeled linker for activation of T cells. PMID:19348772

Manipulating molecular quantum states with classical metal atom inputs: demonstration of a single molecule NOR logic gate.

PubMed

Soe, We-Hyo; Manzano, Carlos; Renaud, Nicolas; de Mendoza, Paula; De Sarkar, Abir; Ample, Francisco; Hliwa, Mohamed; Echavarren, Antonio M; Chandrasekhar, Natarajan; Joachim, Christian

2011-02-22

Quantum states of a trinaphthylene molecule were manipulated by putting its naphthyl branches in contact with single Au atoms. One Au atom carries 1-bit of classical information input that is converted into quantum information throughout the molecule. The Au-trinaphthylene electronic interactions give rise to measurable energy shifts of the molecular electronic states demonstrating a NOR logic gate functionality. The NOR truth table of the single molecule logic gate was characterized by means of scanning tunnelling spectroscopy.

Single-Molecule Sensing with Nanopore Confinement: From Chemical Reactions to Biological Interactions.

PubMed

Lin, Yao; Ying, Yi-Lun; Gao, Rui; Long, Yi-Tao

2018-03-25

The nanopore can generate an electrochemical confinement for single-molecule sensing that help understand the fundamental chemical principle in nanoscale dimensions. By observing the generated ionic current, individual bond-making and bond-breaking steps, single biomolecule dynamic conformational changes and electron transfer processes that occur within pore can be monitored with high temporal and current resolution. These single-molecule studies in nanopore confinement are revealing information about the fundamental chemical and biological processes that cannot be extracted from ensemble measurements. In this Concept article, we introduce and discuss the electrochemical confinement effects on single-molecule covalent reactions, conformational dynamics of individual molecules and host-guest interactions in protein nanopores. Then, we extend the concept of nanopore confinement effects to confine electrochemical redox reactions in solid-state nanopores for developing new sensing mechanisms. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Targeting neurotransmitter receptors with nanoparticles in vivo allows single-molecule tracking in acute brain slices

NASA Astrophysics Data System (ADS)

Varela, Juan A.; Dupuis, Julien P.; Etchepare, Laetitia; Espana, Agnès; Cognet, Laurent; Groc, Laurent

2016-03-01

Single-molecule imaging has changed the way we understand many biological mechanisms, particularly in neurobiology, by shedding light on intricate molecular events down to the nanoscale. However, current single-molecule studies in neuroscience have been limited to cultured neurons or organotypic slices, leaving as an open question the existence of fast receptor diffusion in intact brain tissue. Here, for the first time, we targeted dopamine receptors in vivo with functionalized quantum dots and were able to perform single-molecule tracking in acute rat brain slices. We propose a novel delocalized and non-inflammatory way of delivering nanoparticles (NPs) in vivo to the brain, which allowed us to label and track genetically engineered surface dopamine receptors in neocortical neurons, revealing inherent behaviour and receptor activity regulations. We thus propose a NP-based platform for single-molecule studies in the living brain, opening new avenues of research in physiological and pathological animal models.

Single molecule characterization of DNA binding and strand displacement reactions on lithographic DNA origami microarrays.

PubMed

Scheible, Max B; Pardatscher, Günther; Kuzyk, Anton; Simmel, Friedrich C

2014-03-12

The combination of molecular self-assembly based on the DNA origami technique with lithographic patterning enables the creation of hierarchically ordered nanosystems, in which single molecules are positioned at precise locations on multiple length scales. Based on a hybrid assembly protocol utilizing DNA self-assembly and electron-beam lithography on transparent glass substrates, we here demonstrate a DNA origami microarray, which is compatible with the requirements of single molecule fluorescence and super-resolution microscopy. The spatial arrangement allows for a simple and reliable identification of single molecule events and facilitates automated read-out and data analysis. As a specific application, we utilize the microarray to characterize the performance of DNA strand displacement reactions localized on the DNA origami structures. We find considerable variability within the array, which results both from structural variations and stochastic reaction dynamics prevalent at the single molecule level.

