WorldWideScience

Sample records for ultrafast molecular structure

  1. Molecular-structure control of ultrafast electron injection at cationic porphyrin-CdTe quantum dot interfaces

    KAUST Repository

    Aly, Shawkat Mohammede

    2015-03-05

    Charge transfer (CT) at donor (D)/acceptor (A) interfaces is central to the functioning of photovoltaic and light-emitting devices. Understanding and controlling this process on the molecular level has been proven to be crucial for optimizing the performance of many energy-challenge relevant devices. Here, we report the experimental observations of controlled on/off ultrafast electron transfer (ET) at cationic porphyrin-CdTe quantum dot (QD) interfaces using femto- and nanosecond broad-band transient absorption (TA) spectroscopy. The time-resolved data demonstrate how one can turn on/off the electron injection from porphyrin to the CdTe QDs. With careful control of the molecular structure, we are able to tune the electron injection at the porphyrin-CdTe QD interface from zero to very efficient and ultrafast. In addition, our data demonstrate that the ET process occurs within our temporal resolution of 120 fs, which is one of the fastest times recorded for organic photovoltaics. © 2015 American Chemical Society.

  2. Ultrafast molecular dynamics illuminated with synchrotron radiation

    International Nuclear Information System (INIS)

    Bozek, John D.; Miron, Catalin

    2015-01-01

    Highlights: • Ultrafast molecular dynamics probed with synchrotron radiation. • Core-excitation as probe of ultrafast dynamics through core-hole lifetime. • Review of experimental and theoretical methods in ultrafast dynamics using core-level excitation. - Abstract: Synchrotron radiation is a powerful tool for studying molecular dynamics in small molecules in spite of the absence of natural matching between the X-ray pulse duration and the time scale of nuclear motion. Promoting core level electrons to unoccupied molecular orbitals simultaneously initiates two ultrafast processes, nuclear dynamics on the potential energy surfaces of the highly excited neutral intermediate state of the molecule on the one hand and an ultrafast electronic decay of the intermediate excited state to a cationic final state, characterized by a core hole lifetime. The similar time scales of these processes enable core excited pump-probe-type experiments to be performed with long duration X-ray pulses from a synchrotron source. Recent results obtained at the PLIEADES beamline concerning ultrafast dissociation of core excited states and molecular potential energy curve mapping facilitated by changes in the geometry of the short-lived intermediate core excited state are reviewed. High brightness X-ray beams combined with state-of-the art electron and ion-electron coincidence spectrometers and highly sophisticated theoretical methods are required to conduct these experiments and to achieve a full understanding of the experimental results.

  3. Femtochemistry and femtobiology ultrafast dynamics in molecular science

    CERN Document Server

    Douhal, Abderrazzak

    2002-01-01

    This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol

  4. Molecular-structure control of ultrafast electron injection at cationic porphyrin-CdTe quantum dot interfaces

    KAUST Repository

    Aly, Shawkat Mohammede; Ahmed, Ghada H.; Shaheen, Basamat; Sun, Jingya; Mohammed, Omar F.

    2015-01-01

    Charge transfer (CT) at donor (D)/acceptor (A) interfaces is central to the functioning of photovoltaic and light-emitting devices. Understanding and controlling this process on the molecular level has been proven to be crucial for optimizing

  5. Ultrafast Optical Signal Processing with Bragg Structures

    Directory of Open Access Journals (Sweden)

    Yikun Liu

    2017-05-01

    Full Text Available The phase, amplitude, speed, and polarization, in addition to many other properties of light, can be modulated by photonic Bragg structures. In conjunction with nonlinearity and quantum effects, a variety of ensuing micro- or nano-photonic applications can be realized. This paper reviews various optical phenomena in several exemplary 1D Bragg gratings. Important examples are resonantly absorbing photonic structures, chirped Bragg grating, and cholesteric liquid crystals; their unique operation capabilities and key issues are considered in detail. These Bragg structures are expected to be used in wide-spread applications involving light field modulations, especially in the rapidly advancing field of ultrafast optical signal processing.

  6. Ultrafast Dynamics in Light-Driven Molecular Rotary Motors Probed by Femtosecond Stimulated Raman Spectroscopy

    NARCIS (Netherlands)

    Hall, Christopher R.; Conyard, Jamie; Heisler, Ismael A.; Jones, Garth; Frost, James; Browne, Wesley R.; Feringa, Ben L.; Meech, Stephen R.

    2017-01-01

    Photochemical isomerization in sterically crowded chiral alkenes is the driving force for molecular rotary motors in nanoscale machines. Here the excited-state dynamics and structural evolution of the prototypical light-driven rotary motor are followed on the ultrafast time scale by femtosecond

  7. Ultrafast photoinduced structure phase transition in antimony single crystals

    NARCIS (Netherlands)

    Fausti, Daniele; Misochko, Oleg V.; van Loosdrecht, Paul H. M.

    2009-01-01

    Picosecond Raman scattering is used to study the photoinduced ultrafast dynamics in Peierls distorted antimony. We find evidence for an ultrafast nonthermal reversible structural phase transition. Most surprisingly, we find evidence that this transition evolves toward a lower symmetry in contrast to

  8. Ultrafast phenomena in molecular sciences femtosecond physics and chemistry

    CERN Document Server

    Bañares, Luis

    2014-01-01

    This book presents the latest developments in Femtosecond Chemistry and Physics for the study of ultrafast photo-induced molecular processes. Molecular systems, from the simplest H2 molecule to polymers or biological macromolecules, constitute central objects of interest for Physics, Chemistry and Biology, and despite the broad range of phenomena that they exhibit, they share some common behaviors. One of the most significant of those is that many of the processes involving chemical transformation (nuclear reorganization, bond breaking, bond making) take place in an extraordinarily short time, in or around the femtosecond temporal scale (1 fs = 10-15 s). A number of experimental approaches - very particularly the developments in the generation and manipulation of ultrashort laser pulses - coupled with theoretical progress, provide the ultrafast scientist with powerful tools to understand matter and its interaction with light, at this spatial and temporal scale. This book is an attempt to reunite some of the ...

  9. Ultrafast dissociation: An unexpected tool for probing molecular dynamics

    International Nuclear Information System (INIS)

    Morin, Paul; Miron, Catalin

    2012-01-01

    Highlights: ► Ultrafast dissociation has been investigated by means of XPS and mass spectrometry. ► The interplay between electron relaxation and molecular dynamics is evidenced. ► Extension toward polyatomics, clusters, adsorbed molecules is considered. ► Quantum effects (spectral hole, angular effects) evidence the molecular field anisotropy. -- Abstract: Ultrafast dissociation following core–shell excitation into an antibonding orbital led to the early observation in HBr of atomic Auger lines associated to the decay of dissociated excited atoms. The purpose of this article is to review the very large variety of systems where such a situation has been encountered, extending from simple diatomic molecules toward more complex systems like polyatomics, clusters, or adsorbed molecules. Interestingly, this phenomenon has revealed an extremely rich and powerful tool for probing nuclear dynamics and its subtle interplay with electron relaxation occurring on a comparable time scale. Consequently this review covers a surprisingly large period, starting in 1986 and still ongoing.

  10. Modeling of ultrafast THz interactions in molecular crystals

    DEFF Research Database (Denmark)

    Pedersen, Pernille Klarskov; Clark, Stewart J.; Jepsen, Peter Uhd

    2014-01-01

    In this paper we present a numerical study of terahertz pulses interacting with crystals of cesium iodide. We model the molecular dynamics of the cesium iodide crystals with the Density Functional Theory software CASTEP, where ultrafast terahertz pulses are implemented to the CASTEP software...... to interact with molecular crystals. We investigate the molecular dynamics of cesium iodide crystals when interacting with realistic terahertz pulses of field strengths from 0 to 50 MV/cm. We find nonlinearities in the response of the CsI crystals at field strengths higher than 10 MV/cm....

  11. Ultrafast protein structure-based virtual screening with Panther

    Science.gov (United States)

    Niinivehmas, Sanna P.; Salokas, Kari; Lätti, Sakari; Raunio, Hannu; Pentikäinen, Olli T.

    2015-10-01

    Molecular docking is by far the most common method used in protein structure-based virtual screening. This paper presents Panther, a novel ultrafast multipurpose docking tool. In Panther, a simple shape-electrostatic model of the ligand-binding area of the protein is created by utilizing the protein crystal structure. The features of the possible ligands are then compared to the model by using a similarity search algorithm. On average, one ligand can be processed in a few minutes by using classical docking methods, whereas using Panther processing takes Panther protocol can be used in several applications, such as speeding up the early phases of drug discovery projects, reducing the number of failures in the clinical phase of the drug development process, and estimating the environmental toxicity of chemicals. Panther-code is available in our web pages (http://www.jyu.fi/panther) free of charge after registration.

  12. Roadmap of ultrafast x-ray atomic and molecular physics

    Science.gov (United States)

    Young, Linda; Ueda, Kiyoshi; Gühr, Markus; Bucksbaum, Philip H.; Simon, Marc; Mukamel, Shaul; Rohringer, Nina; Prince, Kevin C.; Masciovecchio, Claudio; Meyer, Michael; Rudenko, Artem; Rolles, Daniel; Bostedt, Christoph; Fuchs, Matthias; Reis, David A.; Santra, Robin; Kapteyn, Henry; Murnane, Margaret; Ibrahim, Heide; Légaré, François; Vrakking, Marc; Isinger, Marcus; Kroon, David; Gisselbrecht, Mathieu; L'Huillier, Anne; Wörner, Hans Jakob; Leone, Stephen R.

    2018-02-01

    X-ray free-electron lasers (XFELs) and table-top sources of x-rays based upon high harmonic generation (HHG) have revolutionized the field of ultrafast x-ray atomic and molecular physics, largely due to an explosive growth in capabilities in the past decade. XFELs now provide unprecedented intensity (1020 W cm-2) of x-rays at wavelengths down to ˜1 Ångstrom, and HHG provides unprecedented time resolution (˜50 attoseconds) and a correspondingly large coherent bandwidth at longer wavelengths. For context, timescales can be referenced to the Bohr orbital period in hydrogen atom of 150 attoseconds and the hydrogen-molecule vibrational period of 8 femtoseconds; wavelength scales can be referenced to the chemically significant carbon K-edge at a photon energy of ˜280 eV (44 Ångstroms) and the bond length in methane of ˜1 Ångstrom. With these modern x-ray sources one now has the ability to focus on individual atoms, even when embedded in a complex molecule, and view electronic and nuclear motion on their intrinsic scales (attoseconds and Ångstroms). These sources have enabled coherent diffractive imaging, where one can image non-crystalline objects in three dimensions on ultrafast timescales, potentially with atomic resolution. The unprecedented intensity available with XFELs has opened new fields of multiphoton and nonlinear x-ray physics where behavior of matter under extreme conditions can be explored. The unprecedented time resolution and pulse synchronization provided by HHG sources has kindled fundamental investigations of time delays in photoionization, charge migration in molecules, and dynamics near conical intersections that are foundational to AMO physics and chemistry. This roadmap coincides with the year when three new XFEL facilities, operating at Ångstrom wavelengths, opened for users (European XFEL, Swiss-FEL and PAL-FEL in Korea) almost doubling the present worldwide number of XFELs, and documents the remarkable progress in HHG capabilities since

  13. Ultrafast molecular imaging by laser-induced electron diffraction

    International Nuclear Information System (INIS)

    Peters, M.; Nguyen-Dang, T. T.; Cornaggia, C.; Saugout, S.; Charron, E.; Keller, A.; Atabek, O.

    2011-01-01

    We address the feasibility of imaging geometric and orbital structures of a polyatomic molecule on an attosecond time scale using the laser-induced electron diffraction (LIED) technique. We present numerical results for the highest molecular orbitals of the CO 2 molecule excited by a near-infrared few-cycle laser pulse. The molecular geometry (bond lengths) is determined within 3% of accuracy from a diffraction pattern which also reflects the nodal properties of the initial molecular orbital. Robustness of the structure determination is discussed with respect to vibrational and rotational motions with a complete interpretation of the laser-induced mechanisms.

  14. Enhanced surface structuring by ultrafast XUV/NIR dual action

    Czech Academy of Sciences Publication Activity Database

    Jakubczak, Krzysztof; Mocek, Tomáš; Chalupský, Jaromír; Lee, G.H.; Kim, T.K.; Park, S.B.; Nam, Ch. H.; Hájková, Věra; Toufarová, Martina; Juha, Libor; Rus, Bedřich

    2011-01-01

    Roč. 13, č. 5 (2011), s. 1-12 ISSN 1367-2630 R&D Projects: GA AV ČR KAN300100702; GA MŠk(CZ) LC528; GA MŠk LA08024; GA ČR GC202/07/J008 Grant - others:AV ČR(CZ) M100100911 Institutional research plan: CEZ:AV0Z10100523 Keywords : XUV beam * ultrafast NIR laser pulses * high-order harmonics * laser-induced periodic surface structures Subject RIV: BH - Optics, Masers, Lasers Impact factor: 4.177, year: 2011 http://iopscience.iop.org/1367-2630/13/5/053049

  15. Ultrafast studies of dynamic & complex systems: Understanding molecular and ionization dynamics

    OpenAIRE

    Hockett, Paul

    2016-01-01

    Presentation given at the ITAMP workshop "Ultrafast atomic and molecular physics with cutting-edge light sources: New opportunities and challenges", held at Kansas State University, Nov. 2013.  A video of the presentation can be found on the ITAMP Youtube channel, https://www.youtube.com/watch?v=x8RWWDWZJpk

  16. Photoelectron diffraction from single oriented molecules: Towards ultrafast structure determination of molecules using x-ray free-electron lasers

    Science.gov (United States)

    Kazama, Misato; Fujikawa, Takashi; Kishimoto, Naoki; Mizuno, Tomoya; Adachi, Jun-ichi; Yagishita, Akira

    2013-06-01

    We provide a molecular structure determination method, based on multiple-scattering x-ray photoelectron diffraction (XPD) calculations. This method is applied to our XPD data on several molecules having different equilibrium geometries. Then it is confirmed that, by our method, bond lengths and bond angles can be determined with a resolution of less than 0.1 Å and 10∘, respectively. Differently from any other scenario of ultrafast structure determination, we measure the two- or three-dimensional XPD of aligned or oriented molecules in the energy range from 100 to 200 eV with a 4π detection velocity map imaging spectrometer. Thanks to the intense and ultrashort pulse properties of x-ray free-electron lasers, our approach exhibits the most probable method for obtaining ultrafast real-time structural information on small to medium-sized molecules consisting of light elements, i.e., a “molecular movie.”

  17. Ultrafast Dynamic Pressure Sensors Based on Graphene Hybrid Structure.

    Science.gov (United States)

    Liu, Shanbiao; Wu, Xing; Zhang, Dongdong; Guo, Congwei; Wang, Peng; Hu, Weida; Li, Xinming; Zhou, Xiaofeng; Xu, Hejun; Luo, Chen; Zhang, Jian; Chu, Junhao

    2017-07-19

    Mechanical flexible electronic skin has been focused on sensing various physical parameters, such as pressure and temperature. The studies of material design and array-accessible devices are the building blocks of strain sensors for subtle pressure sensing. Here, we report a new and facile preparation of a graphene hybrid structure with an ultrafast dynamic pressure response. Graphene oxide nanosheets are used as a surfactant to prevent graphene restacking in aqueous solution. This graphene hybrid structure exhibits a frequency-independent pressure resistive sensing property. Exceeding natural skin, such pressure sensors, can provide transient responses from static up to 10 000 Hz dynamic frequencies. Integrated by the controlling system, the array-accessible sensors can manipulate a robot arm and self-rectify the temperature of a heating blanket. This may pave a path toward the future application of graphene-based wearable electronics.

  18. Protonation-induced ultrafast torsional dynamics in 9-anthrylbenzimidazole: a pH activated molecular rotor.

    Science.gov (United States)

    Nandi, Amitabha; Kushwaha, Archana; Das, Dipanwita; Ghosh, Rajib

    2018-03-07

    We report the photophysical properties and excited state dynamics of 9-anthrylbenzimidazole (ANBI) which exhibits protonation-induced molecular rotor properties. In contrast to the highly emissive behavior of neutral ANBI, protonation of the benzimidazole group of ANBI induces efficient nonradiative deactivation by ultrafast torsional motion around the bond connecting the anthracene and benzimidazole units, as revealed by ultrafast transient absorption and fluorescence spectroscopy. Contrary to viscosity-independent fluorescence of neutral dyes, protonated ANBI is shown to display linear variation of emission yield and lifetime with solvent viscosity. The protonation-induced molecular rotor properties in the studied system are shown to be driven by enhanced charge transfer and are corroborated by quantum chemical calculations. Potential application as a microviscosity sensor of acidic regions in a heterogeneous environment by these proton-activated molecular rotor properties of ANBI is discussed.

  19. Nonlinear ultrafast optical response in organic molecular crystals

    Science.gov (United States)

    Rahman, Talat S.; Turkowski, Volodymyr; Leuenberger, Michael N.

    2012-02-01

    We analyze possible nonlinear excitonic effects in the organic molecule crystals by using a combined time-dependent DFT and many-body approach. In particular, we analyze possible effects of the time-dependent (retarded)interaction between different types of excitations, Frenkel excitons, charge transfer excitons and excimers, on the electric and the optical response of the system. We pay special attention to the case of constant electric field and ultrafast pulses, including that of four-wave mixing experiments. As a specific application we examine the optical excitations of pentacene nanocrystals and compare the results with available experimental data.[1] Our results demostrate that the nonlinear effects can play an important role in the optical response of these systems. [1] A. Kabakchiev, ``Scanning Tunneling Luminescence of Pentacene Nanocrystals'', PhD Thesis (EPFL, Lausanne, 2010).

  20. Ultrafast electron injection at the cationic porphyrin-graphene interface assisted by molecular flattening

    KAUST Repository

    Aly, Shawkat Mohammede; Parida, Manas R.; Alarousu, Erkki; Mohammed, Omar F.

    2014-01-01

    The steady-state and femtosecond (fs) time-resolved data clearly demonstrate that the charge transfer (CT) process at the porphyrin-graphene carboxylate (GC) interfaces can be tuned from zero to very sufficient and ultrafast by changing the electronic structure of the meso unit and the redox properties of the porphyrin cavity. This journal is © the Partner Organisations 2014.

  1. Wavelet analysis of molecular dynamics: Efficient extraction of time-frequency information in ultrafast optical processes

    International Nuclear Information System (INIS)

    Prior, Javier; Castro, Enrique; Chin, Alex W.; Almeida, Javier; Huelga, Susana F.; Plenio, Martin B.