Efficient use of single molecule time traces to resolve kinetic rates, models and uncertainties

NASA Astrophysics Data System (ADS)

Schmid, Sonja; Hugel, Thorsten

2018-03-01

Single molecule time traces reveal the time evolution of unsynchronized kinetic systems. Especially single molecule Förster resonance energy transfer (smFRET) provides access to enzymatically important time scales, combined with molecular distance resolution and minimal interference with the sample. Yet the kinetic analysis of smFRET time traces is complicated by experimental shortcomings—such as photo-bleaching and noise. Here we recapitulate the fundamental limits of single molecule fluorescence that render the classic, dwell-time based kinetic analysis unsuitable. In contrast, our Single Molecule Analysis of Complex Kinetic Sequences (SMACKS) considers every data point and combines the information of many short traces in one global kinetic rate model. We demonstrate the potential of SMACKS by resolving the small kinetic effects caused by different ionic strengths in the chaperone protein Hsp90. These results show an unexpected interrelation between conformational dynamics and ATPase activity in Hsp90.

Single molecule sequencing of the M13 virus genome without amplification

PubMed Central

Zhao, Luyang; Deng, Liwei; Li, Gailing; Jin, Huan; Cai, Jinsen; Shang, Huan; Li, Yan; Wu, Haomin; Xu, Weibin; Zeng, Lidong; Zhang, Renli; Zhao, Huan; Wu, Ping; Zhou, Zhiliang; Zheng, Jiao; Ezanno, Pierre; Yang, Andrew X.; Yan, Qin; Deem, Michael W.; He, Jiankui

2017-01-01

Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single-molecule sequencing platform from Direct Genomics to sequence the genome of the M13 virus. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x, with 100% coverage. We determined a consensus sequence accuracy of 100%. In contrast to GC bias inherent to NGS results, we demonstrated that our single-molecule sequencing method yields minimal GC bias. PMID:29253901

Single molecule sequencing of the M13 virus genome without amplification.

PubMed

Zhao, Luyang; Deng, Liwei; Li, Gailing; Jin, Huan; Cai, Jinsen; Shang, Huan; Li, Yan; Wu, Haomin; Xu, Weibin; Zeng, Lidong; Zhang, Renli; Zhao, Huan; Wu, Ping; Zhou, Zhiliang; Zheng, Jiao; Ezanno, Pierre; Yang, Andrew X; Yan, Qin; Deem, Michael W; He, Jiankui

2017-01-01

Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single-molecule sequencing platform from Direct Genomics to sequence the genome of the M13 virus. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x, with 100% coverage. We determined a consensus sequence accuracy of 100%. In contrast to GC bias inherent to NGS results, we demonstrated that our single-molecule sequencing method yields minimal GC bias.

In situ temperature monitoring in single-molecule FRET experiments

NASA Astrophysics Data System (ADS)

Hartmann, Andreas; Berndt, Frederic; Ollmann, Simon; Krainer, Georg; Schlierf, Michael

2018-03-01

Thermodynamic properties of single molecules including enthalpic and entropic contributions are often determined from experiments by a direct control and precise measurement of the local temperature. However, common temperature monitoring techniques using, for example, ultrafine temperature probes can lead to uncertainties as the probe cannot be placed in the vicinity of the molecule of interest. Here, we devised an approach to measure the local temperature in freely diffusing confocal single-molecule Förster Resonance Energy Transfer (smFRET) experiments in situ by directly adding the temperature-sensitive fluorescent dye Rhodamine B, whose fluorescence lifetime serves as a probe of the local temperature in the confocal volume. We demonstrate that the temperature and FRET efficiencies of static and dynamic molecules can be extracted within one measurement simultaneously, without the need of a reference chamber. We anticipate this technique to be particularly useful in the physicochemical analyses of temperature-dependent biomolecular processes from single-molecule measurements.

Study of the specific features of single-crystal boron microstructure

NASA Astrophysics Data System (ADS)

Blagov, A. E.; Vasil'ev, A. L.; Dmitriev, V. P.; Ivanova, A. G.; Kulikov, A. G.; Marchenkov, N. V.; Popov, P. A.; Presnyakov, M. Yu.; Prosekov, P. A.; Pisarevskii, Yu. V.; Targonskii, A. V.; Chernaya, T. S.; Chernyshov, D. Yu.

2017-09-01

A complex study of the structure of β-boron single crystal grown by the floating-zone method, with sizes significantly exceeding the analogs known in the literature, has been performed. The study includes X-ray diffraction analysis and X-ray diffractometry (measurement of pole figures and rocking curves), performed on both laboratory and synchrotron sources; atomic-resolution scanning transmission electron microscopy with spherical aberration correction; and energy-dispersive microanalysis. X-ray diffraction analysis using synchrotron radiation has been used to refine the β-boron structure and find impurity Si atoms. The relative variations in the unit-cell parameters a and c for the crystal bulk are found to be δ a/ a ≈ 0.4 and δ c/ c ≈ 0.1%. X-ray diffractometry has revealed that the single-crystal growth axis coincides with the [2\\bar 2013] crystallographic axis and makes an angle of 21.12° with the [0001] threefold axis. Electron microscopy data have confirmed that the sample under study is a β-boron crystal, which may contain 0.3-0.4 at % Si as an impurity. Planar defects (stacking faults and dislocations) are found. The results of additional measurements of the temperature dependence of the thermal conductivity of the crystal in the range of 50-300 K are indicative of its high structural quality.

Universality class of non-Fermi-liquid behavior in mixed-valence systems

NASA Astrophysics Data System (ADS)

Zhang, Guang-Ming; Su, Zhao-Bin; Yu, Lu

1996-01-01

A generalized Anderson single-impurity model with off-site Coulomb interactions is derived from the extended three-band Hubbard model, originally proposed to describe the physics of the copper oxides. Using the Abelian bosonization technique and canonical transformations, an effective Hamiltonian is derived in the strong-coupling limit, which is essentially analogous to the Toulouse limit of the ordinary Kondo problem. In this limit, the effective Hamiltonian can be exactly solved, with a mixed-valence quantum critical point separating two different Fermi-liquid phases, i.e., the Kondo phase and the empty orbital phase. In the mixed-valence quantum critical regime, the local moment is only partially quenched and x-ray edge singularities are generated. Around the quantum critical point, a type of non-Fermi-liquid behavior is predicted with an extra specific heat Cimp~T1/4 and a singular spin susceptibility χimp~T-3/4. At the same time, the effective Hamiltonian under single occupancy is transformed into a resonant-level model, from which the correct Kondo physical properties (specific heat, spin susceptibility, and an enhanced Wilson ratio) are easily rederived. Finally, a brief discussion is given to relate these theoretical results to observations in UPdxCu5-x (x=1,1.5) alloys, which show single-impurity critical behavior consistent with our predictions.

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

Jadeja, K.A.; Patel, K.M.; Tanna, R.L., E-mail: kumarpal@ipr.res.in

Low temperature glow discharge wall conditioning (GDC) using H{sub 2} gas is effective in reduction of oxygen and carbon (low-Z) contain impurities on near surface region of vessel wall. The high retention of hydrogen in vessel wall/components due to long operation of H{sub 2} GDC increases hydrogen out-gassing during tokamak operation and affects the production of high temperature plasma. The hydrogen retention can be reduced using inert gas GDC by sputter cleaning for short duration. But in that case the out-gassing rate of inert gas increases, that again impairs the plasma performance. To overcome above problems, the GDC with hydrogen-inertmore » gas mixture can be used for better removal of C and O surface contaminants and low hydrogen retention in surface. In ADITYA tokamak, H{sub 2}-GDC is carried out regularly after plasma operation, while the GDC with argon-hydrogen (Ar-H{sub 2}) mixture has been experimentally tested to observe the reduction of oxygen and carbon impurities along with low hydrogen retention. In Ar-H{sub 2} GDC, the reason being the formation of ArH{sup +} hydride ions, which has quite long life and more energy compared to H{sub 2}{sup +} ions formed in H{sub 2} GDC for breaking the bond of wall molecules. A systematic comparative study of H{sub 2} GDC and Ar-H{sub 2} Mixture GDC by changing the mixture ratio has been carried out in ADITYA tokamak. The relative levels of oxygen and carbon contain impurities have been measured using residual gas analyzer in both GDC's. We have observed a substantial reduction in oxygen and carbon impurities with a significant improvement in wall condition with Ar-H{sub 2} GDC compared to the H{sub 2} GDC. The effect of wall conditioning by Ar-H{sub 2} GDC on the performance of high temperature plasma operation will be presented in this paper. (author)« less

Ferroelectric Tungsten Bronze Bulk Crystals and Epitaxial Thin Films for Electro-Optic Device Applications

DTIC Science & Technology

1984-07-01

improved, they show a considerable enhancement in electro - optic and photorefractive properties, specifically for Ce(3+)-doped SBN:60 crystals. The...concentration of impurity ions increased. Undoped SBN:60 single crystals have also been grown and they are almost striation-free and exhibit excellent electro - optic properties.