    2013-01-01

    New experimental techniques based on nonlinear ultrafast spectroscopies have been developed over the last few years, and have been demonstrated to provide powerful probes of quantum dynamics in different types of molecular aggregates, including both natural and artificial light harvesting complexes. Fourier transform-based spectroscopies have been particularly successful, yet “complete” spectral information normally necessitates the loss of all information on the temporal sequence of events in a signal. This information though is particularly important in transient or multi-stage processes, in which the spectral decomposition of the data evolves in time. By going through several examples of ultrafast quantum dynamics, we demonstrate that the use of wavelets provide an efficient and accurate way to simultaneously acquire both temporal and frequency information about a signal, and argue that this greatly aids the elucidation and interpretation of physical process responsible for non-stationary spectroscopic features, such as those encountered in coherent excitonic energy transport

  2. Ultrafast Structural Dynamics in InSb Probed by Time-Resolved X-Ray Diffraction

    International Nuclear Information System (INIS)

    Chin, A.H.; Shank, C.V.; Chin, A.H.; Schoenlein, R.W.; Shank, C.V.; Glover, T.E.; Leemans, W.P.; Balling, P.

    1999-01-01

    Ultrafast structural dynamics in laser-perturbed InSb are studied using time-resolved x-ray diffraction with a novel femtosecond x-ray source. We report the first observation of a delay in the onset of lattice expansion, which we attribute to energy relaxation processes and lattice strain propagation. In addition, we observe direct indications of ultrafast disordering on a subpicosecond time scale. copyright 1999 The American Physical Society

  3. Nonlinear Optical Spectroscopy in the Time Domain: Studies of Ultrafast Molecular Processes in the Condensed Phase.

    Science.gov (United States)

    Joo, Taiha

    Ultrafast molecular processes in the condensed phase at room temperature are studied in the time domain by four wave mixing spectroscopy. The structure/dynamics of various quantum states can be studied by varying the time ordering of the incident fields, their polarization, their colors, etc. In one, time-resolved coherent Stokes Raman spectroscopy of benzene is investigated at room temperature. The reorientational correlation time of benzene as well as the T_2 time of the nu _1 ring-breathing mode have been measured by using two different polarization geometries. Bohr frequency difference beats have also been resolved between the nu_1 modes of ^ {12}C_6H_6 and ^{12}C_5^{13 }CH_6.. The dephasing dynamics of the nu _1 ring-breathing mode of neat benzene is studied by time-resolved coherent anti-Stokes Raman scattering. Ultrafast time resolution reveals deviation from the conventional exponential decay. The correlation time, tau _{rm c}, and the rms magnitude, Delta, of the Bohr frequency modulation are determined for the process responsible for the vibrational dephasing by Kubo dephasing function analysis. The electronic dephasing of two oxazine dyes in ethylene glycol at room temperature is investigated by photon echo experiments. It was found that at least two stochastic processes are responsible for the observed electronic dephasing. Both fast (homogeneous) and slow (inhomogeneous) dynamics are recovered using Kubo line shape analysis. Moreover, the slow dynamics is found to spectrally diffuse over the inhomogeneous distribution on the time scale around a picosecond. Time-resolved degenerate four wave mixing signal of dyes in a population measurement geometry is reported. The vibrational coherences both in the ground and excited electronic states produced strong oscillations in the signal together with the usual population decay from the excited electronic state. Absolute frequencies and their dephasing times of the vibrational modes at ~590 cm^{-1} are obtained

  4. Earle K. Plyler Prize Lecture: The Three Pillars of Ultrafast Molecular Science - Time, Phase, Intensity

    Science.gov (United States)

    Stolow, Albert

    We discuss the probing and control of molecular wavepacket dynamics in the context of three main `pillars' of light-matter interaction: time, phase, intensity. Time: Using short, coherent laser pulses and perturbative matter-field interactions, we study molecular wavepackets with a focus on the ultrafast non-Born-Oppenheimer dynamics, that is, the coupling of electronic and nuclear motions. Time-Resolved Photoelectron Spectroscopy (TRPES) is a powerful ultrafast probe of these processes in polyatomic molecules because it is sensitive both electronic and vibrational dynamics. Ideally, one would like to observe these ultrafast processes from the molecule's point of view - the Molecular Frame - thereby avoiding loss of information due to orientational averaging. This can be achieved by Time-Resolved Coincidence Imaging Spectroscopy (TRCIS) which images 3D recoil vectors of both photofragments and photoelectrons, in coincidence and as a function of time, permitting direct Molecular Frame imaging of valence electronic dynamics during a molecular dynamics. Phase: Using intermediate strength non-perturbative interactions, we apply the second order (polarizability) Non-Resonant Dynamic Stark Effect (NRDSE) to control molecular dynamics without any net absorption of light. NRDSE is also the interaction underlying molecular alignment and applies to field-free 1D of linear molecules and field-free 3D alignment of general (asymmetric) molecules. Using laser alignment, we can transiently fix a molecule in space, yielding a more general approach to direct Molecular Frame imaging of valence electronic dynamics during a chemical reaction. Intensity: In strong (ionizing) laser fields, a new laser-matter physics emerges for polyatomic systems wherein both the single active electron picture and the adiabatic electron response, both implicit in the standard 3-step models, can fail dramatically. This has important consequences for all attosecond strong field spectroscopies of

  5. Effects of Ultrafast Molecular Rotation on Collisional Decoherence

    Science.gov (United States)

    Milner, Alexander A.; Korobenko, Aleksey; Hepburn, John W.; Milner, Valery

    2014-07-01

    Using an optical centrifuge to control molecular rotation in an extremely broad range of angular momenta, we study coherent rotational dynamics of nitrogen molecules in the presence of collisions. We cover the range of rotational quantum numbers between J=8 and J =66 at room temperature and study a crossover between the adiabatic and nonadiabatic regimes of rotational relaxation, which cannot be easily accessed by thermal means. We demonstrate that the rate of rotational decoherence changes by more than an order of magnitude in this range of J values and show that its dependence on J can be described by a simplified scaling law.

  6. PREFACE: Ultrafast biophotonics Ultrafast biophotonics

    Science.gov (United States)

    Gu, Min; Reid, Derryck; Ben-Yakar, Adela

    2010-08-01

    reduced chromatic aberration effects. These extensive advantages have led to further exploration of nonlinear processes including second-harmonic generation (SHG) microscopy and third-harmonic generation (THG) microscopy. Second-harmonic generation has provided biologists with an extremely powerful tool for generating contrast in biological imaging, with the additional benefit of non-invasive three-dimensional imaging. The recent popularity of THG microscopy is largely due to the fact that three-dimensional imaging is achievable without the need for any labels, but rather relying on the intrinsic properties of the biological specimen itself. This optical nonlinear technique has attracted much attention recently from the biological community due to its non-invasive capabilities. Users of ultrafast lasers in the biological and medical fields are becoming a fast-growing community, employing pulse-shaping microscopy, resolution-enhancing microscopy techniques, linear and nonlinear micro-spectroscopy, functional deep-tissue imaging, optical coherence tomography, nonlinear fluorescence microscopy, molecular imaging and control, harmonic microscopy and femtosecond lifetime imaging, for cutting-edge research concerning the interaction of light with biological dynamics. The adaptability of ultrafast lasers to interact with a large array of materials through nonlinear excitation has enabled precise control of laser fluence allowing for highly localized material interactions, permitting micro-structured fabricated surfaces. The resultant multi-dimensional fabricated micro-structures are capable of replicating and/or manipulating microenvironments for controlled cell biology. In this special issue of Journal of Optics readers have a chance to view a collection of new contributions to the growing research field of ultrafast biophotonics. They are presented with recent advances in ultrafast technology applied to biological and medical investigations, where topics include advances in

  7. Exploring Ultrafast Structural Dynamics for Energetic Enhancement or Disruption

    Science.gov (United States)

    2016-03-01

    it. In a pump -push/ dump probe experiment, a secondary laser pulse (push/ dump ) is used after the initial perturbation due to the pump pulse. The...increased. The pump -push/ dump probe technique is a difficult experiment that requires a highly stable laser source. Ultrafast pump -probe experiments...decomposition of solids. Journal of Applied Physics. 2001;89:4156–4166. 17. Kee TW. Femtosecond pump -push-probe and pump - dump -probe spectroscopy of

  8. Ultrafast fragmentation dynamics of triply charged carbon dioxide: Vibrational-mode-dependent molecular bond breakage

    Science.gov (United States)

    Yang, HongJiang; Wang, Enliang; Dong, WenXiu; Gong, Maomao; Shen, Zhenjie; Tang, Yaguo; Shan, Xu; Chen, Xiangjun

    2018-05-01

    The a b i n i t i o molecular dynamics (MD) simulations using an atom-centered density matrix propagation method have been carried out to investigate the fragmentation of the ground-state triply charged carbon dioxide, CO23 +→C+ + Oa+ + Ob+ . Ten thousands of trajectories have been simulated. By analyzing the momentum correlation of the final fragments, it is demonstrated that the sequential fragmentation dominates in the three-body dissociation, consistent with our experimental observations which were performed by electron collision at impact energy of 1500 eV. Furthermore, the MD simulations allow us to have detailed insight into the ultrafast evolution of the molecular bond breakage at a very early stage, within several tens of femtoseconds, and the result shows that the initial nuclear vibrational mode plays a decisive role in switching the dissociation pathways.

  9. Capturing Structural Snapshots during Photochemical Reactions with Ultrafast Raman Spectroscopy: From Materials Transformation to Biosensor Responses.

    Science.gov (United States)

    Fang, Chong; Tang, Longteng; Oscar, Breland G; Chen, Cheng

    2018-06-21

    Chemistry studies the composition, structure, properties, and transformation of matter. A mechanistic understanding of the pertinent processes is required to translate fundamental knowledge into practical applications. The current development of ultrafast Raman as a powerful time-resolved vibrational technique, particularly femtosecond stimulated Raman spectroscopy (FSRS), has shed light on the structure-energy-function relationships of various photosensitive systems. This Perspective reviews recent work incorporating optical innovations, including the broad-band up-converted multicolor array (BUMA) into a tunable FSRS setup, and demonstrates its resolving power to watch metal speciation and photolysis, leading to high-quality thin films, and fluorescence modulation of chimeric protein biosensors for calcium ion imaging. We discuss advantages of performing FSRS in the mixed time-frequency domain and present strategies to delineate mechanisms by tracking low-frequency modes and systematically modifying chemical structures with specific functional groups. These unique insights at the chemical-bond level have started to enable the rational design and precise control of functional molecular machines in optical, materials, energy, and life sciences.

  10. Vibrational energy on surfaces: Ultrafast flash-thermal conductance of molecular monolayers

    Science.gov (United States)

    Dlott, Dana

    2008-03-01

    Vibrational energy flow through molecules remains a perennial problem in chemical physics. Usually vibrational energy dynamics are viewed through the lens of time-dependent level populations. This is natural because lasers naturally pump and probe vibrational transitions, but it is also useful to think of vibrational energy as being conducted from one location in a molecule to another. We have developed a new technique where energy is driven into a specific part of molecules adsorbed on a metal surface, and ultrafast nonlinear coherent vibrational spectroscopy is used to watch the energy arrive at another part. This technique is the analog of a flash thermal conductance apparatus, except it probes energy flow with angstrom spatial and femtosecond temporal resolution. Specific examples to be presented include energy flow along alkane chains, and energy flow into substituted benzenes. Ref: Z. Wang, J. A. Carter, A. Lagutchev, Y. K. Koh, N.-H. Seong, D. G. Cahill, and D. D. Dlott, Ultrafast flash thermal conductance of molecular chains, Science 317, 787-790 (2007). This material is based upon work supported by the National Science Foundation under award DMR 0504038 and the Air Force Office of Scientific Research under award FA9550-06-1-0235.

  11. Valency and molecular structure

    CERN Document Server

    Cartmell, E

    1977-01-01

    Valency and Molecular Structure, Fourth Edition provides a comprehensive historical background and experimental foundations of theories and methods relating to valency and molecular structures. In this edition, the chapter on Bohr theory has been removed while some sections, such as structures of crystalline solids, have been expanded. Details of structures have also been revised and extended using the best available values for bond lengths and bond angles. Recent developments are mostly noted in the chapter on complex compounds, while a new chapter has been added to serve as an introduction t

  12. Structural Transformation of LiFePO4 during Ultrafast Delithiation.

    Science.gov (United States)

    Kuss, Christian; Trinh, Ngoc Duc; Andjelic, Stefan; Saulnier, Mathieu; Dufresne, Eric M; Liang, Guoxian; Schougaard, Steen B

    2017-12-21

    The prolific lithium battery electrode material lithium iron phosphate (LiFePO 4 ) stores and releases lithium ions by undergoing a crystallographic phase change. Nevertheless, it performs unexpectedly well at high rate and exhibits good cycling stability. We investigate here the ultrafast charging reaction to resolve the underlying mechanism while avoiding the limitations of prevailing electrochemical methods by using a gaseous oxidant to deintercalate lithium from the LiFePO 4 structure. Oxidizing LiFePO 4 with nitrogen dioxide gas reveals structural changes through in situ synchrotron X-ray diffraction and electronic changes through in situ UV/vis reflectance spectroscopy. This study clearly shows that ultrahigh rates reaching 100% state of charge in 10 s does not lead to a particle-wide union of the olivine and heterosite structures. An extensive solid solution phase is therefore not a prerequisite for ultrafast charge/discharge.

  13. Probing Photoinduced Structural Phase Transitions by Fast or Ultra-Fast Time-Resolved X-Ray Diffraction

    Science.gov (United States)

    Cailleau, Hervé Collet, Eric; Buron-Le Cointe, Marylise; Lemée-Cailleau, Marie-Hélène Koshihara, Shin-Ya

    A new frontier in the field of structural science is the emergence of the fast and ultra-fast X-ray science. Recent developments in time-resolved X-ray diffraction promise direct access to the dynamics of electronic, atomic and molecular motions in condensed matter triggered by a pulsed laser irradiation, i.e. to record "molecular movies" during the transformation of matter initiated by light pulse. These laser pump and X-ray probe techniques now provide an outstanding opportunity for the direct observation of a photoinduced structural phase transition as it takes place. The use of X-ray short-pulse of about 100ps around third-generation synchrotron sources allows structural investigations of fast photoinduced processes. Other new X-ray sources, such as laser-produced plasma ones, generate ultra-short pulses down to 100 fs. This opens the way to femtosecond X-ray crystallography, but with rather low X-ray intensities and more limited experimental possibilities at present. However this new ultra-fast science rapidly progresses around these sources and new large-scale projects exist. It is the aim of this contribution to overview the state of art and the perspectives of fast and ultra-fast X-ray scattering techniques to study photoinduced phase transitions (here, the word ultra-fast is used for sub-picosecond time resolution). In particular we would like to largely present the contribution of crystallographic methods in comparison with optical methods, such as pump-probe reflectivity measurements, the reader being not necessary familiar with X-ray scattering. Thus we want to present which type of physical information can be obtained from the positions of the Bragg peaks, their intensity and their shape, as well as from the diffuse scattering beyond Bragg peaks. An important physical feature is to take into consideration the difference in nature between a photoinduced phase transition and conventional homogeneous photoinduced chemical or biochemical processes where

  14. Photoionization and molecular structure

    International Nuclear Information System (INIS)

    Palma, A.

    1983-01-01

    A presentation is here given of the theoretical work on photoionization and molecular structure carried out by the author and coworkers. The implications of the photoionization process on the molecular geometry are emphasized. In particular, the ionization effect on deep orbitals is considered and it is shown that, contrary to traditional thinking, these orbitals have relevant effects on the molecular geometry. The problem of calculating photoionization relative intensities for the full spectrum is also considered, and the results of the present model are compared with experimental and other theoretical results. (author)

  15. Understanding molecular structure from molecular mechanics.

    Science.gov (United States)

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  16. Generation of nanoclusters by ultrafast laser ablation of Al: Molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Miloshevsky, Alexander; Phillips, Mark C.; Harilal, Sivanandan S.; Dressman, Phillip; Miloshevsky, Gennady

    2017-11-01

    The laser ablation of materials induced by an ultrashort femtosecond pulse is a complex phenomenon, which depends on both the material properties and the properties of the laser pulse. The unique capability of a combination of molecular dynamics (MD) and Momentum Scaling Model (MSM) methods is developed and applied to a large atomic system for studying the process of ultrafast laser-material interactions, behavior of matter in a highly non-equilibrium state, material disintegration, and formation of nanoparticles (NPs). Laser pulses with several fluences in the range from 500 J/m2 to 5000 J/m2 interacting with a large system of aluminum atoms are simulated. The response of Al material to the laser energy deposition is investigated within the finite-size laser spot. It is found that the shape of the plasma plume is dynamically changing during an expansion process. At several tens of picoseconds it can be characterized as a long hollow ellipsoid surrounded by atomized and nano-clustered particles. The time evolution of NP clusters in the plume is investigated. The collisions between the single Al atoms and generated NPs and fragmentation of large NPs determine the fractions of different-size NP clusters in the plume. The MD-MSM simulations show that laser fluence greatly affects the size distribution of NPs, their polar angles, magnitude and direction vectors of NP velocities. These results and predictions are supported by the experimental data and previous MD simulations.

  17. Observing Structure and Motion in Molecules with Ultrafast Strong Field and Short Wavelength Laser Radiation

    Energy Technology Data Exchange (ETDEWEB)

    Bucksbaum, Philip H

    2011-04-13

    The term "molecular movie" has come to describe efforts to track and record Angstrom-scale coherent atomic and electronic motion in a molecule. The relevant time scales for this range cover several orders of magnitude, from sub-femtosecond motion associated with electron-electron correlations, to 100-fs internal vibrations, to multi-picosecond motion associated with the dispersion and quantum revivals of molecular reorientation. Conventional methods of cinematography do not work well in this ultrafast and ultrasmall regime, but stroboscopic "pump and probe" techniques can reveal this motion with high fidelity. This talk will describe some of the methods and recent progress in exciting and controlling this motion, using both laboratory lasers and the SLAC Linac Coherent Light Source x-ray free electron laser, and will further try to relate the date to the goal of molecular movies.

  18. First-principles assessment of potential ultrafast laser-induced structural transition in Ni

    Energy Technology Data Exchange (ETDEWEB)

    Bévillon, E.; Colombier, J.P., E-mail: jean.philippe.colombier@univ-st-etienne.fr; Stoian, R.