Procedure for normalization of cDNA libraries

DOEpatents

Bonaldo, M.D.; Soares, M.B.

1997-12-30

This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library. 1 fig.

Discovery of iron group impurity ion spin states in single crystal Y{sub 2}SiO{sub 5} with strong coupling to whispering gallery photons

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

Goryachev, Maxim; Farr, Warrick G.; Carmo Carvalho, Natalia do

2015-06-08

Interaction of Whispering Gallery Modes (WGMs) with dilute spin ensembles in solids is an interesting paradigm of Hybrid Quantum Systems potentially beneficial for Quantum Signal Processing applications. Unexpected ion transitions are measured in single crystal Y{sub 2}SiO{sub 5} using WGM spectroscopy with large Zero Field Splittings at 14.7 GHz, 18.4 GHz, and 25.4 GHz, which also feature considerable anisotropy of the g-tensors as well as two inequivalent lattice sites, indicating spins from Iron Group Ion (IGI) impurities. The comparison of undoped and Rare-Earth doped crystals reveal that the IGIs are introduced during co-doping of Eu{sup 3+} or Er{sup 3+} with concentration at muchmore » lower levels of order 100 ppb. The strong coupling regime between an ensemble of IGI spins and WGM photons have been demonstrated at 18.4 GHz and near zero field. This approach together with useful optical properties of these ions opens avenues for “spins-in-solids” Quantum Electrodynamics.« less

Magnetic moment in single crystalline BaFe2-xZnxAs2

NASA Astrophysics Data System (ADS)

Guo, Yanfeng; Wang, Xia; Li, Jun; Yamaura, Kazunari; Takayama-Muromachi, Eiji

2012-02-01

Nature of the magnetism for iron-based superconductors (FeSCs) has been actively studied since the discovery of this new family of compounds in 2008, largely owing to its significance for interpreting the paring mechanism. The approach through impurity substitution to shed light into this issue is always one of major ways. The substitution shows distinct responses to species of impurities, where partially replacement of Fe in parent FeSCs with a variety of d-metals like Co, Ni Ru, Rh, Pd, Ir, and Pt generally results in superconductivity, while recent progress in Zn doped FeSCs gives rather contrary result, where Zn severely degenerates the TC. Herein we show the magnetic and electrical studies on BaFe2-xZnxAs2 single crystals. Nonmagnetic Zn doping progressively suppresses the SDW without resulting in superconductivity, while it alternatively develops the spin-glass state, possibly suggestive of local magnetic moment around the Fe sites induced by Zn. The characterizations by X-ray diffraction, magnetic and electrical transport properties, specific heat capacity, and Hall coefficient have been done and the results will be discussed in detail.

Thermal bleaching in single fluorescent molecules under two-photon excitation regime

NASA Astrophysics Data System (ADS)

Chirico, Giuseppe; Cannone, Fabio; Baldini, Giancarlo; Diaspro, Alberto

2003-07-01

Single molecule spectroscopy often requires the immobilization of the molecules onto solid or quasi-solid substrates and the use of relatively high excitation intensity We have studied the fluorescence emission of four common dyes used for bio-imaging studies, rhodamine 6G, fluorescein, pyrene and indo-1 at the single molecule level under two-photon excitation regime. We focus on two-photon excitation thermal effects on the stability of the single molecules, influencing the internal photo-dynamics and the total duration of the fluorescent emission. Single dye molecules, spread on a glass substrate by spin coating, show a constant fluorescence output till a sudden transition to a dark state very close to the background. The bleaching time that is found to vary in the series pyrene, Indo-1, fluorescein and rhodamine 6G from the fastest to the slowest one respectively, has a Gaussian distribution suggesting that bleaching is not due to photo-bleaching. Moreover it shows a correlation to the amount of absorbed power not re-irradiated as fluorescence and to the complexity of the molecule. These observations are interpreted as thermal bleaching where the temperature increase is induced by the two-photon excitation process. This study should be extended to different trapping media of interest in single molecule basic research and applications, such as silica and polyacrylamide gels or nanosctructured polyelectrolyte matrices. We think that the observed behavior and the correlations found to the molecular chemical and physical parameters, may be of some help for the design of molecules with switching on-off behavior of longer duration.