    2016-06-30

    Highlights: • First-principles theory calculations in nonequilibrium conditions. • Electronic temperatures fully and consistently taken into account. • Evaluation of an ultrafast laser-induced solid-to-solid transition in Ni. • Relative energies, phonon spectra and energy path are evaluated. • Discussion on the generation of non-thermal forces in metals. - Abstract: The possibility to trigger ultrafast solid-to-solid transitions in transition metals under femtosecond laser irradiation is investigated by means of first-principles calculations. Electronic heating can drastically modify screening, charge distribution and atomic binding features, potentially determining new structural relaxation paths in the solid phase, before thermodynamic solid-to-liquid transformations set in. Consequently, we evaluate here the effect of electronic excitation on structural stability and conditions for structural transitions. Ni is chosen as a case study for the probability of a solid transition, and the stability of its FCC phase is compared to the non-standard HCP structure while accounting for the heating of the electronic subsystem. From a phonon spectra analysis, we show that the thermodynamic stability order reverses at an electronic temperature of around 10{sup 4} K. Both structures exhibit a dynamic stability, indicating they present a metastability depending on the heating. However, the general hardening of phonon modes with the increase of the electronic temperature points out that no transformation will occur, as confirmed by the study of a typical FCC to HCP diffusionless transformation path, showing an increasing energy barrier. Finally, based on electronic density of states interpretation, the tendency of different metal categories to undergo or not an ultrafast laser-induced structural transition is discussed.

  19. Novel radio-frequency gun structures for ultrafast relativistic electron diffraction.

    Science.gov (United States)

    Musumeci, P; Faillace, L; Fukasawa, A; Moody, J T; O'Shea, B; Rosenzweig, J B; Scoby, C M

    2009-08-01

    Radio-frequency (RF) photoinjector-based relativistic ultrafast electron diffraction (UED) is a promising new technique that has the potential to probe structural changes at the atomic scale with sub-100 fs temporal resolution in a single shot. We analyze the limitations on the temporal and spatial resolution of this technique considering the operating parameters of a standard 1.6 cell RF gun (which is the RF photoinjector used for the first experimental tests of relativistic UED at Stanford Linear Accelerator Center; University of California, Los Angeles; Brookhaven National Laboratory), and study the possibility of employing novel RF structures to circumvent some of these limits.

  20. Ultrafast isomerization dynamics of a unidirectional molecular rotor revealed by femtosecond stimulated raman spectroscopy (FSRS)

    NARCIS (Netherlands)

    Hall, Christopher R.; Conyard, Jamie; Laptenok, Siarhei; Browne, Wesley R.; Feringa, Ben L.; Heisler, Ismael A.; Meech, Stephen R.

    2016-01-01

    Unidirectional molecular rotors based on chiral overcrowded alkenes operate via sequential photochemical- and thermal-activated steps. Over the last decade the rotation rate limiting thermal step has been optimized through modification of the molecular structure. In recent years we have shown the

  1. Measurements of ionic structure in shock compressed lithium hydride from ultrafast x-ray Thomson scattering.

    Science.gov (United States)

    Kritcher, A L; Neumayer, P; Brown, C R D; Davis, P; Döppner, T; Falcone, R W; Gericke, D O; Gregori, G; Holst, B; Landen, O L; Lee, H J; Morse, E C; Pelka, A; Redmer, R; Roth, M; Vorberger, J; Wünsch, K; Glenzer, S H

    2009-12-11

    We present the first ultrafast temporally, spectrally, and angularly resolved x-ray scattering measurements from shock-compressed matter. The experimental spectra yield the absolute elastic and inelastic scattering intensities from the measured density of free electrons. Laser-compressed lithium-hydride samples are well characterized by inelastic Compton and plasmon scattering of a K-alpha x-ray probe providing independent measurements of temperature and density. The data show excellent agreement with the total intensity and structure when using the two-species form factor and accounting for the screening of ion-ion interactions.

  2. Taking MAD to the extreme: ultrafast protein structure determination

    International Nuclear Information System (INIS)

    Walsh, M.A.; Dementieva, I.; Evans, G.; Sanishvili, R.; Joachimiak, A.

    1999-01-01

    Multiwavelength anomalous diffraction data were measured in 23 min from a 16 kDa selenomethionyl-substituted protein, producing experimental phases to 2.25 (angstrom) resolution. The data were collected on a mosaic 3 x 3 charge-coupled device using undulator radiation from the Structural Biology Center 19ID beamline at the Argonne National Laboratory's Advanced Photon Source. The phases were independently obtained semiautomatically by two crystallographic program suites, CCP4 and CNS. The quality and speed of this data acquisition exemplify the opportunities at third-generation synchrotron sources for high-throughput protein crystal structure determination

  3. Structural dynamics of surfaces by ultrafast electron crystallography: experimental and multiple scattering theory.

    Science.gov (United States)

    Schäfer, Sascha; Liang, Wenxi; Zewail, Ahmed H

    2011-12-07

    Recent studies in ultrafast electron crystallography (UEC) using a reflection diffraction geometry have enabled the investigation of a wide range of phenomena on the femtosecond and picosecond time scales. In all these studies, the analysis of the diffraction patterns and their temporal change after excitation was performed within the kinematical scattering theory. In this contribution, we address the question, to what extent dynamical scattering effects have to be included in order to obtain quantitative information about structural dynamics. We discuss different scattering regimes and provide diffraction maps that describe all essential features of scatterings and observables. The effects are quantified by dynamical scattering simulations and examined by direct comparison to the results of ultrafast electron diffraction experiments on an in situ prepared Ni(100) surface, for which structural dynamics can be well described by a two-temperature model. We also report calculations for graphite surfaces. The theoretical framework provided here allows for further UEC studies of surfaces especially at larger penetration depths and for those of heavy-atom materials. © 2011 American Institute of Physics

  4. Molecular Structure of Nucleic Acids

    Indian Academy of Sciences (India)

    Molecular Structure of Nucleic Acids. A Structure for Deoxyribose Nucleic Acid. J. D. Watson and F. H. C. Crick. Medical Research Council Unit for the Study of the Molecular Structure of Biological. Systems, Cavendish Laboratory, Cambridge. April 2. We wish to suggest a structure for the salt of deoxyribose nucleic acid ...

  5. Spectrally selective molecular doped solids: spectroscopy, photophysics and their application to ultrafast optical pulse processing

    International Nuclear Information System (INIS)

    Galaup, Jean-Pierre

    2005-01-01

    The persistent spectral hole-burning (PSHB) phenomenon observed in molecular doped polymers cooled down to liquid helium temperatures allows the engraving of spectral structures in the inhomogeneous absorption profile of the material. This phenomenon known since 1974 has became a fruitful field for the study of the intimacy of complex molecular systems in the solid state, revealing high-resolution spectroscopy, photophysics, photochemistry and dynamics of molecular doped amorphous media, organic as well as inorganic. A PSHB molecular doped solid can be programmed in spectral domain and therefore, it can be converted in an optical processor capable to achieve user-defined optical functions. Some aspects of this field are illustrated in the present paper. An application is presented where a naphthalocyanine doped polymer film is used in a demonstrative experiment to prove that temporal aberration free re-compression of ultra-short light pulses is feasible. Perspectives for the coherent control of light fields or photochemical processes are also evoked

  6. Structural Molecular Biology 2017 | SSRL

    Science.gov (United States)

    Highlights Training Workshops & Summer Schools Summer Students Structural Molecular Biology Illuminating experimental driver for structural biology research, serving the needs of a large number of academic and — Our Mission The SSRL Structural Molecular Biology program operates as an integrated resource and has

  7. 1H CSA parameters by ultrafast MAS NMR: Measurement and applications to structure refinement.

    Science.gov (United States)

    Miah, Habeeba K; Cresswell, Rosalie; Iuga, Dinu; Titman, Jeremy J

    2017-10-01

    A 1 H anisotropic-isotropic chemical shift correlation experiment which employs symmetry-based recoupling sequences to reintroduce the chemical shift anisotropy in ν 1 and ultrafast MAS to resolve 1 H sites in ν 2 is described. This experiment is used to measure 1 H shift parameters for L-ascorbic acid, a compound with a relatively complex hydrogen-bonding network in the solid. The 1 H CSAs of hydrogen-bonded sites with resolved isotropic shifts can be extracted directly from the recoupled lineshapes. In combination with DFT calculations, hydrogen positions in crystal structures obtained from X-ray and neutron diffraction are refined by comparison with simulations of the full two-dimensional NMR spectrum. The improved resolution afforded by the second dimension allows even unresolved hydrogen-bonded sites 1 H to be assigned and their shift parameters to be obtained. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. "Ultra"-Fast Fracture Strength of Advanced Structural Ceramic Materials Studied at Elevated Temperatures

    Science.gov (United States)

    Choi, Sung R.; Gyekenyesi, John P.

    1999-01-01

    The accurate determination of inert strength is important in reliable life prediction of structural ceramic components. At ambient temperature, the inert strength of a brittle material is typically regarded as free of the effects of slow crack growth due to stress corrosion. Therefore, the inert strength can be determined either by eliminating active species, especially moisture, with an appropriate inert medium, or by using a very high test rate. However, at elevated temperatures, the concept or definition of the inert strength of brittle ceramic materials is not clear, since temperature itself is a degrading environment, resulting in strength degradation through slow crack growth and/or creep. Since the mechanism to control strength is rate-dependent viscous flow, the only conceivable way to determine the inert strength at elevated temperatures is to utilize a very fast test rate that either minimizes the time for or eliminates slow crack growth. Few experimental studies have measured the elevated-temperature, inert (or "ultra"-fast fracture) strength of advanced ceramics. At the NASA Lewis Research Center, an experimental study was initiated to better understand the "ultra"-fast fracture strength behavior of advanced ceramics at elevated temperatures. Fourteen advanced ceramics - one alumina, eleven silicon nitrides, and two silicon carbides - have been tested using constant stress-rate (dynamic fatigue) testing in flexure with a series of stress rates including the "ultra"-fast stress rate of 33 000 MPa/sec with digitally controlled test frames. The results for these 14 advanced ceramics indicate that, notwithstanding possible changes in flaw populations as well as flaw configurations because of elevated temperatures, the strength at 33 000 MPa/sec approached the room-temperature strength or reached a higher value than that determined at the conventional test rate of 30 MPa/sec. On the basis of the experimental data, it can be stated that the elevated

  9. Comparative investigation of third- and fifth-harmonic generation in atomic and molecular gases driven by midinfrared ultrafast laser pulses

    Energy Technology Data Exchange (ETDEWEB)

    Ni Jielei; Yao Jinping; Zeng Bin; Chu Wei; Li Guihua; Zhang Haisu; Jing Chenrui [State Key Laboratory of High Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, P.O. Box 800-211, Shanghai 201800 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100039 (China); Chin, S. L. [Department of Physics, Engineering Physics and Optics, and Center for Optics, Photonics and Laser (COPL), Laval University, Laval, Quebec, G1K 7P4 (Canada); Cheng, Y.; Xu, Z. [State Key Laboratory of High Field Laser Physics, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, P.O. Box 800-211, Shanghai 201800 (China)

    2011-12-15

    We report on the comparative experimental investigation on third- and fifth-harmonic generation (THG and FHG) in atomic and molecular gases driven by midinfrared ultrafast laser pulses at a wavelength of {approx}1500 nm. We observe that the conversion efficiencies of both the THG and FHG processes saturate at similar peak intensities close to {approx}1.5 x 10{sup 14} W/cm{sup 2} for argon, nitrogen, and air, whose ionization potentials are close to each other. Near the saturation intensity, the ratio of yields of the FHG and THG reaches {approx}10{sup -1} for all the gases. Our results show that high-order Kerr effect seems to exist; however, contribution from the fourth-order Kerr refractive index coefficient alone is insufficient to balance the Kerr self-focusing without the assistance of plasma generation.

  10. Electronic and structural response of nanomaterials to ultrafast and ultraintense laser pulses.

    Science.gov (United States)

    Jiang, Chen-Wei; Zhou, Xiang; Lin, Zhibin; Xie, Rui-Hua; Li, Fu-Li; Allen, Roland E

    2014-02-01

    The interaction of materials with ultrafast and ultraintense laser pulses is a current frontier of science both experimentally and theoretically. In this review, we briefly discuss some recent theoretical studies by the present authors with our method of semiclassical electron-radiation-ion dynamics (SERID). In particular, Zhou et al. and Jiang et al. respectively, determined the optimal duration and optimal timing for a series of femtosecond scale laser pulses to excite a specific vibrational mode in a general chemical system. A set of such modes can be used as a "fingerprint" for characterizing a particular molecule or a complex in a solid. One can therefore envision many applications, ranging from fundamental studies to detection of chemical or biological agents. Allen et al. proved that dimers are preferentially emitted during photofragmentation of C60 under an ultrafast and ultraintense laser pulse. For interactions between laser pulses and semiconductors, e.g., GaAs, Si and InSb, besides experimentally accessible optical properties--epsilon(omega) and chi(2)-Allen et al. offered many other indicators to confirm the nonthermal nature of structural changes driven by electronic excitations and occurring during the first few hundred femtoseconds. Lin et al. found that, after the application of a femtosecond laser pulse, excited electrons in materials automatically equilibrate to a Fermi-Dirac distribution within roughly 100 fs, solely because of their coupling to the nuclear motion, even though the resulting electronic temperature is one to two orders of magnitude higher than the kinetic temperature defined by the nuclear motion.

  11. Single-order laser high harmonics in XUV for ultrafast photoelectron spectroscopy of molecular wavepacket dynamics

    Directory of Open Access Journals (Sweden)

    Mizuho Fushitani

    2016-11-01

    Full Text Available We present applications of extreme ultraviolet (XUV single-order laser harmonics to gas-phase ultrafast photoelectron spectroscopy. Ultrashort XUV pulses at 80 nm are obtained as the 5th order harmonics of the fundamental laser at 400 nm by using Xe or Kr as the nonlinear medium and separated from other harmonic orders by using an indium foil. The single-order laser harmonics is applied for real-time probing of vibrational wavepacket dynamics of I2 molecules in the bound and dissociating low-lying electronic states and electronic-vibrational wavepacket dynamics of highly excited Rydberg N2 molecules.

  12. Ultrafast static and diffusion-controlled electron transfer at Ag 29 nanocluster/molecular acceptor interfaces

    KAUST Repository

    Aly, Shawkat Mohammede; AbdulHalim, Lina G.; Besong, Tabot M.D.; Soldan, Giada; Bakr, Osman; Mohammed, Omar F.

    2015-01-01

    Efficient absorption of visible light and a long-lived excited state lifetime of silver nanoclusters (Ag29 NCs) are integral properties for these new clusters to serve as light-harvesting materials. Upon optical excitation, electron injection at Ag29 NC/methyl viologen (MV2+) interfaces is very efficient and ultrafast. Interestingly, our femto- and nanosecond time-resolved results demonstrate clearly that both dynamic and static electron transfer mechanisms are involved in photoluminescence quenching of Ag29 NCs. © 2016 The Royal Society of Chemistry.

  13. Ultrafast static and diffusion-controlled electron transfer at Ag 29 nanocluster/molecular acceptor interfaces

    KAUST Repository

    Aly, Shawkat Mohammede

    2015-10-29

    Efficient absorption of visible light and a long-lived excited state lifetime of silver nanoclusters (Ag29 NCs) are integral properties for these new clusters to serve as light-harvesting materials. Upon optical excitation, electron injection at Ag29 NC/methyl viologen (MV2+) interfaces is very efficient and ultrafast. Interestingly, our femto- and nanosecond time-resolved results demonstrate clearly that both dynamic and static electron transfer mechanisms are involved in photoluminescence quenching of Ag29 NCs. © 2016 The Royal Society of Chemistry.

  14. Single-order laser high harmonics in XUV for ultrafast photoelectron spectroscopy of molecular wavepacket dynamics.

    Science.gov (United States)

    Fushitani, Mizuho; Hishikawa, Akiyoshi

    2016-11-01

    We present applications of extreme ultraviolet (XUV) single-order laser harmonics to gas-phase ultrafast photoelectron spectroscopy. Ultrashort XUV pulses at 80 nm are obtained as the 5th order harmonics of the fundamental laser at 400 nm by using Xe or Kr as the nonlinear medium and separated from other harmonic orders by using an indium foil. The single-order laser harmonics is applied for real-time probing of vibrational wavepacket dynamics of I 2 molecules in the bound and dissociating low-lying electronic states and electronic-vibrational wavepacket dynamics of highly excited Rydberg N 2 molecules.

  15. Femtosecond X-Ray Scattering Study of Ultrafast Photoinduced Structural Dynamics in Solvated [Co(terpy)2]2+

    DEFF Research Database (Denmark)

    Biasin, Elisa; Brandt van Driel, Tim; Kjær, Kasper Skov

    2016-01-01

    We study the structural dynamics of photoexcited [Co(terpy)2]2+ in an aqueous solution with ultrafast x-ray diffuse scattering experiments conducted at the Linac Coherent Light Source. Through direct comparisons with density functional theory calculations, our analysis shows that the photoexcitat......We study the structural dynamics of photoexcited [Co(terpy)2]2+ in an aqueous solution with ultrafast x-ray diffuse scattering experiments conducted at the Linac Coherent Light Source. Through direct comparisons with density functional theory calculations, our analysis shows...... find that the equilibrium bond-elongated structure of the high spin state is established on a single-picosecond time scale and that this state has a lifetime of ∼7 ps....

  16. Ultrafast spectroscopy on DNA-cleavage by endonuclease in molecular crowding.

    Science.gov (United States)

    Singh, Priya; Choudhury, Susobhan; Dutta, Shreyasi; Adhikari, Aniruddha; Bhattacharya, Siddhartha; Pal, Debasish; Pal, Samir Kumar

    2017-10-01

    The jam-packed intracellular environments differ the activity of a biological macromolecule from that in laboratory environments (in vitro) through a number of mechanisms called molecular crowding related to structure, function and dynamics of the macromolecule. Here, we have explored the structure, function and dynamics of a model enzyme protein DNase I in molecular crowing of polyethylene glycol (PEG; MW 3350). We have used steady state and picosecond resolved dynamics of a well-known intercalator ethidium bromide (EB) in a 20-mer double-stranded DNA (dsDNA) to monitor the DNA-cleavage by the enzyme in absence and presence PEG. We have also labelled the enzyme by a well-known fluorescent probe 8-anilino-1-naphthalenesulfonic acid ammonium salt (ANS) to study the molecular mechanism of the protein-DNA association through exited state relaxation of the probe in absence (dictated by polarity) and presence of EB in the DNA (dictated by Förster resonance energy transfer (FRET)). The overall and local structures of the protein in presence of PEG have been followed by circular dichroism and time resolved polarization gated spectroscopy respectively. The enhanced dynamical flexibility of protein in presence of PEG as revealed from excited state lifetime and polarization gated anisotropy of ANS has been correlated with the stronger DNA-binding for the higher nuclease activity. We have also used conventional experimental strategy of agarose gel electrophoresis to monitor DNA-cleavage and found consistent results of enhanced nuclease activities both on synthetic 20-mer oligonucleotide and long genomic DNA from calf thymus. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Structure and Ultrafast Dynamics of White-Light-Emitting CdSe Nanocrystals

    International Nuclear Information System (INIS)

    Bowers, Michael J.; McBride, James; Garrett, Maria Danielle; Sammons, Jessica A.; Dukes, Albert; Schreuder, Michael A.; Watt, Tony L.; Lupini, Andrew R.; Pennycook, Stephen J.; Rosenthal, Sandra

    2009-01-01

    White-light emission from ultrasmall CdSe nanocrystals offers an alternative approach to the realization of solid-state lighting as an appealing technology for consumers. Unfortunately, their extremely small size limits the feasibility of traditional methods for nanocrystal characterization. This paper reports the first images of their structure, which were obtained using aberration-corrected atomic number contrast scanning transmission electron microscopy (Z-STEM). With subangstrom resolution, Z-STEM is one of the few available methods that can be used to directly image the nanocrystal's structure. The initial images suggest that they are crystalline and approximately four lattice planes in diameter. In addition to the structure, for the first time, the exciton dynamics were measured at different wavelengths of the white-light spectrum using ultrafast fluorescence upconversion spectroscopy. The data suggest that a myriad of trap states are responsible for the broad-spectrum emission. It is hoped that the information presented here will provide a foundation for the future development and improvement of white-light-emitting nanocrystals.