Spin doping using transition metal phthalocyanine molecules

PubMed Central

Atxabal, A.; Ribeiro, M.; Parui, S.; Urreta, L.; Sagasta, E.; Sun, X.; Llopis, R.; Casanova, F.; Hueso, L. E.

2016-01-01

Molecular spins have become key enablers for exploring magnetic interactions, quantum information processes and many-body effects in metals. Metal-organic molecules, in particular, let the spin state of the core metal ion to be modified according to its organic environment, allowing localized magnetic moments to emerge as functional entities with radically different properties from its simple atomic counterparts. Here, using and preserving the integrity of transition metal phthalocyanine high-spin complexes, we demonstrate the magnetic doping of gold thin films, effectively creating a new ground state. We demonstrate it by electrical transport measurements that are sensitive to the scattering of itinerant electrons with magnetic impurities, such as Kondo effect and weak antilocalization. Our work expands in a simple and powerful way the classes of materials that can be used as magnetic dopants, opening a new channel to couple the wide range of molecular properties with spin phenomena at a functional scale. PMID:27941810

Silicon photon-counting avalanche diodes for single-molecule fluorescence spectroscopy

PubMed Central

Michalet, Xavier; Ingargiola, Antonino; Colyer, Ryan A.; Scalia, Giuseppe; Weiss, Shimon; Maccagnani, Piera; Gulinatti, Angelo; Rech, Ivan; Ghioni, Massimo

2014-01-01

Solution-based single-molecule fluorescence spectroscopy is a powerful experimental tool with applications in cell biology, biochemistry and biophysics. The basic feature of this technique is to excite and collect light from a very small volume and work in a low concentration regime resulting in rare burst-like events corresponding to the transit of a single molecule. Detecting photon bursts is a challenging task: the small number of emitted photons in each burst calls for high detector sensitivity. Bursts are very brief, requiring detectors with fast response time and capable of sustaining high count rates. Finally, many bursts need to be accumulated to achieve proper statistical accuracy, resulting in long measurement time unless parallelization strategies are implemented to speed up data acquisition. In this paper we will show that silicon single-photon avalanche diodes (SPADs) best meet the needs of single-molecule detection. We will review the key SPAD parameters and highlight the issues to be addressed in their design, fabrication and operation. After surveying the state-of-the-art SPAD technologies, we will describe our recent progress towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. The potential of this approach is illustrated with single-molecule Förster resonance energy transfer measurements. PMID:25309114

Development of new photon-counting detectors for single-molecule fluorescence microscopy.

PubMed

Michalet, X; Colyer, R A; Scalia, G; Ingargiola, A; Lin, R; Millaud, J E; Weiss, S; Siegmund, Oswald H W; Tremsin, Anton S; Vallerga, John V; Cheng, A; Levi, M; Aharoni, D; Arisaka, K; Villa, F; Guerrieri, F; Panzeri, F; Rech, I; Gulinatti, A; Zappa, F; Ghioni, M; Cova, S

2013-02-05

Two optical configurations are commonly used in single-molecule fluorescence microscopy: point-like excitation and detection to study freely diffusing molecules, and wide field illumination and detection to study surface immobilized or slowly diffusing molecules. Both approaches have common features, but also differ in significant aspects. In particular, they use different detectors, which share some requirements but also have major technical differences. Currently, two types of detectors best fulfil the needs of each approach: single-photon-counting avalanche diodes (SPADs) for point-like detection, and electron-multiplying charge-coupled devices (EMCCDs) for wide field detection. However, there is room for improvements in both cases. The first configuration suffers from low throughput owing to the analysis of data from a single location. The second, on the other hand, is limited to relatively low frame rates and loses the benefit of single-photon-counting approaches. During the past few years, new developments in point-like and wide field detectors have started addressing some of these issues. Here, we describe our recent progresses towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. We also discuss our development of large area photon-counting cameras achieving subnanosecond resolution for fluorescence lifetime imaging applications at the single-molecule level.

Development of new photon-counting detectors for single-molecule fluorescence microscopy

PubMed Central

Michalet, X.; Colyer, R. A.; Scalia, G.; Ingargiola, A.; Lin, R.; Millaud, J. E.; Weiss, S.; Siegmund, Oswald H. W.; Tremsin, Anton S.; Vallerga, John V.; Cheng, A.; Levi, M.; Aharoni, D.; Arisaka, K.; Villa, F.; Guerrieri, F.; Panzeri, F.; Rech, I.; Gulinatti, A.; Zappa, F.; Ghioni, M.; Cova, S.