  18. Photoinduced molecular chirality probed by ultrafast resonant X-ray spectroscopy

    Directory of Open Access Journals (Sweden)

    Jérémy R. Rouxel

    2017-07-01

    Full Text Available Recently developed circularly polarized X-ray light sources can probe the ultrafast chiral electronic and nuclear dynamics through spatially localized resonant core transitions. We present simulations of time-resolved circular dichroism signals given by the difference of left and right circularly polarized X-ray probe transmission following an excitation by a circularly polarized optical pump with the variable time delay. Application is made to formamide which is achiral in the ground state and assumes two chiral geometries upon optical excitation to the first valence excited state. Probes resonant with various K-edges (C, N, and O provide different local windows onto the parity breaking geometry change thus revealing the enantiomer asymmetry.

  19. Ultrafast Hydro-Micromechanical Synthesis of Calcium Zincate: Structural and Morphological Characterizations

    Directory of Open Access Journals (Sweden)

    Vincent Caldeira

    2017-01-01

    Full Text Available Calcium zincate is a compound with a large panel of application: mainly known as an advantageous replacement of zinc oxide in negative electrodes for air-zinc or nickel-zinc batteries, it is also used as precursor catalyst in biodiesel synthesis and as antifungal compound for the protection of limestone monuments. However, its synthesis is not optimized yet. In this study, it was elaborated using an ultrafast synthesis protocol: Hydro-Micromechanical Synthesis. Two other synthesis methods, Hydrochemical Synthesis and Hydrothermal Synthesis, were used for comparison. In all cases, the as-synthesized samples were analyzed by X-ray diffraction, scanning electron microscopy, and LASER diffraction particle size analysis. Rietveld method was used to refine various structural parameters and obtain an average crystallite size, on a Hydro-Micromechanical submicronic sample. X-ray single crystal structure determination was performed on a crystal obtained by Hydrochemical Synthesis. It has been shown that regardless of the synthesis protocol, the prepared samples always crystallize in the same crystal lattice, with P21/c space group and only differ from their macroscopic textural parameters. Nevertheless, only the Hydro-Micromechanical method is industrially scalable and enables a precise control of the textural parameters of the obtained calcium zincate.

  20. Optical Detection in Ultrafast Short Wavelength Science

    International Nuclear Information System (INIS)

    Fullagar, Wilfred K.; Hall, Chris J.

    2010-01-01

    A new approach to coherent detection of ionising radiation is briefly motivated and recounted. The approach involves optical scattering of coherent light fields by colour centres in transparent solids. It has significant potential for diffractive imaging applications that require high detection dynamic range from pulsed high brilliance short wavelength sources. It also motivates new incarnations of Bragg's X-ray microscope for pump-probe studies of ultrafast molecular structure-dynamics.

  1. Molecular Structure of Membrane Tethers

    NARCIS (Netherlands)

    Baoukina, Svetlana; Marrink, Siewert J.; Tieleman, D. Peter

    2012-01-01

    Membrane tethers are nanotubes formed by a lipid bilayer. They play important functional roles in cell biology and provide an experimental window on lipid properties. Tethers have been studied extensively in experiments and described by theoretical models, but their molecular structure remains

  2. Scattering properties of ultrafast laser-induced refractive index shaping lenticular structures in hydrogels

    Science.gov (United States)

    Wozniak, Kaitlin T.; Germer, Thomas A.; Butler, Sam C.; Brooks, Daniel R.; Huxlin, Krystel R.; Ellis, Jonathan D.

    2018-02-01

    We present measurements of light scatter induced by a new ultrafast laser technique being developed for laser refractive correction in transparent ophthalmic materials such as cornea, contact lenses, and/or intraocular lenses. In this new technique, called intra-tissue refractive index shaping (IRIS), a 405 nm femtosecond laser is focused and scanned below the corneal surface, inducing a spatially-varying refractive index change that corrects vision errors. In contrast with traditional laser correction techniques, such as laser in-situ keratomileusis (LASIK) or photorefractive keratectomy (PRK), IRIS does not operate via photoablation, but rather changes the refractive index of transparent materials such as cornea and hydrogels. A concern with any laser eye correction technique is additional scatter induced by the process, which can adversely affect vision, especially at night. The goal of this investigation is to identify sources of scatter induced by IRIS and to mitigate possible effects on visual performance in ophthalmic applications. Preliminary light scattering measurements on patterns written into hydrogel showed four sources of scatter, differentiated by distinct behaviors: (1) scattering from scanned lines; (2) scattering from stitching errors, resulting from adjacent scanning fields not being aligned to one another; (3) diffraction from Fresnel zone discontinuities; and (4) long-period variations in the scans that created distinct diffraction peaks, likely due to inconsistent line spacing in the writing instrument. By knowing the nature of these different scattering errors, it will now be possible to modify and optimize the design of IRIS structures to mitigate potential deficits in visual performance in human clinical trials.

  3. Ultrafast gain and index dynamics of quantum dash structures emitting at 1.55 mu m

    DEFF Research Database (Denmark)

    Poel, Mike van der; Mørk, Jesper; Somers, A.

    2006-01-01

    The authors systematically characterize the ultrafast gain and index recovery of a quantum dash semiconductor optical amplifier after it has amplified a strong femtosecond pulse. The results show a recovery dominated by a fast time constant of 1.4 ps with an ultimate recovery taking place on a 150...

  4. Ultrafast Excited State Dynamics in Molecular Motors : Coupling of Motor Length to Medium Viscosity

    NARCIS (Netherlands)

    Conyard, Jamie; Stacko, Peter; Chen, Jiawen; McDonagh, Sophie; Hall, Christopher R.; Laptenok, Sergey P.; Browne, Wesley R.; Feringa, Ben L.; Meech, Stephen R.

    2017-01-01

    Photochemically driven molecular motors convert the energy of incident radiation to intramolecular rotational motion. The motor molecules considered here execute four step unidirectional rotational motion. This comprises a pair of successive light induced isomerizations to a metastable state

  5. Prediction of molecular crystal structures

    International Nuclear Information System (INIS)

    Beyer, Theresa

    2001-01-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol -1 of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  6. Prediction of molecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, Theresa

    2001-07-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  7. Ultrafast Electron Transfer at Organic Semiconductor Interfaces: Importance of Molecular Orientation

    KAUST Repository

    Ayzner, Alexander L.

    2015-01-02

    © 2014 American Chemical Society. Much is known about the rate of photoexcited charge generation in at organic donor/acceptor (D/A) heterojunctions overaged over all relative arrangements. However, there has been very little experimental work investigating how the photoexcited electron transfer (ET) rate depends on the precise relative molecular orientation between D and A in thin solid films. This is the question that we address in this work. We find that the ET rate depends strongly on the relative molecular arrangement: The interface where the model donor compound copper phthalocyanine is oriented face-on with respect to the fullerene C60 acceptor yields a rate that is approximately 4 times faster than that of the edge-on oriented interface. Our results suggest that the D/A electronic coupling is significantly enhanced in the face-on case, which agrees well with theoretical predictions, underscoring the importance of controlling the relative interfacial molecular orientation.

  8. Ultrafast Electron Transfer at Organic Semiconductor Interfaces: Importance of Molecular Orientation

    KAUST Repository

    Ayzner, Alexander L.; Nordlund, Dennis; Kim, Do-Hwan; Bao, Zhenan; Toney, Michael F.

    2015-01-01

    © 2014 American Chemical Society. Much is known about the rate of photoexcited charge generation in at organic donor/acceptor (D/A) heterojunctions overaged over all relative arrangements. However, there has been very little experimental work investigating how the photoexcited electron transfer (ET) rate depends on the precise relative molecular orientation between D and A in thin solid films. This is the question that we address in this work. We find that the ET rate depends strongly on the relative molecular arrangement: The interface where the model donor compound copper phthalocyanine is oriented face-on with respect to the fullerene C60 acceptor yields a rate that is approximately 4 times faster than that of the edge-on oriented interface. Our results suggest that the D/A electronic coupling is significantly enhanced in the face-on case, which agrees well with theoretical predictions, underscoring the importance of controlling the relative interfacial molecular orientation.

  9. Infrared studies of impurity states and ultrafast carrier dynamics in semiconductor quantum structures

    Energy Technology Data Exchange (ETDEWEB)

    Stehr, D.

    2007-12-28

    This thesis deals with infrared studies of impurity states, ultrafast carrier dynamics as well as coherent intersubband polarizations in semiconductor quantum structures such as quantum wells and superlattices, based on the GaAs/AlGaAs material system. In the first part it is shown that the 2p{sub z} confined impurity state of a semiconductor quantum well develops into an excited impurity band in the case of a superlattice. This is studied by following theoretically the transition from a single to a multiple quantum well or superlattice by exactly diagonalizing the three-dimensional Hamiltonian for a quantum well system with random impurities. These results also require reinterpretation of previous experimental data. The relaxation dynamics of interminiband transitions in doped GaAs/AlGaAs superlattices in the mid-IR are studied. This involves single-color pump-probe measurements to explore the dynamics at different wavelengths, which is performed with the Rossendorf freeelectron laser (FEL), providing picosecond pulses in a range from 3-200 {mu}m and are used for the first time within this thesis. In these experiments, a fast bleaching of the interminiband transition is observed followed by thermalization and subsequent relaxation, whose time constants are determined to be 1-2 picoseconds. This is followed by an additional component due to carrier cooling in the lower miniband. In the second part, two-color pump-probe measurements are performed, involving the FEL as the pump source and a table-top broad-band tunable THz source for probing the transmission changes. In addition, the dynamics of excited electrons within the minibands is explored and their contribution quantitatively extracted from the measurements. Intersubband absorption experiments of photoexcited carriers in single quantum well structures, measured directly in the time-domain, i.e. probing coherently the polarization between the first and the second subband, are presented. By varying the carrier

  10. Ultrafast Spectroscopy of Energetic Materials: Toward a Molecular Understanding of Impact Sensitivity

    National Research Council Canada - National Science Library

    Dlott, Dana D

    2005-01-01

    ... with 1.5 Angstrom resolution. With 3D spectroscopy we have studied vibrational energy transfer in water and for the first time we have been able to watch vibrational energy flow across the interface between a molecular nanostructure and its surroundings.

  11. Ultrathin graphene-based membrane with precise molecular sieving and ultrafast solvent permeation

    Science.gov (United States)

    Yang, Q.; Su, Y.; Chi, C.; Cherian, C. T.; Huang, K.; Kravets, V. G.; Wang, F. C.; Zhang, J. C.; Pratt, A.; Grigorenko, A. N.; Guinea, F.; Geim, A. K.; Nair, R. R.

    2017-12-01

    Graphene oxide (GO) membranes continue to attract intense interest due to their unique molecular sieving properties combined with fast permeation. However, their use is limited to aqueous solutions because GO membranes appear impermeable to organic solvents, a phenomenon not yet fully understood. Here, we report efficient and fast filtration of organic solutions through GO laminates containing smooth two-dimensional (2D) capillaries made from large (10-20 μm) flakes. Without modification of sieving characteristics, these membranes can be made exceptionally thin, down to ~10 nm, which translates into fast water and organic solvent permeation. We attribute organic solvent permeation and sieving properties to randomly distributed pinholes interconnected by short graphene channels with a width of 1 nm. With increasing membrane thickness, organic solvent permeation rates decay exponentially but water continues to permeate quickly, in agreement with previous reports. The potential of ultrathin GO laminates for organic solvent nanofiltration is demonstrated by showing >99.9% rejection of small molecular weight organic dyes dissolved in methanol. Our work significantly expands possibilities for the use of GO membranes in purification and filtration technologies.

  12. Single-shot mega-electronvolt ultrafast electron diffraction for structure dynamic studies of warm dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Mo, M. Z., E-mail: mmo09@slac.stanford.edu; Shen, X.; Chen, Z.; Li, R. K.; Dunning, M.; Zheng, Q.; Weathersby, S. P.; Reid, A. H.; Coffee, R.; Makasyuk, I.; Edstrom, S.; McCormick, D.; Jobe, K.; Hast, C.; Glenzer, S. H.; Wang, X. [SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025 (United States); Sokolowski-Tinten, K. [Faculty of Physics and Centre for Nanointegration Duisburg-Essen, University of Duisburg-Essen, Lotharstrasse 1, D-47048 Duisburg (Germany)

    2016-11-15

    We have developed a single-shot mega-electronvolt ultrafast-electron-diffraction system to measure the structural dynamics of warm dense matter. The electron probe in this system is featured by a kinetic energy of 3.2 MeV and a total charge of 20 fC, with the FWHM pulse duration and spot size at sample of 350 fs and 120 μm respectively. We demonstrate its unique capability by visualizing the atomic structural changes of warm dense gold formed from a laser-excited 35-nm freestanding single-crystal gold foil. The temporal evolution of the Bragg peak intensity and of the liquid signal during solid-liquid phase transition are quantitatively determined. This experimental capability opens up an exciting opportunity to unravel the atomic dynamics of structural phase transitions in warm dense matter regime.

  13. CSMB | Center For Structural Molecular Biology

    Data.gov (United States)

    Federal Laboratory Consortium — The Center for Structural Molecular Biologyat ORNL is dedicated to developing instrumentation and methods for determining the 3-dimensional structures of proteins,...

  14. Coherent phonon excitation and linear thermal expansion in structural dynamics and ultrafast electron diffraction of laser-heated metals.

    Science.gov (United States)

    Tang, Jau

    2008-04-28

    In this study, we examine the ultrafast structural dynamics of metals induced by a femtosecond laser-heating pulse as probed by time-resolved electron diffraction. Using the two-temperature model and the Grüneisen relationship we calculate the electron temperature, phonon temperature, and impulsive force at each atomic site in the slab. Together with the Fermi-Pasta-Ulam anharmonic chain model we calculate changes of bond distance and the peak shift of Bragg spots or Laue rings. A laser-heated thin slab is shown to exhibit "breathing" standing-wave behavior, with a period equal to the round-trip time for sound wave and a wavelength twice the slab thickness. The peak delay time first increases linearly with the thickness (linear thermal expansion due to lattice temperature jump are shown to contribute to the overall structural changes. Differences between these two mechanisms and their dependence on film thickness and other factors are discussed.

  15. Photoelectron photoion coincidence imaging of ultrafast control in multichannel molecular dynamics.

    Science.gov (United States)

    Lehmann, C Stefan; Ram, N Bhargava; Irimia, Daniel; Janssen, Maurice H M

    2011-01-01

    The control of multichannel ionic fragmentation dynamics in CF3I is studied by femtosecond pulse shaping and velocity map photoelectron photoion coincidence imaging. When CF3I is photoexcited with femtosecond laser pulses around 540 nm there are two major ions observed in the time-of-flight mass spectrum, the parent CF3I+ ion and the CF3+ fragment ion. In this first study we focussed on the influence of LCD-shaped laser pulses on the molecular dynamics. The three-dimensional recoil distribution of electrons and ions were imaged in coincidence using a single time-of-flight delay line detector. By fast switching of the voltages on the various velocity map ion lenses after detection of the electron, both the electron and the coincident ion are measured with the same imaging detector. These results demonstrate that a significant simplification of a photoelectron-photoion coincidence imaging apparatus is in principle possible using switched lens voltages. It is observed that shaped laser fields like chirped pulses, double pulses, and multiple pulses can enhance the CF3+CF3I+ ratio by up to 100%. The total energetics of the dynamics is revealed by analysis of the coincident photoelectron spectra and the kinetic energy of the CF3+ and I fragments. Both the parent CF3I+ and the CF3+ fragment result from a five-photon excitation process. The fragments are formed with very low kinetic energy. The photoelectron spectra and CF3+/CF3I+ ratio vary with the center wavelength of the shaped laser pulses. An optimal enhancement of the CF3+/CF3I+ ratio by about 60% is observed for the double pulse excitation when the pulses are spaced 60 fs apart. We propose that the control mechanism is determined by dynamics on neutral excited states and we discuss the results in relation to the location of electronically excited (Rydberg) states of CF3I.

  16. Uncertainties of Molecular Structural Parameters

    International Nuclear Information System (INIS)

    Császár, Attila G.

    2014-01-01

    performed. Simply, there are significant disagreements between the same bond lengths measured by different techniques. These disagreements are, however, systematic and can be computed via techniques of quantum chemistry which deal not only with the motions of the electrons (electronic structure theory) but also with the often large amplitude motions of the nuclei. As to the relevant quantum chemical computations, since about 1970 electronic structure theory has become able to make quantitative predictions and thus challenge (or even overrule) many experiments. Nevertheless, quantitative agreement of quantum chemical results with experiment can only be expected when the motions of the atoms are also considered. In the fourth age of quantum chemistry we are living in an era where one can bridge quantitatively the gap between ‘effective’, experimental and ‘equilibrium’, computed structures at even elevated temperatures of interest thus minimizing any real uncertainties of structural parameters. The connections mentioned are extremely important as they help to understand the true uncertainty of measured structural parameters. Traditionally it is microwave (MW) and millimeterwave (MMW) spectroscopy, as well as gas-phase electron diffraction (GED), which yielded the most accurate structural parameters of molecules. The accuracy of the MW and GED experiments approached about 0.001Å and 0.1º under ideal circumstances, worse, sometimes considerably worse, in less than ideal and much more often encountered situations. Quantum chemistry can define both highly accurate equilibrium (so-called Born-Oppenheimer, r_e"B"O, and semiexperimental, r_e"S"E) structures and, via detailed investigation of molecular motions, accurate temperature-dependent rovibrationally averaged structures. Determining structures is still a rich field for research, understanding the measured or computed uncertainties of structures and structural parameters is still a challenge but there are firm and well

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-08-15

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

  18. Physical mechanisms of SiNx layer structuring with ultrafast lasers by direct and confined laser ablation

    International Nuclear Information System (INIS)

    Rapp, S.; Heinrich, G.; Wollgarten, M.; Huber, H. P.; Schmidt, M.

    2015-01-01

    In the production process of silicon microelectronic devices and high efficiency silicon solar cells, local contact openings in thin dielectric layers are required. Instead of photolithography, these openings can be selectively structured with ultra-short laser pulses by confined laser ablation in a fast and efficient lift off production step. Thereby, the ultrafast laser pulse is transmitted by the dielectric layer and absorbed at the substrate surface leading to a selective layer removal in the nanosecond time domain. Thermal damage in the substrate due to absorption is an unwanted side effect. The aim of this work is to obtain a deeper understanding of the physical laser-material interaction with the goal of finding a damage-free ablation mechanism. For this, thin silicon nitride (SiN x ) layers on planar silicon (Si) wafers are processed with infrared fs-laser pulses. Two ablation types can be distinguished: The known confined ablation at fluences below 300 mJ/cm 2 and a combined partial confined and partial direct ablation at higher fluences. The partial direct ablation process is caused by nonlinear absorption in the SiN x layer in the center of the applied Gaussian shaped laser pulses. Pump-probe investigations of the central area show ultra-fast reflectivity changes typical for direct laser ablation. Transmission electron microscopy results demonstrate that the Si surface under the remaining SiN x island is not damaged by the laser ablation process. At optimized process parameters, the method of direct laser ablation could be a good candidate for damage-free selective structuring of dielectric layers on absorbing substrates

  19. Adlayer structure dependent ultrafast desorption dynamics in carbon monoxide adsorbed on Pd (111)

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Sung-Young; Camillone, Nina R.; Camillone, Nicholas, E-mail: nicholas@bnl.gov [Chemistry Department, Brookhaven National Laboratory, Upton, New York 11973 (United States); Xu, Pan [Department of Chemistry, Stony Brook University, Stony Brook, New York 11794 (United States); White, Michael G. [Chemistry Department, Brookhaven National Laboratory, Upton, New York 11973 (United States); Department of Chemistry, Stony Brook University, Stony Brook, New York 11794 (United States)

    2016-07-07

    We report our ultrafast photoinduced desorption investigation of the coverage dependence of substrate–adsorbate energy transfer in carbon monoxide adlayers on the (111) surface of palladium. As the CO coverage is increased, the adsorption site population shifts from all threefold hollows (up to 0.33 ML), to bridge and near bridge (>0.5 to 0.6 ML) and finally to mixed threefold hollow plus top site (at saturation at 0.75 ML). We show that between 0.24 and 0.75 ML this progression of binding site motifs is accompanied by two remarkable features in the ultrafast photoinduced desorption of the adsorbates: (i) the desorption probability increases roughly two orders magnitude, and (ii) the adsorbate–substrate energy transfer rate observed in two-pulse correlation experiments varies nonmonotonically, having a minimum at intermediate coverages. Simulations using a phenomenological model to describe the adsorbate–substrate energy transfer in terms of frictional coupling indicate that these features are consistent with an adsorption-site dependent electron-mediated energy coupling strength, η{sub el}, that decreases with binding site in the order: three-fold hollow > bridge and near bridge > top site. This weakening of η{sub el} largely counterbalances the decrease in the desorption activation energy that accompanies this progression of adsorption site motifs, moderating what would otherwise be a rise of several orders of magnitude in the desorption probability. Within this framework, the observed energy transfer rate enhancement at saturation coverage is due to interadsorbate energy transfer from the copopulation of molecules bound in three-fold hollows to their top-site neighbors.

  20. Ultrafast re-structuring of the electronic landscape of transparent dielectrics: new material states (Die-Met)

    Science.gov (United States)

    Gamaly, E. G.; Rode, A. V.

    2018-03-01

    Swift excitation of transparent dielectrics by ultrashort and highly intense laser pulse leads to ultra-fast re-structuring of the electronic landscape and generates many transient material states, which are continuously reshaped in accord with the changing pulse intensity. These unconventional transient material states, which exhibit simultaneously both dielectric and metallic properties, we termed here as the `Die-Met' states. The excited material is transparent and conductive at the same time. The real part of permittivity of the excited material changes from positive to negative values with the increase of excitation, which affects strongly the interaction process during the laser pulse. When the incident field has a component along the permittivity gradient, the amplitude of the field increases resonantly near the point of zero permittivity, which dramatically changes the interaction mode and increases absorption in a way that is similar to the resonant absorption in plasma. The complex 3D structure of the permittivity makes a transparent part of the excited dielectric (at ɛ 0 > ɛ re > 0) optically active. The electro-magnetic wave gets a twisted trajectory and accrues the geometric phase while passing through such a medium. Both the phase and the rotation of the polarisation plane depend on the 3D permittivity structure. Measuring the transmission, polarisation and the phase of the probe beam allows one to quantitatively identify these new transient states. We discuss the revelations of this effect in different experimental situations and their possible applications.

  1. Watching ultrafast responses of structure and magnetism in condensed matter with momentum-resolved probes

    Directory of Open Access Journals (Sweden)

    S. L. Johnson

    2017-11-01

    Full Text Available We present a non-comprehensive review of some representative experimental studies in crystalline condensed matter systems where the effects of intense ultrashort light pulses are probed using x-ray diffraction and photoelectron spectroscopy. On an ultrafast (sub-picosecond time scale, conventional concepts derived from the assumption of thermodynamic equilibrium must often be modified in order to adequately describe the time-dependent changes in material properties. There are several commonly adopted approaches to this modification, appropriate in different experimental circumstances. One approach is to treat the material as a collection of quasi-thermal subsystems in thermal contact with each other in the so-called “N-temperature” models. On the other extreme, one can also treat the time-dependent changes as fully coherent dynamics of a sometimes complex network of excitations. Here, we present examples of experiments that fall into each of these categories, as well as experiments that partake of both models. We conclude with a discussion of the limitations and future potential of these concepts.

  2. Ultrafast biophotonics

    CERN Document Server

    Vasa, P

    2016-01-01

    This book presents emerging contemporary optical techniques of ultrafast science which have opened entirely new vistas for probing biological entities and processes. The spectrum reaches from time-resolved imaging and multiphoton microscopy to cancer therapy and studies of DNA damage. The book displays interdisciplinary research at the interface of physics and biology. Emerging topics on the horizon are also discussed, like the use of squeezed light, frequency combs and terahertz imaging as the possibility of mimicking biological systems. The book is written in a manner to make it readily accessible to researchers, postgraduate biologists, chemists, engineers, and physicists and students of optics, biomedical optics, photonics and biotechnology.

  3. Molecular Structure of Nucleic Acids

    Indian Academy of Sciences (India)

    chain, that is, after 34 A. The distance of a phosphorus atom from the fibre axis is 10. A. As the phosphates are on the outside, cations have easy access to them. The structure is an open one, and its water content is rather high. At lower water contents we would expect the bases to tilt so that the structure could become more.

  4. Exploring RNA structure by integrative molecular modelling

    DEFF Research Database (Denmark)

    Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice

    2010-01-01

    RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based...... on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...

  5. The Molecular Structure of Penicillin

    Science.gov (United States)

    Bentley, Ronald

    2004-01-01

    Overviews of the observations that constitute a structure proof for penicillin, specifically aimed at the general student population, are presented. Melting points and boiling points were criteria of purity and a crucial tool was microanalysis leading to empirical formulas.

  6. Developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy.

    Science.gov (United States)

    Doust, Alexander B; Marai, Christopher N J; Harrop, Stephen J; Wilk, Krystyna E; Curmi, Paul M G; Scholes, Gregory D

    2004-11-12

    Cryptophyte algae differ from cyanobacteria and red algae in the architecture of their photosynthetic light harvesting systems, even though all three are evolutionarily related. Central to cryptophyte light harvesting is the soluble antenna protein phycoerythrin 545 (PE545). The ultrahigh resolution crystal structure of PE545, isolated from a unicellular cryptophyte Rhodomonas CS24, is reported at both 1.1A and 0.97A resolution, revealing details of the conformation and environments of the chromophores. Absorption, emission and polarized steady state spectroscopy (298K, 77K), as well as ultrafast (20fs time resolution) measurements of population dynamics are reported. Coupled with complementary quantum chemical calculations of electronic transitions of the bilins, these enable assignment of spectral absorption characteristics to each chromophore in the structure. Spectral differences between the tetrapyrrole pigments due to chemical differences between bilins, as well as their binding and interaction with the local protein environment are described. Based on these assignments, and considering customized optical properties such as strong coupling, a model for light harvesting by PE545 is developed which explains the fast, directional harvesting of excitation energy. The excitation energy is funnelled from four peripheral pigments (beta158,beta82) into a central chromophore dimer (beta50/beta61) in approximately 1ps. Those chromophores, in turn, transfer the excitation energy to the red absorbing molecules located at the periphery of the complex in approximately 4ps. A final resonance energy transfer step sensitizes just one of the alpha19 bilins on a time scale of 22ps. Furthermore, it is concluded that binding of PE545 to the thylakoid membrane is not essential for efficient energy transfer to the integral membrane chlorophyll a-containing complexes associated with PS-II.

  7. STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

    Energy Technology Data Exchange (ETDEWEB)

    Sawada, Tsuyoshi [Joint ALMA Office, Alonso de Cordova 3107, Vitacura, Santiago 763-0355 (Chile); Hasegawa, Tetsuo [NAOJ Chile Observatory, Joaquin Montero 3000 Oficina 702, Vitacura, Santiago 763-0409 (Chile); Koda, Jin, E-mail: sawada.tsuyoshi@nao.ac.jp [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800 (United States)

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  8. Fano resonance control in a photonic crystal structure and its application to ultrafast switching

    DEFF Research Database (Denmark)

    Yu, Yi; Heuck, Mikkel; Hu, Hao

    2014-01-01

    We experimentally demonstrate a photonic crystal structure that allows easy and robust control of the Fano spectrum. Its operation relies on controlling the amplitude of light propagating along one of the light paths in the structure from which the Fano resonance is obtained. Short-pulse dynamic ...... reshaping effect of the nonlinear Fano transfer function. As an example, we present a system application of a Fano structure, demonstrating its advantages by the experimental realiza- tion of 10 Gbit/s all-optical modulation with optical control power less than 1mW.......We experimentally demonstrate a photonic crystal structure that allows easy and robust control of the Fano spectrum. Its operation relies on controlling the amplitude of light propagating along one of the light paths in the structure from which the Fano resonance is obtained. Short-pulse dynamic...

  9. The multi-phase winds of Markarian 231: from the hot, nuclear, ultra-fast wind to the galaxy-scale, molecular outflow

    Science.gov (United States)

    Feruglio, C.; Fiore, F.; Carniani, S.; Piconcelli, E.; Zappacosta, L.; Bongiorno, A.; Cicone, C.; Maiolino, R.; Marconi, A.; Menci, N.; Puccetti, S.; Veilleux, S.

    2015-11-01

    Mrk 231 is a nearby ultra-luminous IR galaxy exhibiting a kpc-scale, multi-phase AGN-driven outflow. This galaxy represents the best target to investigate in detail the morphology and energetics of powerful outflows, as well as their still poorly-understood expansion mechanism and impact on the host galaxy. In this work, we present the best sensitivity and angular resolution maps of the molecular disk and outflow of Mrk 231, as traced by CO(2-1) and (3-2) observations obtained with the IRAM/PdBI. In addition, we analyze archival deep Chandra and NuSTAR X-ray observations. We use this unprecedented combination of multi-wavelength data sets to constrain the physical properties of both the molecular disk and outflow, the presence of a highly-ionized ultra-fast nuclear wind, and their connection. The molecular CO(2-1) outflow has a size of 1 kpc, and extends in all directions around the nucleus, being more prominent along the south-west to north-east direction, suggesting a wide-angle biconical geometry. The maximum projected velocity of the outflow is nearly constant out to 1 kpc, thus implying that the density of the outflowing material must decrease from the nucleus outwards as r-2. This suggests that either a large part of the gas leaves the flow during its expansion or that the bulk of the outflow has not yet reached out to 1 kpc, thus implying a limit on its age of 1 Myr. Mapping the mass and energy rates of the molecular outflow yields dot {M} OF = [500-1000] M⊙ yr-1 and Ėkin,OF = [7-10] × 1043 erg s-1. The total kinetic energy of the outflow is Ekin,OF is of the same order of the total energy of the molecular disk, Edisk. Remarkably, our analysis of the X-ray data reveals a nuclear ultra-fast outflow (UFO) with velocity -20 000 km s-1, dot {M}UFO = [0.3-2.1] M⊙ yr-1, and momentum load dot {P}UFO/ dot {P}rad = [0.2-1.6]. We find Ėkin,UFO Ėkin,OF as predicted for outflows undergoing an energy conserving expansion. This suggests that most of the UFO

  10. Hierarchically structured lithium titanate for ultrafast charging in long-life high capacity batteries

    Science.gov (United States)

    Odziomek, Mateusz; Chaput, Frédéric; Rutkowska, Anna; Świerczek, Konrad; Olszewska, Danuta; Sitarz, Maciej; Lerouge, Frédéric; Parola, Stephane

    2017-05-01

    High-performance Li-ion batteries require materials with well-designed and controlled structures on nanometre and micrometre scales. Electrochemical properties can be enhanced by reducing crystallite size and by manipulating structure and morphology. Here we show a method for preparing hierarchically structured Li4Ti5O12 yielding nano- and microstructure well-suited for use in lithium-ion batteries. Scalable glycothermal synthesis yields well-crystallized primary 4-8 nm nanoparticles, assembled into porous secondary particles. X-ray photoelectron spectroscopy reveals presence of Ti+4 only; combined with chemical analysis showing lithium deficiency, this suggests oxygen non-stoichiometry. Electron microscopy confirms hierarchical morphology of the obtained material. Extended cycling tests in half cells demonstrates capacity of 170 mAh g-1 and no sign of capacity fading after 1,000 cycles at 50C rate (charging completed in 72 s). The particular combination of nanostructure, microstructure and non-stoichiometry for the prepared lithium titanate is believed to underlie the observed electrochemical performance of material.

  11. Learning surface molecular structures via machine vision

    Science.gov (United States)

    Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

    2017-08-01

    Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

  12. Rotational structure in molecular infrared spectra

    CERN Document Server

    di Lauro, Carlo

    2013-01-01

    Recent advances in infrared molecular spectroscopy have resulted in sophisticated theoretical and laboratory methods that are difficult to grasp without a solid understanding of the basic principles and underlying theory of vibration-rotation absorption spectroscopy. Rotational Structure in Molecular Infrared Spectra fills the gap between these recent, complex topics and the most elementary methods in the field of rotational structure in the infrared spectra of gaseous molecules. There is an increasing need for people with the skills and knowledge to interpret vibration-rotation spectra in many scientific disciplines, including applications in atmospheric and planetary research. Consequently, the basic principles of vibration-rotation absorption spectroscopy are addressed for contemporary applications. In addition to covering operational quantum mechanical methods, spherical tensor algebra, and group theoretical methods applied to molecular symmetry, attention is also given to phase conventions and their effe...

  13. Ultrafast quenching of tryptophan fluorescence in proteins: Interresidue and intrahelical electron transfer

    Energy Technology Data Exchange (ETDEWEB)

    Qiu Weihong; Li Tanping; Zhang Luyuan; Yang Yi; Kao Yating; Wang Lijuan [Department of Physics, Chemistry, and Biochemistry, Program of Biophysics, Chemical Physics, and Biochemistry, Ohio State University, Columbus, OH 43210 (United States); Zhong Dongping [Department of Physics, Chemistry, and Biochemistry, Program of Biophysics, Chemical Physics, and Biochemistry, Ohio State University, Columbus, OH 43210 (United States)], E-mail: dongping@mps.ohio-state.edu

    2008-06-23

    Quenching of tryptophan fluorescence in proteins has been critical to the understanding of protein dynamics and enzyme reactions using tryptophan as a molecular optical probe. We report here our systematic examinations of potential quenching residues with more than 40 proteins. With site-directed mutation, we placed tryptophan to desired positions or altered its neighboring residues to screen quenching groups among 20 amino acid residues and of peptide backbones. With femtosecond resolution, we observed the ultrafast quenching dynamics within 100 ps and identified two ultrafast quenching groups, the carbonyl- and sulfur-containing residues. The former is glutamine and glutamate residues and the later is disulfide bond and cysteine residue. The quenching by the peptide-bond carbonyl group as well as other potential residues mostly occurs in longer than 100 ps. These ultrafast quenching dynamics occur at van der Waals distances through intraprotein electron transfer with high directionality. Following optimal molecular orbital overlap, electron jumps from the benzene ring of the indole moiety in a vertical orientation to the LUMO of acceptor quenching residues. Molecular dynamics simulations were invoked to elucidate various correlations of quenching dynamics with separation distances, relative orientations, local fluctuations and reaction heterogeneity. These unique ultrafast quenching pairs, as recently found to extensively occur in high-resolution protein structures, may have significant biological implications.

  14. Molecular Structure of Human-Liver Glycogen.

    Directory of Open Access Journals (Sweden)

    Bin Deng

    Full Text Available Glycogen is a highly branched glucose polymer which is involved in maintaining blood-sugar homeostasis. Liver glycogen contains large composite α particles made up of linked β particles. Previous studies have shown that the binding which links β particles into α particles is impaired in diabetic mice. The present study reports the first molecular structural characterization of human-liver glycogen from non-diabetic patients, using transmission electron microscopy for morphology and size-exclusion chromatography for the molecular size distribution; the latter is also studied as a function of time during acid hydrolysis in vitro, which is sensitive to certain structural features, particularly glycosidic vs. proteinaceous linkages. The results are compared with those seen in mice and pigs. The molecular structural change during acid hydrolysis is similar in each case, and indicates that the linkage of β into α particles is not glycosidic. This result, and the similar morphology in each case, together imply that human liver glycogen has similar molecular structure to those of mice and pigs. This knowledge will be useful for future diabetes drug targets.