2013-01-01

Two optical configurations are commonly used in single-molecule fluorescence microscopy: point-like excitation and detection to study freely diffusing molecules, and wide field illumination and detection to study surface immobilized or slowly diffusing molecules. Both approaches have common features, but also differ in significant aspects. In particular, they use different detectors, which share some requirements but also have major technical differences. Currently, two types of detectors best fulfil the needs of each approach: single-photon-counting avalanche diodes (SPADs) for point-like detection, and electron-multiplying charge-coupled devices (EMCCDs) for wide field detection. However, there is room for improvements in both cases. The first configuration suffers from low throughput owing to the analysis of data from a single location. The second, on the other hand, is limited to relatively low frame rates and loses the benefit of single-photon-counting approaches. During the past few years, new developments in point-like and wide field detectors have started addressing some of these issues. Here, we describe our recent progresses towards increasing the throughput of single-molecule fluorescence spectroscopy in solution using parallel arrays of SPADs. We also discuss our development of large area photon-counting cameras achieving subnanosecond resolution for fluorescence lifetime imaging applications at the single-molecule level. PMID:23267185

Precision analysis for standard deviation measurements of immobile single fluorescent molecule images.

PubMed

DeSantis, Michael C; DeCenzo, Shawn H; Li, Je-Luen; Wang, Y M

2010-03-29

Standard deviation measurements of intensity profiles of stationary single fluorescent molecules are useful for studying axial localization, molecular orientation, and a fluorescence imaging system's spatial resolution. Here we report on the analysis of the precision of standard deviation measurements of intensity profiles of single fluorescent molecules imaged using an EMCCD camera.We have developed an analytical expression for the standard deviation measurement error of a single image which is a function of the total number of detected photons, the background photon noise, and the camera pixel size. The theoretical results agree well with the experimental, simulation, and numerical integration results. Using this expression, we show that single-molecule standard deviation measurements offer nanometer precision for a large range of experimental parameters.

Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

DOEpatents

Sansinena, Jose-Maria [Los Alamos, NM; Redondo, Antonio [Los Alamos, NM; Olazabal, Virginia [Los Alamos, NM; Hoffbauer, Mark A [Los Alamos, NM; Akhadov, Elshan A [Los Alamos, NM

2009-12-29

A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

Single DNA molecule detection using nanopipettes and nanoparticles.

PubMed

Karhanek, Miloslav; Kemp, Jennifer T; Pourmand, Nader; Davis, Ronald W; Webb, Chris D

2005-02-01

Single DNA molecules labeled with nanoparticles can be detected by blockades of ionic current as they are translocated through a nanopipette tip formed by a pulled glass capillary. The nanopipette detection technique can provide not only tools for detection and identification of single DNA and protein molecules but also deeper insight and understanding of stochastic interactions of various biomolecules with their environment.

Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

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

Sansinena, Jose-Maria; Redondo, Antonio; Olazabal, Virginia

2017-09-12

A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

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

Sansinena, Jose-Maria; Redondo, Antonio; Olazabal, Virginia

2017-07-18

A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

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

Sansinena, Jose-Maria; Redondo, Antonio; Olazabal, Virginia

A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

Single-Molecule Bioelectronics

PubMed Central

Rosenstein, Jacob K.; Lemay, Serge G.; Shepard, Kenneth L.

2014-01-01

Experimental techniques which interface single biomolecules directly with microelectronic systems are increasingly being used in a wide range of powerful applications, from fundamental studies of biomolecules to ultra-sensitive assays. Here we review several technologies which can perform electronic measurements of single molecules in solution: ion channels, nanopore sensors, carbon nanotube field-effect transistors, electron tunneling gaps, and redox cycling. We discuss the shared features among these techniques that enable them to resolve individual molecules, and discuss their limitations. Recordings from each of these methods all rely on similar electronic instrumentation, and we discuss the relevant circuit implementations and potential for scaling these single-molecule bioelectronic interfaces to high-throughput arrayed sensing platforms. PMID:25529538

Stiffness, working stroke, and force of single-myosin molecules in skeletal muscle: elucidation of these mechanical properties via nonlinear elasticity evaluation.