  15. Ultrafast laser induced electronic and structural modifications in bulk fused silica

    Energy Technology Data Exchange (ETDEWEB)

    Mishchik, K.; D' Amico, C.; Velpula, P. K.; Mauclair, C.; Boukenter, A.; Ouerdane, Y.; Stoian, R. [Laboratoire Hubert Curien, UMR 5516 CNRS, Université de Lyon, Université Jean Monnet, 42000 Saint Etienne (France)

    2013-10-07

    Ultrashort laser pulses can modify the inner structure of fused silica, generating refractive index changes varying from soft positive (type I) light guiding forms to negative (type II) values with void presence and anisotropic sub-wavelength modulation. We investigate electronic and structural material changes in the type I to type II transition via coherent and incoherent secondary light emission reflecting free carrier behavior and post-irradiation material relaxation in the index change patterns. Using phase contrast microscopy, photoluminescence, and Raman spectroscopy, we determine in a space-resolved manner defect formation, redistribution and spatial segregation, and glass network reorganization paths in conditions marking the changeover between type I and type II photoinscription regimes. We first show characteristic patterns of second harmonic generation in type I and type II traces, indicating the collective involvement of free carriers and polarization memory. Second, incoherent photoemission from resonantly and non-resonantly excited defect states reveals accumulation of non-bridging oxygen hole centers (NBOHCs) in positive index domains and oxygen deficiency centers (ODCs) with O{sub 2}{sup −} ions segregation in void-like regions and in the nanostructured domains, reflecting the interaction strength. Complementary Raman investigations put into evidence signatures of the different environments where photo-chemical densification (bond rearrangements) and mechanical effects can be indicated. NBOHCs setting in before visible index changes serve as precursors for subsequent compaction build-up, indicating a scenario of cold, defect-assisted densification for the soft type I irradiation regime. Additionally, we observe hydrodynamic effects and severe bond-breaking in type II zones with indications of phase transition. These observations illuminate densification paths in fused silica in low power irradiation regimes, and equally in energetic ranges

  16. Ultra-Fast RAFT-HDA Click Conjugation: An Efficient Route to High Molecular Weight Block Copolymers.

    Science.gov (United States)

    Inglis, Andrew J; Stenzel, Martina H; Barner-Kowollik, Christopher

    2009-11-02

    The use of the reversible addition fragmentation chain transfer-hetero Diels-Alder (RAFT-HDA) click reaction for the modular construction of block copolymers is extended to the generation of high molecular weight materials. Cyclopentadienyl end-functionalized polystyrene (PS-Cp) prepared via both atom transfer radical polymerization (ATRP) and the RAFT process are conjugated to poly(isobornyl acrylate) (PiBoA) (also prepared via RAFT polymerization) to achieve well-defined block copolymers with molecular weights ranging from 34 000 to over 100 000 g · mol(-1) and with small polydispersities (PDI HDA click chemistry can provide access to high molecular weight block copolymers in a simple and straight-forward fashion. Copyright © 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Ultrafast hydrogen exchange reveals specific structural events during the initial stages of folding of cytochrome c.

    Science.gov (United States)

    Fazelinia, Hossein; Xu, Ming; Cheng, Hong; Roder, Heinrich

    2014-01-15

    Many proteins undergo a sharp decrease in chain dimensions during early stages of folding, prior to the rate-limiting step in folding. However, it remains unclear whether compact states are the result of specific folding events or a general hydrophobic collapse of the poly peptide chain driven by the change in solvent conditions. To address this fundamental question, we extended the temporal resolution of NMR-detected H/D exchange labeling experiments into the microsecond regime by adopting a microfluidics approach. By observing the competition between H/D exchange and folding as a function of labeling pH, coupled with direct measurement of exchange rates in the unfolded state, we were able to monitor hydrogen-bond formation for over 50 individual backbone NH groups within the initial 140 microseconds of folding of horse cytochrome c. Clusters of solvent-shielded amide protons were observed in two α-helical segments in the C-terminal half of the protein, while the N-terminal helix remained largely unstructured, suggesting that proximity in the primary structure is a major factor in promoting helix formation and association at early stages of folding, while the entropically more costly long-range contacts between the N- and C-terminal helices are established only during later stages. Our findings clearly indicate that the initial chain condensation in cytochrome c is driven by specific interactions among a subset of α-helical segments rather than a general hydrophobic collapse.

  18. Ultrafast electron dynamics at alkali/ice structures adsorbed on a metal surface

    International Nuclear Information System (INIS)

    Meyer, Michael

    2011-01-01

    The goal of this work is to study the interaction between excess electrons in water ice structures adsorbed on metal surfaces and other charged or neutral species, like alkali ions, or chemically reactive molecules, like chlorofluorocarbons (CFC), respectively. The excess electrons in the ice can interact with the ions directly or indirectly via the hydrogen bonded water molecules. In both cases the presence of the alkali influences the population, localization, and lifetime of electronic states of excess electrons in the ice adlayer. These properties are of great relevance when considering the highly reactive character of the excess electrons, which can mediate chemical reactions by dissociative electron attachment (DEA). The influence of alkali adsorption on electron solvation and transfer dynamics in ice structures is investigated for two types of adsorption configurations using femtosecond time-resolved two-photon photoelectron spectroscopy. In the first system alkali atoms are coadsorbed on top of a wetting amorphous ice film adsorbed on Cu(111). At temperatures between 60 and 100 K alkali adsorption leads to the formation of positively charged alkali ions at the ice/vacuum interface. The interaction between the alkali ions at the surface and the dipole moments of the surrounding water molecules results in a reorientation of the water molecules. As a consequence new electron trapping sites, i.e. at local potential minima, are formed. Photoinjection of excess electrons into these alkali-ion covered amorphous ice layers, results in the trapping of a solvated electron at an alkali-ion/water complex. In contrast to solvation in pure amorphous ice films, where the electrons are located in the bulk of the ice layer, solvated electrons at alkali-ion/water complexes are located at the ice/vacuum interface. They exhibit lifetimes of several picoseconds and show a fast energetic stabilization. With ongoing solvation, i.e. pump-probe time delay, the electron transfer is

  19. Characteristics studies of molecular structures in drugs

    Directory of Open Access Journals (Sweden)

    Wei Gao

    2017-05-01

    Full Text Available In theoretical medicine, topological indices are defined to test the medicine and pharmacy characteristics, such as melting point, boiling point, toxicity and other biological activities. As basic molecular structures, hexagonal jagged-rectangle and distance-regular structure are widely appeared in medicine, pharmacy and biology engineering. In this paper, we study the chemical properties of hexagonal jagged-rectangle from the mathematical point of view. Several vertex distance-based indices are determined. Furthermore, the Wiener related indices of distance-regular structure are also considered.

  20. Progress in Ultrafast Intense Laser Science II

    CERN Document Server

    Yamanouchi, Kaoru; Agostini, Pierre; Ferrante, Gaetano

    2007-01-01

    This book series addresses a newly emerging interdisciplinary research field, Ultrafast Intense Laser Science, spanning atomic and molecular physics, molecular science, and optical science. Its progress is being stimulated by the recent development of ultrafast laser technologies. Highlights of this second volume include Coulomb explosion and fragmentation of molecules, control of chemical dynamics, high-order harmonic generation, propagation and filamentation, and laser-plasma interaction. All chapters are authored by foremost experts in their fields and the texts are written at a level accessible to newcomers and graduate students, each chapter beginning with an introductory overview.

  1. Progress in ultrafast intense laser science XI

    CERN Document Server

    Yamanouchi, Kaoru; Martin, Philippe

    2014-01-01

    The PUILS series delivers up-to-date reviews of progress in Ultrafast Intense Laser Science, a newly emerging interdisciplinary research field spanning atomic and molecular physics, molecular science and optical science, which has been stimulated by the recent developments in ultrafast laser technologies. Each volume compiles peer-reviewed articles authored by researchers at the forefront of each their own subfields of UILS. Every chapter opens with an overview of the topics to be discussed, so that researchers unfamiliar to the subfield, as well as graduate students, can grasp the importance

  2. Progress in ultrafast intense laser science

    CERN Document Server

    Yamanouchi, Kaoru; Mathur, Deepak

    2014-01-01

    The PUILS series delivers up-to-date reviews of progress in Ultrafast Intense Laser Science, a newly emerging interdisciplinary research field spanning atomic and molecular physics, molecular science, and optical science, which has been stimulated by the recent developments in ultrafast laser technologies. Each volume compiles peer-reviewed articles authored by researchers at the forefront of each their own subfields of UILS. Every chapter opens with an overview of the topics to be discussed, so that researchers unfamiliar to the subfield, as well as graduate students, can grasp the importance

  3. Marine Biotoxins: Laboratory Culture and Molecular Structure

    Science.gov (United States)

    1991-01-21

    ciguateric carnivorous fishes in concentrations ranging from I to 10 ppb. Its molecular structure has been elucidated. It has been isolated from toxic...American Chemical Society, Washington, DC, 1984, pp 217-329. 6. Med. J. Australia 1986, 145 (11/12), 558; 584-5M). 7. "Toxic Plants and Animals A Guide...isolated and grown in the laboratory. Lethality of crude acetone and methanol extracts were assa~ed by ip injection into mice. In vitro cytotoxicity and

  4. Evidences from electron momentum spectroscopy for ultra-fast charge transfers and structural reorganizations in a floppy molecule: Ethanol

    International Nuclear Information System (INIS)

    Deleuze, Michael S; Hajgato, Balazs; Morini, Filippo

    2009-01-01

    Calculations of electron momentum distributions employing advanced Dyson orbital theories and statistical thermodynamics beyond the RRHO approximation fail to quantitatively reproduce the outermost momentum profile inferred from experiments on ethanol employing high resolution Electron Momentum Spectroscopy [1]. Study of the influence of nuclear dynamics in the initial ground state and final ionized state indicates that this discrepancy between theory and experiment reflects a charge transfer occurring during an ultra-fast dissociation of the ethanol radical cation into a methyl radical and H 2 C=O-H + .

  5. Optimal laser control of ultrafast photodissociation of I2- in water: Mixed quantum/classical molecular dynamics simulation

    International Nuclear Information System (INIS)

    Nishiyama, Yoshikazu; Kato, Tsuyoshi; Ohtsuki, Yukiyoshi; Fujimura, Yuichi

    2004-01-01

    A linearized optimal control method in combination with mixed quantum/classical molecular dynamics simulation is used for numerically investigating the possibility of controlling photodissociation wave packets of I 2 - in water. Optimal pulses are designed using an ensemble of photodissociation samples, aiming at the creation of localized dissociation wave packets. Numerical results clearly show the effectiveness of the control although the control achievement is reduced with an increase in the internuclear distance associated with a target region. We introduce effective optimal pulses that are designed using a statistically averaged effective dissociation potential, and show that they semiquantitatively reproduce the control achievements calculated by using optimal pulses. The control mechanisms are interpreted from the time- and frequency-resolved spectra of the effective optimal pulses

  6. Molecular structure of the lecithin ripple phase

    Science.gov (United States)

    de Vries, Alex H.; Yefimov, Serge; Mark, Alan E.; Marrink, Siewert J.

    2005-04-01

    Molecular dynamics simulations of lecithin lipid bilayers in water as they are cooled from the liquid crystalline phase show the spontaneous formation of rippled bilayers. The ripple consists of two domains of different length and orientation, connected by a kink. The organization of the lipids in one domain of the ripple is found to be that of a splayed gel; in the other domain the lipids are gel-like and fully interdigitated. In the concave part of the kink region between the domains the lipids are disordered. The results are consistent with the experimental information available and provide an atomic-level model that may be tested by further experiments. molecular dynamics simulation | structural model

  7. Tracking the ultrafast motion of a single molecule by femtosecond orbital imaging

    Science.gov (United States)

    Cocker, Tyler L.; Peller, Dominik; Yu, Ping; Repp, Jascha; Huber, Rupert

    2016-11-01

    Watching a single molecule move on its intrinsic timescale has been one of the central goals of modern nanoscience, and calls for measurements that combine ultrafast temporal resolution with atomic spatial resolution. Steady-state experiments access the requisite spatial scales, as illustrated by direct imaging of individual molecular orbitals using scanning tunnelling microscopy or the acquisition of tip-enhanced Raman and luminescence spectra with sub-molecular resolution. But tracking the intrinsic dynamics of a single molecule directly in the time domain faces the challenge that interactions with the molecule must be confined to a femtosecond time window. For individual nanoparticles, such ultrafast temporal confinement has been demonstrated by combining scanning tunnelling microscopy with so-called lightwave electronics, which uses the oscillating carrier wave of tailored light pulses to directly manipulate electronic motion on timescales faster even than a single cycle of light. Here we build on ultrafast terahertz scanning tunnelling microscopy to access a state-selective tunnelling regime, where the peak of a terahertz electric-field waveform transiently opens an otherwise forbidden tunnelling channel through a single molecular state. It thereby removes a single electron from an individual pentacene molecule’s highest occupied molecular orbital within a time window shorter than one oscillation cycle of the terahertz wave. We exploit this effect to record approximately 100-femtosecond snapshot images of the orbital structure with sub-ångström spatial resolution, and to reveal, through pump/probe measurements, coherent molecular vibrations at terahertz frequencies directly in the time domain. We anticipate that the combination of lightwave electronics and the atomic resolution of our approach will open the door to visualizing ultrafast photochemistry and the operation of molecular electronics on the single-orbital scale.

  8. Molecular Models of Genetic and Organismic Structures

    CERN Document Server

    Baianu, I C

    2004-01-01

    In recent studies we showed that the earlier relational theories of organismic sets (Rashevsky,1967), Metabolic-Replication (M,R)-systems (Rosen,1958)and molecular sets (Bartholomay,1968) share a joint foundation that can be studied within a unified categorical framework of functional organismic structures (Baianu,1980. This is possible because all relational theories have a biomolecular basis, that is, complex structures such as genomes, cells,organs and biological organisms are mathematically represented in terms of biomolecular properties and entities,(that are often implicit in their representation axioms. The definition of organismic sets, for example, requires that certain essential quantities be determined from experiment: these are specified by special sets of values of general observables that are derived from physicochemical measurements(Baianu,1970; Baianu,1980; Baianu et al, 2004a.)Such observables are context-dependent and lead directly to natural transformations in categories and Topoi, that are...

  9. Projected quasiparticle theory for molecular electronic structure

    Science.gov (United States)

    Scuseria, Gustavo E.; Jiménez-Hoyos, Carlos A.; Henderson, Thomas M.; Samanta, Kousik; Ellis, Jason K.

    2011-09-01

    We derive and implement symmetry-projected Hartree-Fock-Bogoliubov (HFB) equations and apply them to the molecular electronic structure problem. All symmetries (particle number, spin, spatial, and complex conjugation) are deliberately broken and restored in a self-consistent variation-after-projection approach. We show that the resulting method yields a comprehensive black-box treatment of static correlations with effective one-electron (mean-field) computational cost. The ensuing wave function is of multireference character and permeates the entire Hilbert space of the problem. The energy expression is different from regular HFB theory but remains a functional of an independent quasiparticle density matrix. All reduced density matrices are expressible as an integration of transition density matrices over a gauge grid. We present several proof-of-principle examples demonstrating the compelling power of projected quasiparticle theory for quantum chemistry.

  10. Molecular motion and structure in plastics

    International Nuclear Information System (INIS)

    Doolan, K.R.; Baxter, M.

    2000-01-01

    Full text: When molten thermoplastics solidify, the polymeric chains form a completely amorphous structure or a mixture of crystalline and amorphous regions. Measurement of Nuclear Magnetic Resonance (NMR) relaxation times provides information about the configuration and molecular motion of polymeric chains in solid plastics. We are currently measuring the NMR relaxation times T 1 , T 2 , T 2 and T 1p as a function of temperature using a Bruker High Power pulsed NMR Spectrometer for several different classes of thermoplastics containing varying concentrations of inorganic filler materials. We present data here for T 1 , and T 2 obtained for polyethylenes, polypropylenes, polystyrenes and acrylics in the temperature range 100 K to 450 K. At temperatures below 320 K, all of the polyethylenes and polypropylenes and some of the polystyrenes and acrylics produced NMR signals after a single radio frequency (RF) pulse with rapidly and slowly decaying components corresponding to the rigid and flexible regions within the plastic. From these results we have estimated using Mathematica the amount of crystallinity within the polyethylenes and polypropylenes. For the impact modified polystyrenes and acrylics studied we have estimated the amounts of elastomeric phases present. We find that the initial rapid decay signal produced by polyethylenes and polypropylenes is Gaussian while the long tail is Lorentzian. All of the signal components from the polystyrenes and the acrylics were fitted using Lorentzian functions indicating their structures are highly amorphous. Addition of CaCO 3 filler to polypropylene resins appears to reduce the crystallinity of the material. We also present data for the activation energy of the molecular motion inducing longitudinal relaxation, from T 1 measurements

  11. Molecular structure input on the web

    Directory of Open Access Journals (Sweden)

    Ertl Peter

    2010-02-01

    Full Text Available Abstract A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential. The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

  12. Molecular structure and vibrational spectroscopy of isoproturon

    Science.gov (United States)

    Vrielynck, L.; Dupuy, N.; Kister, J.; Nowogrocki, G.

    2006-05-01

    The crystal structure of isoproturon [ N-(4-isopropylphenyl)- N', N'-dimethylurea] has been determined: the compound crystallizes in the space group Pbca with unit cell parameters a=10.186(2) Å, b=11.030(2) Å, c=20.981(4) Å. The structure was solved and refined down to R1=0.0508 and ωR2=0.12470 for 3056 reflections. The crystalline molecular network of this pesticide is stabilized, as for many molecules of the same family, by π-π interactions but especially by a medium-strong N-H⋯C dbnd6 O intermolecular hydrogen bond (2.14 Å). The X-ray parameters were then compared with the results of DFT quantum chemical calculation computed with the GAUSSIAN 94 package. A tentative assignment of the ATR-FT-IR and Raman spectra was proposed supported by vibrational mode calculation and spectroscopic data on benzenic and urea derivatives available in the literature. The presence of a tight band around 3300 cm -1, which can be assigned to the NH bond stretching mode as well as the low frequency position of the amide I band at 1640 cm -1, sensitive to solvent polarity, confirms the existence of a quite strong intermolecular hydrogen bond between neighboring molecules in the crystal of isoproturon.

  13. Ultrafast electron microscopy integrated with a direct electron detection camera

    Directory of Open Access Journals (Sweden)

    Young Min Lee

    2017-07-01

    Full Text Available In the past decade, we have witnessed the rapid growth of the field of ultrafast electron microscopy (UEM, which provides intuitive means to watch atomic and molecular motions of matter. Yet, because of the limited current of the pulsed electron beam resulting from space-charge effects, observations have been mainly made to periodic motions of the crystalline structure of hundreds of nanometers or higher by stroboscopic imaging at high repetition rates. Here, we develop an advanced UEM with robust capabilities for circumventing the present limitations by integrating a direct electron detection camera for the first time which allows for imaging at low repetition rates. This approach is expected to promote UEM to a more powerful platform to visualize molecular and collective motions and dissect fundamental physical, chemical, and materials phenomena in space and time.

  14. Ultrafast electron microscopy integrated with a direct electron detection camera.

    Science.gov (United States)

    Lee, Young Min; Kim, Young Jae; Kim, Ye-Jin; Kwon, Oh-Hoon

    2017-07-01

    In the past decade, we have witnessed the rapid growth of the field of ultrafast electron microscopy (UEM), which provides intuitive means to watch atomic and molecular motions of matter. Yet, because of the limited current of the pulsed electron beam resulting from space-charge effects, observations have been mainly made to periodic motions of the crystalline structure of hundreds of nanometers or higher by stroboscopic imaging at high repetition rates. Here, we develop an advanced UEM with robust capabilities for circumventing the present limitations by integrating a direct electron detection camera for the first time which allows for imaging at low repetition rates. This approach is expected to promote UEM to a more powerful platform to visualize molecular and collective motions and dissect fundamental physical, chemical, and materials phenomena in space and time.

  15. Molecular structures and intramolecular dynamics of pentahalides

    Science.gov (United States)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  16. Ultrafast spectroscopy of model biological membranes

    NARCIS (Netherlands)

    Ghosh, Avishek

    2009-01-01

    In this PhD thesis, I have described the novel time-resolved sum-frequency generation (TR-SFG) spectroscopic technique that I developed during the course of my PhD research and used it study the ultrafast vibrational, structural and orientational dynamics of water molecules at model biological

  17. Novel Aspects of Materials Processing by Ultrafast Lasers: From Electronic to Biological and Cultural Heritage Applications

    International Nuclear Information System (INIS)

    Fotakis, C; Zorba, V; Stratakis, E; Athanassiou, A; Tzanetakis, P; Zergioti, I; Papagoglou, D G; Sambani, K; Filippidis, G; Farsari, M; Pouli, V; Bounos, G; Georgiou, S

    2007-01-01

    Materials processing by ultrafast lasers offers several distinct possibilities for micro/nano scale applications. This is due to the unique characteristics of the laser-matter interactions involved, when sub-picosecond pulses are employed. Prospects arising will be discussed in the context of surface and in bulk laser induced modifications. In particular, examples of diverse applications including the development and functionalization of laser engineered surfaces, the laser transfer of biomolecules and the functionalization of 3D structures constructed by three-photon stereolithography will be presented. Furthermore, the removal of molecular substrates by ultrafast laser ablation will be discussed with emphasis placed on assessing the photochemical changes induced in the remaining bulk material. The results indicate that in femtosecond laser processing of organic materials, besides the well acknowledged morphological advantages, a second fundamental factor responsible for its success pertains to the selective chemical effects. This is crucial for the laser cleaning of sensitive painted artworks

  18. Molecular structure and motion in zero field magnetic resonance

    International Nuclear Information System (INIS)

    Jarvie, T.P.

    1989-10-01

    Zero field magnetic resonance is well suited for the determination of molecular structure and the study of motion in disordered materials. Experiments performed in zero applied magnetic field avoid the anisotropic broadening in high field nuclear magnetic resonance (NMR) experiments. As a result, molecular structure and subtle effects of motion are more readily observed

  19. Progress in ultrafast intense laser science XIII

    CERN Document Server

    III, Wendell; Paulus, Gerhard

    2017-01-01

    This thirteenth volume covers a broad range of topics from this interdisciplinary research field, focusing on atoms, molecules, and clusters interacting in intense laser field and high-order harmonics generation and their applications. The PUILS series delivers up-to-date reviews of progress in Ultrafast Intense Laser Science, the interdisciplinary research field spanning atomic and molecular physics, molecular science, and optical science, which has been stimulated by the recent developments in ultrafast laser technologies. Each volume compiles peer-reviewed articles authored by researchers at the forefront of each their own subfields of UILS. Every chapter opens with an overview of the topics to be discussed, so that researchers unfamiliar to the subfield, as well as graduate students, can grasp the importance and attractions of the research topic at hand; these are followed by reports of cutting-edge discoveries.   .

  20. Progress in Ultrafast Intense Laser Science

    CERN Document Server

    Yamanouchi, Kaoru; Li, Ruxin; Chin, See Leang

    2009-01-01

    The PUILS series presents Progress in Ultrafast Intense Laser Science, a newly emerging interdisciplinary research field spanning atomic and molecular physics, molecular science, and optical science. PUILS has been stimulated by the recent development of ultrafast laser technologies. Each volume contains approximately 15 chapters, authored by researchers at the forefront. Each chapter opens with an overview of the topics to be discussed, so that researchers, who are not experts in the specific topics, as well as graduate students can grasp the importance and attractions of this sub-field of research, and these are followed by reports of cutting-edge discoveries. This fourth volume covers a broad range of topics from this interdisciplinary research field, focusing on strong field ionization of atoms; excitation, ionization and fragmentation of molecules; nonlinear intense optical phenomena and attosecond pulses; and laser - solid interactions and photoemission.

  1. Progress in Ultrafast Intense Laser Science III

    CERN Document Server

    Yamanouchi, Kaoru; Agostini, Pierre; Ferrante, Gaetano

    2008-01-01

    The PUILS series presents Progress in Ultrafast Intense Laser Science, a newly emerging interdisciplinary research field spanning atomic and molecular physics, molecular science, and optical science. PUILS has been stimulated by the recent development of ultrafast laser technologies. Each volume contains approximately 15 chapters, authored by researchers at the forefront. Each chapter opens with an overview of the topics to be discussed, so that researchers, who are not experts in the specific topics, as well as graduate students can grasp the importance and attractions of this sub-field of research, and these are followed by reports of cutting-edge discoveries. This third volume covers a diverse range of disciplines, focusing on such topics as strong field ionization of atoms, ionization and fragmentation of molecules and clusters, generation of high-order harmonics and attosecond pulses, filamentation and laser plasma interaction, and the development of ultrashort and ultrahigh-intensity light sources.

  2. Progress in Ultrafast Intense Laser Science VIII

    CERN Document Server

    Nisoli, Mauro; Hill, Wendell; III, III

    2012-01-01

    The PUILS series delivers up-to-date reviews of progress in Ultrafast Intense Laser Science, a newly emerging interdisciplinary research field spanning atomic and molecular physics, molecular science and optical science which has been stimulated by the recent developments in ultrafast laser technologies. Each volume compiles peer-reviewed articles authored by researchers at the forefront of each their own subfields of UILS. Every chapter opens with an overview of the topics to be discussed, so that researchers unfamiliar to the subfield as well as graduate students can grasp the importance and attractions of the research topic at hand. These are followed by reports of cutting-edge discoveries. This eighth volume covers a broad range of topics from this interdisciplinary research field, focusing on molecules interacting with ultrashort and intense laser fields, advanced technologies for the characterization of ultrashort laser pulses and their applications, laser plasma formation and laser acceleration.

  3. Progress in Ultrafast Intense Laser Science VI

    CERN Document Server

    Yamanouchi, Kaoru; Bandrauk, André D

    2010-01-01

    The PUILS series delivers up-to-date reviews of progress in Ultrafast Intense Laser Science, a newly emerging interdisciplinary research field spanning atomic and molecular physics, molecular science, and optical science, which has been stimulated by the recent developments in ultrafast laser technologies. Each volume compiles peer-reviewed articles authored by researchers at the forefront of each their own subfields of UILS. Every chapter opens with an overview of the topics to be discussed, so that researchers unfamiliar to the subfield, as well as graduate students, can grasp the importance and attractions of the research topic at hand; these are followed by reports of cutting-edge discoveries. This sixth volume covers a broad range of topics from this interdisciplinary research field, focusing on responses of molecules to ultrashort intense laser pulses, generation and characterization of attosecond pulses and high-order harmonics, and filamentation and laser-plasma interaction.

  4. Progress in ultrafast intense laser science XII

    CERN Document Server

    Roso, Luis; Li, Ruxin; Mathur, Deepak; Normand, Didier

    2015-01-01

    This  volume covers a broad range of topics focusing on atoms, molecules, and clusters interacting in intense laser field, laser induced filamentation, and laser plasma interaction and application. The PUILS series delivers up-to-date reviews of progress in Ultrafast Intense Laser Science, a newly emerging interdisciplinary research field spanning atomic and molecular physics, molecular science, and optical science, which has been stimulated by the recent developments in ultrafast laser technologies. Each volume compiles peer-reviewed articles authored by researchers at the forefront of each their own subfields of UILS. Every chapter opens with an overview of the topics to be discussed, so that researchers unfamiliar to the subfield, as well as graduate students, can grasp the importance and attractions of the research topic at hand; these are followed by reports of cutting-edge discoveries. .

  5. Ultrafast nonlinear optics

    CERN Document Server

    Leburn, Christopher; Reid, Derryck

    2013-01-01

    The field of ultrafast nonlinear optics is broad and multidisciplinary, and encompasses areas concerned with both the generation and measurement of ultrashort pulses of light, as well as those concerned with the applications of such pulses. Ultrashort pulses are extreme events – both in terms of their durations, and also the high peak powers which their short durations can facilitate. These extreme properties make them powerful experiment tools. On one hand, their ultrashort durations facilitate the probing and manipulation of matter on incredibly short timescales. On the other, their ultrashort durations can facilitate high peak powers which can drive highly nonlinear light-matter interaction processes. Ultrafast Nonlinear Optics covers a complete range of topics, both applied and fundamental in nature, within the area of ultrafast nonlinear optics. Chapters 1 to 4 are concerned with the generation and measurement of ultrashort pulses. Chapters 5 to 7 are concerned with fundamental applications of ultrasho...

  6. Molecular clouds and galactic spiral structure

    International Nuclear Information System (INIS)

    Dame, T.M.

    1984-02-01

    Galactic CO line emission at 115 GHz was surveyed in order to study the distribution of molecular clouds in the inner galaxy. Comparison of this survey with similar H1 data reveals a detailed correlation with the most intense 21 cm features. To each of the classical 21 cm H1 spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is devised for the galactic distribution of molecular clouds. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide

  7. Molecular catalysts structure and functional design

    CERN Document Server

    Gade, Lutz H

    2014-01-01

    Highlighting the key aspects and latest advances in the rapidly developing field of molecular catalysis, this book covers new strategies to investigate reaction mechanisms, the enhancement of the catalysts' selectivity and efficiency, as well as the rational design of well-defined molecular catalysts. The interdisciplinary author team with an excellent reputation within the community discusses experimental and theoretical studies, along with examples of improved catalysts, and their application in organic synthesis, biocatalysis, and supported organometallic catalysis. As a result, readers wil

  8. MOLECULAR STRUCTURE AND VIBRATIONAL FREQUENCIES OF

    Directory of Open Access Journals (Sweden)

    Fatih UCUN

    2009-02-01

    Full Text Available Abstract: The molecular structure, vibrational frequencies and the corresponding assignments of N-aminophthalimide (NAPH in the ground state have been calculated using the Hartree-Fock (HF and density functional methods (B3LYP with 6-31G (d, p basis set. The calculations were utilized in the CS symmetry of NAPH. The obtained vibrational frequencies and optimized geometric parameters (bond lengths and bond angles were seen to be in good agreement with the experimental data. The comparison of the observed and calculated results showed that B3LYP is superior to the scaled HF method. Theoretical infrared intensities and Raman activities were also reported. Key words: N-aminophthalimide; vibrations; IR spectra; Raman spectra; HF; DFT N-AMİNOFİTALOMİD'İN MOLEKÜLER YAPISI VE TİTREŞİM FREKANSLARI Özet: Temel haldeki N-aminofitalamidin (NAPH moleküler yapısı, titreşim frekansları ve uygun mod tanımlamaları, 6-31 G (d, p temel setli Hartree-Fock (HF ve yoğunluk fonksiyonu metodları (B3LYP kullanılarak hesaplandı. Hesaplamalar, NAPH'ın CS simetrisine uyarlandı. Elde edilen titreşim frekansları ve optimize geometrik parametreleri (bağ uzunlukları ve bağ açıları, deneysel değerlerle iyi bir uyum içinde olduğu görüldü. Deneysel ve teorik sonuçların karşılaştırılması, B3LYP'nin HF metodundan daha üstün olduğunu gösterdi. Ayrıca teorik infrared şiddetleri ve Raman aktiviteleri verildi. Anahtar Kelimeler: N-aminofitalamidin; titreşimler; IR spektrumu; Raman Spektrumu; HF; DFT

  9. Molecular structure of the lecithin ripple phase

    NARCIS (Netherlands)

    de Vries, AH; Yefimov, S; Mark, AE; Marrink, SJ

    2005-01-01

    Molecular dynamics simulations of lecithin lipid bilayers in water as they are cooled from the liquid crystalline phase show the spontaneous formation of rippled bilayers. The ripple consists of two domains of different length and orientation, connected by a kink. The organization of the lipids in

  10. Ultrafast gas switching experiments

    International Nuclear Information System (INIS)

    Frost, C.A.; Martin, T.H.; Patterson, P.E.; Rinehart, L.F.; Rohwein, G.J.; Roose, L.D.; Aurand, J.F.; Buttram, M.T.

    1993-01-01

    We describe recent experiments which studied the physics of ultrafast gas breakdown under the extreme overvoltages which occur when a high pressure gas switch is pulse charged to hundreds of kV in 1 ns or less. The highly overvolted peaking gaps produce powerful electromagnetic pulses with risetimes Khz at > 100 kV/m E field

  11. Nuclear molecular structure in heavy mass systems

    International Nuclear Information System (INIS)

    Arctaedius, T.; Bargholtz, C.

    1989-04-01

    A study is made of nuclear molecular configurations involving one heavy mass partner. The stability of these configurations to mass flow and to fission is investigated as well as their population in fusion reactions. It is concluded that shell effects in combination with the effects of angular momentum may be important in stabilizing certain configurations. A possible relation of these configurations to the so called superdeformed states is pointed out. The spectrum of rotational and vibrational trasitions within molecular configurations is investigated. For sufficiently mass-asymmetric systems the engergies of vibrational transitions are comparable to the neutron separation energy. Gamma radiation from such transitions may then be observable above the background of statistical transitions. The gamma spectrum and the directional distribution of the radioation following fusion reactions with 12 C and 16 O are calculated. (authors)

  12. The hierarchical structure of molecular clouds

    International Nuclear Information System (INIS)

    Chieze, J.P.

    1987-01-01

    The mass-radius-velocity dispersion relations observed among the members of cool molecular complexes is interpreted in terms of fragmentation at the gravitational instability threshold in a roughly constant pressure environment. The mass range of the self-similar fragmentation hierarchy is governed by the thermal instability thresholds. Using a realistic equation of state, the gravitational stability of thermally stable clumps is analysed as a function of both the local gas pressure and extinction of the mean interstellar radiation field

  13. Quantum modeling of ultrafast photoinduced charge separation

    Science.gov (United States)

    Rozzi, Carlo Andrea; Troiani, Filippo; Tavernelli, Ivano

    2018-01-01

    Phenomena involving electron transfer are ubiquitous in nature, photosynthesis and enzymes or protein activity being prominent examples. Their deep understanding thus represents a mandatory scientific goal. Moreover, controlling the separation of photogenerated charges is a crucial prerequisite in many applicative contexts, including quantum electronics, photo-electrochemical water splitting, photocatalytic dye degradation, and energy conversion. In particular, photoinduced charge separation is the pivotal step driving the storage of sun light into electrical or chemical energy. If properly mastered, these processes may also allow us to achieve a better command of information storage at the nanoscale, as required for the development of molecular electronics, optical switching, or quantum technologies, amongst others. In this Topical Review we survey recent progress in the understanding of ultrafast charge separation from photoexcited states. We report the state-of-the-art of the observation and theoretical description of charge separation phenomena in the ultrafast regime mainly focusing on molecular- and nano-sized solar energy conversion systems. In particular, we examine different proposed mechanisms driving ultrafast charge dynamics, with particular regard to the role of quantum coherence and electron-nuclear coupling, and link experimental observations to theoretical approaches based either on model Hamiltonians or on first principles simulations.

  14. Ultrafast stimulated Raman spectroscopy in the near-infrared region

    International Nuclear Information System (INIS)

    Takaya, Tomohisa

    2016-01-01

    A number of electronic transitions in the near-infrared wavelength region are associated with migration or delocalization of electrons in large molecules or molecular systems. Time-resolved near-infrared Raman spectroscopy will be a powerful tool for investigating the structural dynamic of samples with delocalized electrons. However, the sensitivity of near-infrared spontaneous Raman spectrometers is significantly low due to an extremely small probability of Raman scattering and a low sensitivity of near-infrared detectors. Nonlinear Raman spectroscopy is one of the techniques that can overcome the sensitivity problems and enable us to obtain time-resolved Raman spectra in resonance with near-IR transitions. In this article, the author introduces recent progress of ultrafast time-resolved near-infrared stimulated Raman spectroscopy. Optical setup, spectral and temporal resolution, and applications of the spectrometer are described. (author)

  15. Molecular structure and DFT investigations on new cobalt(II ...

    Indian Academy of Sciences (India)

    tion process was demonstrated.9 Late-transition metals, especially Ni, Pd ..... in table S2 (Supplementary Information). Most of the ... to molecular system because of atomic charges affect ... structure, acidity–basicity behavior and other proper-.

  16. The Role of Molecular Structure and Conformation in Polymer Electronics

    NARCIS (Netherlands)

    von Hauff, Elizabeth

    2011-01-01

    ABSTRACT Conjugated polymers have unique material properties that make them promising for a wide range of applications. The potential lies in the virtually infinite possibilities for creating new materials for specific applications by simply chemically tuning the molecular structure. Conjugated

  17. Crystal structure and pair potentials: A molecular-dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Parrinello, M.; Rahman, A.

    1980-10-06

    With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

  18. Molecular clouds and galactic spiral structure

    International Nuclear Information System (INIS)

    Dame, T.M.

    1983-01-01

    Galactic CO line emission at 115 GHz has been surveyed in the region 12 0 less than or equal to l less than or equal to 60 0 and -1 0 less than or equal to b less than or equal to 1 0 in order to study the distribution of molecular clouds in the inner galaxy; an inner strip 0 0 .5 wide has been sampled every beamwidth (0 0 .125), the rest every two beamwidths. Comparison of the survey with similar HI data reveals a detailed correlation with the most intense 21-cm features, implying that the CO and HI trace the same galactic features and have the same large-scale kinematics. To each of the classical 21-cm (HI) spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is developed in which all of the CO emission from the inner galaxy arises from spiral arms. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide. A variety of methods are employed to estimate distances and masses for the largest clouds detected by the inner-galaxy survey and a catalogue is compiled. The catalogued clouds, the largest of which have masses of several 10 6 M/sub sunmass/ and linear dimensions in excess of 100 pc, are found to be excellent spiral-arm tracers. One of the nearest of the clouds, that associated with the supernova remnant W44, is fully mapped in both CO and 13 CO and is discussed in detail

  19. Instructional Approach to Molecular Electronic Structure Theory

    Science.gov (United States)

    Dykstra, Clifford E.; Schaefer, Henry F.

    1977-01-01

    Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

  20. Systematic analysis of crystal and molecular structures

    Czech Academy of Sciences Publication Activity Database

    Hašek, Jindřich; Dohnálek, Jan

    2012-01-01

    Roč. 19, č. 2 (2012), s. 86-87 ISSN 1211-5894. [Struktura 2012. Kolokvium Krystalografické společnosti. 11.06.2012-14.06.2012, Klatovy] R&D Projects: GA ČR GA310/09/1407 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : structure databases * structure-function relations * organic and inorganic materials Subject RIV: EE - Microbiology, Virology

  1. Ultrafast magnetization dynamics

    OpenAIRE

    Woodford, Simon

    2008-01-01

    This thesis addresses ultrafast magnetization dynamics from a theoretical perspective. The manipulation of magnetization using the inverse Faraday effect has been studied, as well as magnetic relaxation processes in quantum dots. The inverse Faraday effect – the generation of a magnetic field by nonresonant, circularly polarized light – offers the possibility to control and reverse magnetization on a timescale of a few hundred femtoseconds. This is important both for the technological advant...