PubMed

Kaya, Motoshi; Higuchi, Hideo

2013-11-01

In muscles, the arrays of skeletal myosin molecules interact with actin filaments and continuously generate force at various contraction speeds. Therefore, it is crucial for myosin molecules to generate force collectively and minimize the interference between individual myosin molecules. Knowledge of the elasticity of myosin molecules is crucial for understanding the molecular mechanisms of muscle contractions because elasticity directly affects the working and drag (resistance) force generation when myosin molecules are positively or negatively strained. The working stroke distance is also an important mechanical property necessary for elucidation of the thermodynamic efficiency of muscle contractions at the molecular level. In this review, we focus on these mechanical properties obtained from single-fiber and single-molecule studies and discuss recent findings associated with these mechanical properties. We also discuss the potential molecular mechanisms associated with reduction of the drag effect caused by negatively strained myosin molecules.

Current rectification in a single molecule diode: the role of electrode coupling.

PubMed

Sherif, Siya; Rubio-Bollinger, Gabino; Pinilla-Cienfuegos, Elena; Coronado, Eugenio; Cuevas, Juan Carlos; Agraït, Nicolás

2015-07-24

We demonstrate large rectification ratios (> 100) in single-molecule junctions based on a metal-oxide cluster (polyoxometalate), using a scanning tunneling microscope (STM) both at ambient conditions and at low temperature. These rectification ratios are the largest ever observed in a single-molecule junction, and in addition these junctions sustain current densities larger than 10(5) A cm(-2). By following the variation of the I-V characteristics with tip-molecule separation we demonstrate unambiguously that rectification is due to asymmetric coupling to the electrodes of a molecule with an asymmetric level structure. This mechanism can be implemented in other type of molecular junctions using both organic and inorganic molecules and provides a simple strategy for the rational design of molecular diodes.

Current rectification in a single molecule diode: the role of electrode coupling

NASA Astrophysics Data System (ADS)

Sherif, Siya; Rubio-Bollinger, Gabino; Pinilla-Cienfuegos, Elena; Coronado, Eugenio; Cuevas, Juan Carlos; Agraït, Nicolás

2015-07-01

We demonstrate large rectification ratios (\\gt 100) in single-molecule junctions based on a metal-oxide cluster (polyoxometalate), using a scanning tunneling microscope (STM) both at ambient conditions and at low temperature. These rectification ratios are the largest ever observed in a single-molecule junction, and in addition these junctions sustain current densities larger than 105 A cm-2. By following the variation of the I-V characteristics with tip-molecule separation we demonstrate unambiguously that rectification is due to asymmetric coupling to the electrodes of a molecule with an asymmetric level structure. This mechanism can be implemented in other type of molecular junctions using both organic and inorganic molecules and provides a simple strategy for the rational design of molecular diodes.

Distinguishing Lead and Molecule States in Graphene-Based Single-Electron Transistors

PubMed Central

2017-01-01

Graphene provides a two-dimensional platform for contacting individual molecules, which enables transport spectroscopy of molecular orbital, spin, and vibrational states. Here we report single-electron tunneling through a molecule that has been anchored to two graphene leads. Quantum interference within the graphene leads gives rise to an energy-dependent transmission and fluctuations in the sequential tunnel-rates. The lead states are electrostatically tuned by a global back-gate, resulting in a distinct pattern of varying intensity in the measured conductance maps. This pattern could potentially obscure transport features that are intrinsic to the molecule under investigation. Using ensemble averaged magneto-conductance measurements, lead and molecule states are disentangled, enabling spectroscopic investigation of the single molecule. PMID:28423272

DNA-psoralen interaction: a single molecule experiment.

PubMed

Rocha, M S; Viana, N B; Mesquita, O N

2004-11-15

By attaching one end of a single lambda-DNA molecule to a microscope coverslip and the other end to a polystyrene microsphere trapped by an optical tweezers, we can study the entropic elasticity of the lambda-DNA by measuring force versus extension as we stretch the molecule. This powerful method permits single molecule studies. We are particularly interested in the effects of the photosensitive drug psoralen on the elasticity of the DNA molecule. We have illuminated the sample with different light sources, studying how the different wavelengths affect the psoralen-DNA linkage. To do this, we measure the persistence length of individual DNA-psoralen complexes.

Quantum design rules for single molecule logic gates.

PubMed

Renaud, N; Hliwa, M; Joachim, C

2011-08-28

Recent publications have demonstrated how to implement a NOR logic gate with a single molecule using its interaction with two surface atoms as logical inputs [W. Soe et al., ACS Nano, 2011, 5, 1436]. We demonstrate here how this NOR logic gate belongs to the general family of quantum logic gates where the Boolean truth table results from a full control of the quantum trajectory of the electron transfer process through the molecule by very local and classical inputs practiced on the molecule. A new molecule OR gate is proposed for the logical inputs to be also single metal atoms, one per logical input.

Single-molecule fluorescence microscopy review: shedding new light on old problems

PubMed Central

Shashkova, Sviatlana

2017-01-01

Fluorescence microscopy is an invaluable tool in the biosciences, a genuine workhorse technique offering exceptional contrast in conjunction with high specificity of labelling with relatively minimal perturbation to biological samples compared with many competing biophysical techniques. Improvements in detector and dye technologies coupled to advances in image analysis methods have fuelled recent development towards single-molecule fluorescence microscopy, which can utilize light microscopy tools to enable the faithful detection and analysis of single fluorescent molecules used as reporter tags in biological samples. For example, the discovery of GFP, initiating the so-called ‘green revolution’, has pushed experimental tools in the biosciences to a completely new level of functional imaging of living samples, culminating in single fluorescent protein molecule detection. Today, fluorescence microscopy is an indispensable tool in single-molecule investigations, providing a high signal-to-noise ratio for visualization while still retaining the key features in the physiological context of native biological systems. In this review, we discuss some of the recent discoveries in the life sciences which have been enabled using single-molecule fluorescence microscopy, paying particular attention to the so-called ‘super-resolution’ fluorescence microscopy techniques in live cells, which are at the cutting-edge of these methods. In particular, how these tools can reveal new insights into long-standing puzzles in biology: old problems, which have been impossible to tackle using other more traditional tools until the emergence of new single-molecule fluorescence microscopy techniques. PMID:28694303

Nanomanipulation of Single RNA Molecules by Optical Tweezers

PubMed Central

Stephenson, William; Wan, Gorby; Tenenbaum, Scott A.; Li, Pan T. X.

2014-01-01

A large portion of the human genome is transcribed but not translated. In this post genomic era, regulatory functions of RNA have been shown to be increasingly important. As RNA function often depends on its ability to adopt alternative structures, it is difficult to predict RNA three-dimensional structures directly from sequence. Single-molecule approaches show potentials to solve the problem of RNA structural polymorphism by monitoring molecular structures one molecule at a time. This work presents a method to precisely manipulate the folding and structure of single RNA molecules using optical tweezers. First, methods to synthesize molecules suitable for single-molecule mechanical work are described. Next, various calibration procedures to ensure the proper operations of the optical tweezers are discussed. Next, various experiments are explained. To demonstrate the utility of the technique, results of mechanically unfolding RNA hairpins and a single RNA kissing complex are used as evidence. In these examples, the nanomanipulation technique was used to study folding of each structural domain, including secondary and tertiary, independently. Lastly, the limitations and future applications of the method are discussed. PMID:25177917

Homebuilt single-molecule scanning confocal fluorescence microscope studies of single DNA/protein interactions.

PubMed

Zheng, Haocheng; Goldner, Lori S; Leuba, Sanford H

2007-03-01

Many technical improvements in fluorescence microscopy over the years have focused on decreasing background and increasing the signal to noise ratio (SNR). The scanning confocal fluorescence microscope (SCFM) represented a major improvement in these efforts. The SCFM acquires signal from a thin layer of a thick sample, rejecting light whose origin is not in the focal plane thereby dramatically decreasing the background signal. A second major innovation was the advent of high quantum-yield, low noise, single-photon counting detectors. The superior background rejection of SCFM combined with low-noise, high-yield detectors makes it possible to detect the fluorescence from single-dye molecules. By labeling a DNA molecule or a DNA/protein complex with a donor/acceptor dye pair, fluorescence resonance energy transfer (FRET) can be used to track conformational changes in the molecule/complex itself, on a single molecule/complex basis. In this methods paper, we describe the core concepts of SCFM in the context of a study that uses FRET to reveal conformational fluctuations in individual Holliday junction DNA molecules and nucleosomal particles. We also discuss data processing methods for SCFM.