  2. Molecular and structural aspects of oocyte maturation

    NARCIS (Netherlands)

    Hölzenspies, J.J.

    2009-01-01

    In the mammalian ovary, oocytes are contained within follicles, specialized structures that facilitate oocyte growth and development. During the reproductive cycle, several follicles are recruited into growth, and through a process of selection, one (human, cow) or several (mouse, pig) of these

  3. Synthesis, molecular structure, spectroscopic investigations and ...

    Indian Academy of Sciences (India)

    MS received 29 December 2015; revised 9 April 2016; accepted 25 May 2016 ... B, open form blue. Scheme 1. Structures and Photochromic reaction of the title compound. 2. Experimental. 2.1 Materials and measurements. The mid-IR spectra were obtained in the ... segment is put between two parallel Au(111) surfaces,.

  4. Synthesis, Crystal Structure, Density Function Theory, Molecular ...

    African Journals Online (AJOL)

    Tropical Journal of Pharmaceutical Research ... Purpose: To determine the exact structure and antimicrobial activity of 2-(3-(4 phenylpiperazin-1-yl) ... Besides HOMO– LUMO energy gap was performed at B3LYP/6-31G (d,p) level of theory.

  5. Molecular dynamics of the structure and thermodynamics of dusty ...

    African Journals Online (AJOL)

    The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...

  6. Molecular dynamic analysis of the structure of dendrimers

    Energy Technology Data Exchange (ETDEWEB)

    Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.

  7. Molecular dynamic analysis of the structure of dendrimers

    International Nuclear Information System (INIS)

    Canetta, E.; Maino, G.

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques

  8. Resolving molecular vibronic structure using high-sensitivity two-dimensional electronic spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Bizimana, Laurie A.; Brazard, Johanna; Carbery, William P.; Gellen, Tobias; Turner, Daniel B., E-mail: dturner@nyu.edu [Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003 (United States)

    2015-10-28

    Coherent multidimensional optical spectroscopy is an emerging technique for resolving structure and ultrafast dynamics of molecules, proteins, semiconductors, and other materials. A current challenge is the quality of kinetics that are examined as a function of waiting time. Inspired by noise-suppression methods of transient absorption, here we incorporate shot-by-shot acquisitions and balanced detection into coherent multidimensional optical spectroscopy. We demonstrate that implementing noise-suppression methods in two-dimensional electronic spectroscopy not only improves the quality of features in individual spectra but also increases the sensitivity to ultrafast time-dependent changes in the spectral features. Measurements on cresyl violet perchlorate are consistent with the vibronic pattern predicted by theoretical models of a highly displaced harmonic oscillator. The noise-suppression methods should benefit research into coherent electronic dynamics, and they can be adapted to multidimensional spectroscopies across the infrared and ultraviolet frequency ranges.

  9. Evidence for an ultrafast breakdown of the BeO band structure due to swift argon and xenon ions.

    Science.gov (United States)

    Schiwietz, G; Czerski, K; Roth, M; Grande, P L; Koteski, V; Staufenbiel, F

    2010-10-29

    Auger-electron spectra associated with Be atoms in the pure metal lattice and in the stoichiometric oxide have been investigated for different incident charged particles. For fast incident electrons, for Ar7+ and Ar15+ ions as well as Xe15+ and Xe31+ ions at velocities of 6% to 10% the speed of light, there are strong differences in the corresponding spectral distributions of Be-K Auger lines. These differences are related to changes in the local electronic band structure of BeO on a femtosecond time scale after the passage of highly charged heavy ions.

  10. Molecular Eigensolution Symmetry Analysis and Fine Structure

    Directory of Open Access Journals (Sweden)

    William G. Harter

    2013-01-01

    Full Text Available Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES. Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES used in Born-Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v, then applied to families of Oh clusters in SF6 spectra and to extreme clusters.

  11. Ultrafast photo-initiated molecular quantum dynamics in the DNA dinucleotide d(ApG) revealed by broadband transient absorption spectroscopy.

    Science.gov (United States)

    Stuhldreier, Mayra C; Temps, Friedrich

    2013-01-01

    The ultrafast photo-initiated quantum dynamics of the adenine-guanine dinucleotide d(ApG) in aqueous solution (pH 7) has been studied by femtosecond time-resolved spectroscopy after excitation at lambda = 260 nm. The results reveal a hierarchy of processes on time scales from tau 100 ps. Characteristic spectro-temporal signatures are observed indicating the transformation of the molecules in the electronic relaxation from the photo-excited state to a long-lived exciplex. In particular, broadband UV/VIS excited-state absorption (ESA) measurements detected a distinctive absorption by the excited dinucleotide around lambda = 335 nm, approximately 0.5 eV to the blue compared to the maximum of the broad and unstructured ESA spectrum after excitation of an equimolar mixture of the mononucleotides dAMP and dGMP. A similar feature has been identified as signature of the excimer in the dynamics of the adenine dinucleotide d(ApA). The lifetime of the d(ApG) exciplex was found to be tau = 124 +/- 4 ps both from the ESA decay time and from the ground-state recovery time, far longer than the sub-picosecond lifetimes of excited dAMP or dGMP. Fluorescence-time profiles measured by the up-conversion technique indicate that the exciplex state is reached around approximately 6 ps after excitation. Very weak residual fluorescence at longer times red-shifted to the emission from the photo-excited state shows that the exciplex is almost optically dark, but still has enough oscillator strength to give rise to the dual fluorescence of the dinucleotide in the static fluorescence spectrum.

  12. Structures of Life: The Role of Molecular Structures in Scientists' Work

    NARCIS (Netherlands)

    Vyas, Dhaval; Kulyk, Olga Anatoliyivna; van der Vet, P.E.; Nijholt, Antinus; van der Veer, Gerrit C.; Jorge, J

    2008-01-01

    The visual and multidimensional representations like images and graphical structures related to biology provide great insights into understanding the complexities of different organisms. Especially, life scientists use different representations of molecular structures to answer biological questions

  13. Ionization probes of molecular structure and chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, P.M. [State Univ. of New York, Stony Brook (United States)

    1993-12-01

    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  14. Chemistry, photophysics, and ultrafast kinetics of two structurally related Schiff bases containing the naphthalene or quinoline ring

    Science.gov (United States)

    Fita, P.; Luzina, E.; Dziembowska, T.; Radzewicz, Cz.; Grabowska, A.

    2006-11-01

    The two structurally related Schiff bases, 2-hydroxynaphthylidene-(8-aminoquinoline) (HNAQ) and 2-hydroxynaphthylidene-1'-naphthylamine (HNAN), were studied by means of steady-state and time resolved optical spectroscopies as well as time-dependent density functional theory (TDDFT) calculations. The first one, HNAQ, is stable as a keto tautomer in the ground state and in the excited state in solutions, therefore it was used as a model of a keto tautomer of HNAN which exists mainly in its enol form in the ground state at room temperature. Excited state intramolecular proton transfer in the HNAN molecule leads to a very weak (quantum yield of the order of 10-4) strongly Stokes-shifted fluorescence. The characteristic time of the proton transfer (about 30fs) was estimated from femtosecond transient absorption data supported by global analysis and deconvolution techniques. Approximately 35% of excited molecules create a photochromic form whose lifetime was beyond the time window of the experiment (2ns). The remaining ones reach the relaxed S1 state (of a lifetime of approximately 4ps), whose emission is present in the decay associated difference spectra. Some evidence for the back proton transfer from the ground state of the keto form with the characteristic time of approximately 13ps was also found. The energies and orbital characteristics of main electronic transitions in both molecules calculated by TDDFT method are also discussed.

  15. Tuning the morphology and structure of nanocarbons with activating agents for ultrafast ionic liquid-based supercapacitors

    Science.gov (United States)

    Cui, Yongpeng; Wang, Huanlei; Mao, Nan; Yu, Wenhua; Shi, Jing; Huang, Minghua; Liu, Wei; Chen, Shougang; Wang, Xin

    2017-09-01

    The increasing demand for supercapacitors with high energy and power density has attracted extensive attention in designing advanced carbon materials with high accessible surface area, hierarchical porosity, and 2D/3D morphology. Here, we report a new approach to tune the morphology and structure of the nanocarbons by using methyl cellulose as the precursor. Due to the varying effect of different activating agents, the interconnected sheet-like carbon with a high surface area of up to 2285 m2 g-1 and a thickness down to ∼4 nm can be obtained. These important characteristics make the nanocarbons demonstrate a high capacitance of 144 F g-1 at 1 A g-1 and 20 °C, and an excellent capacitance retention ratio of 64% at 100 A g-1 in ionic liquid. Because of the high fraction of meso/macropores for nanocarbons, an outstanding capacitance of 116 F g-1 can be achieved at 0 °C, with a high capacitance retention ratio of 39% at 100 A g-1. A high energy of 16-17 and 9-10 W h kg-1 can be maintained at 20 and 0 °C when the supercapacitor is charged in less than 1s. The excellent electrochemical response of nanocarbons suggests that the proposed preparation process is promising for developing advanced carbon electrodes.

  16. Crystal and molecular structure of 2-thiouridine

    Energy Technology Data Exchange (ETDEWEB)

    Hawkinson, S W

    1977-01-01

    The ''minor'' nucleoside 2-thiouridine, C/sub 9/H/sub 12/O/sub 5/N/sub 2/S, crystallizes in a monoclinic cell, space group P2/sub 1/ with a = 5.049 (2), b = 7.526 (2), c = 14.050 (3) A, ..beta.. = 90.17 (2)/sup 0/, and d = 1.619 g cm/sup -3/ (for Z = 2) at 22 +- 2/sup 0/C. The structure was derived from 1334 unique intensities measured with an Oak Ridge computer-controlled diffractometer to a limit of sin theta/lambda = 0.65 A/sup -1/ with Nb-filtered Mo K..cap alpha.. radiation. Atomic parameters were obtained by a combination of Patterson and Fourier techniques and refined by full-matrix least squares to a final R(F) value of 0.023 for all data. The bond lengths and angles in the molecule agree well with those of other thiopyrimidines (C(2) - S = 1.677 A). The conformation of the sugar ring relative to the base is anti with a torsion angle chi(O(1')--C(1') ..-->.. N(1)--C(6)) of 17/sup 0/. The sugar exists in the 3'-endo conformation. The O(5')--C(5') bond is gauche to C(4) - O(1') and trans to C(4')--C(3') (torsion angles of 74 and -169/sup 0/ respectively). The molecules are linked together in the crystal by hydrogen bonds in an intricate network which is identical to that inferred by Kojic-Prodic, Liminga, Sljukic and Ruzic-Toros (Acta Cryst. (1974), B30, 1550-1555) for the crystal structure of 5,6-dihydro-2-thiouridine. 2 figures; 6 tables.

  17. Suppressing Energy Loss due to Triplet Exciton Formation in Organic Solar Cells: The Role of Chemical Structures and Molecular Packing

    KAUST Repository

    Chen, Xiankai; Wang, Tonghui; Bredas, Jean-Luc

    2017-01-01

    In the most efficient solar cells based on blends of a conjugated polymer (electron donor) and a fullerene derivative (electron acceptor),ultrafast formation of charge-transfer (CT) electronic states at the donor-acceptor interfaces and efficient separation of these CT states into free charges, lead to internal quantum efficiencies near 100%. However, there occur substantial energy losses due to the non-radiative recombinations of the charges, mediated by the loweset-energy (singlet and triplet) CT states; for example, such recombinations can lead to the formation of triplet excited electronic states on the polymer chains, which do not generate free charges. This issue remains a major factor limiting the power conversion efficiencies (PCE) of these devices. The recombination rates are, however, difficult to quantify experimentally. To shed light on these issues, here, an integrated multi-scale theoretical approach that combines molecular dynamics simulations with quantum chemistry calculations is employed in order to establish the relationships among chemical structures, molecular packing, and non-radiative recombination losses mediated by the lowest-energy charge-transfer states.

  18. Suppressing Energy Loss due to Triplet Exciton Formation in Organic Solar Cells: The Role of Chemical Structures and Molecular Packing

    KAUST Repository

    Chen, Xiankai

    2017-04-21

    In the most efficient solar cells based on blends of a conjugated polymer (electron donor) and a fullerene derivative (electron acceptor),ultrafast formation of charge-transfer (CT) electronic states at the donor-acceptor interfaces and efficient separation of these CT states into free charges, lead to internal quantum efficiencies near 100%. However, there occur substantial energy losses due to the non-radiative recombinations of the charges, mediated by the loweset-energy (singlet and triplet) CT states; for example, such recombinations can lead to the formation of triplet excited electronic states on the polymer chains, which do not generate free charges. This issue remains a major factor limiting the power conversion efficiencies (PCE) of these devices. The recombination rates are, however, difficult to quantify experimentally. To shed light on these issues, here, an integrated multi-scale theoretical approach that combines molecular dynamics simulations with quantum chemistry calculations is employed in order to establish the relationships among chemical structures, molecular packing, and non-radiative recombination losses mediated by the lowest-energy charge-transfer states.

  19. RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

    Science.gov (United States)

    Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

    2011-09-01

    Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

  20. Electronic structure of molecular Rydberg states of some small molecules and molecular ion

    International Nuclear Information System (INIS)

    Sun Biao; Li Jiaming

    1993-01-01

    Based on an independent-particle-approximation (i.e. the multiple scattering self-consistent-field theory), the electronic structures of Rydberg states of the small diatomic molecules H 2 , He 2 and the He 2 + molecular ion were studied. The principal quantum number of the first state of the Rydberg series is determined from a convention of the limit of the molecular electronic configuration. The dynamics of the excited molecules and molecular ion has been elucidated. The theoretical results are in fair agreement with the existing experimental measurements, thus they can serve as a reliable basis for future refined treatment such as the configuration interaction calculation

  1. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

    Directory of Open Access Journals (Sweden)

    Rong Shen

    2015-10-01

    Full Text Available The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels, each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good

  2. Molecular structure of dextran sulphate sodium in aqueous environment

    Science.gov (United States)

    Yu, Miao; Every, Hayley A.; Jiskoot, Wim; Witkamp, Geert-Jan; Buijs, Wim

    2018-03-01

    Here we propose a 3D-molecular structural model for dextran sulphate sodium (DSS) in a neutral aqueous environment based on the results of a molecular modelling study. The DSS structure is dominated by the stereochemistry of the 1,6-linked α-glucose units and the presence of two sulphate groups on each α-glucose unit. The structure of DSS can be best described as a helix with various patterns of di-sulphate substitution on the glucose rings. The presence of a side chain does not alter the 3D-structure of the linear main chain much, but affects the overall spatial dimension of the polymer. The simulated polymers have a diameter similar to or in some cases even larger than model α-hemolysin nano-pores for macromolecule transport in many biological processes, indicating a size-limited translocation through such pores. All results of the molecular modelling study are in line with previously reported experimental data. This study establishes the three-dimensional structure of DSS and summarizes the spatial dimension of the polymer, serving as the basis for a better understanding on the molecular level of DSS-involved electrostatic interaction processes with biological components like proteins and cell pores.

  3. Nanohashtag structures based on carbon nanotubes and molecular linkers

    Science.gov (United States)

    Frye, Connor W.; Rybolt, Thomas R.

    2018-03-01

    Molecular mechanics was used to study the noncovalent interactions between single-walled carbon nanotubes and molecular linkers. Groups of nanotubes have the tendency to form tight, parallel bundles (||||). Molecular linkers were introduced into our models to stabilize nanostructures with carbon nanotubes held in perpendicular orientations. Molecular mechanics makes it possible to estimate the strength of noncovalent interactions holding these structures together and to calculate the overall binding energy of the structures. A set of linkers were designed and built around a 1,3,5,7-cyclooctatetraene tether with two corannulene containing pincers that extend in opposite directions from the central cyclooctatetraene portion. Each pincer consists of a pairs of "arms." These molecular linkers were modified so that the "hand" portions of each pair of "arms" could close together to grab and hold two carbon nanotubes in a perpendicular arrangement. To illustrate the possibility of more complicated and open perpendicular CNTs structures, our primary goal was to create a model of a nanohashtag (#) CNT conformation that is more stable than any parallel CNT arrangements with bound linker molecules forming clumps of CNTs and linkers in non-hashtag arrangements. This goal was achieved using a molecular linker (C280H96) that utilizes van der Waals interactions to two perpendicular oriented CNTs. Hydrogen bonding was then added between linker molecules to augment the stability of the hashtag structure. In the hashtag structure with hydrogen bonding, four (5,5) CNTs of length 4.46 nm (18 rings) and four linkers (C276H92N8O8) stabilized the hashtag so that the average binding energy per pincer was 118 kcal/mol.

  4. Learning Molecular Structures in a Tangible Augmented Reality Environment

    Science.gov (United States)

    Asai, Kikuo; Takase, Norio

    2011-01-01

    This article presents the characteristics of using a tangible table top environment produced by augmented reality (AR), aimed at improving the environment in which learners observe three-dimensional molecular structures. The authors perform two evaluation experiments. A performance test for a user interface demonstrates that learners with a…

  5. Molecular epidemiology and population structure of bovine Streptococcus uberis

    DEFF Research Database (Denmark)

    Rato, M G; Bexiga, R; Nunes, S F

    2008-01-01

    The molecular epidemiology and population structure of 30 bovine subclinical mastitis field isolates of Streptococcus uberis, collected from 6 Portuguese herds (among 12 farms screened) during 2002 and 2003, were examined by using pulsed-field gel electrophoresis (PFGE) for clustering of the isol...

  6. Structure of hydrogenated amorphous silicon from ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Buda, F. (Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, Ohio (USA)); Chiarotti, G.L. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Laboratorio Tecnologie Avanzate Superfici e Catalisi del Consorzio Interuniversitario Nazionale di Fisica della Materia, Padriciano 99, I-34012 Trieste (Italy)); Car, R. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Institut Romard de Recherche Numerique en Physique des Materiaux, CH-1015 Lausanne, Switzerland Department of Condensed Matter Physics, University of Geneva, CH-1211 Geneva (Switzerland)); Parrinello, M. (IBM Research Division, Zurich Research Laboratory, CH-8803 Rueschlikon (Switzerland))

    1991-09-15

    We have generated a model of hydrogenated amorphous silicon by first-principles molecular dynamics. Our results are in good agreement with the available experimental data and provide new insight into the microscopic structure of this material. The calculation lends support to models in which monohydride complexes are prevalent, and indicates a strong tendency of hydrogen to form small clusters.

  7. Structural changes in polytetrafluoroethylene molecular chains upon sliding against steel

    NARCIS (Netherlands)

    Shen, J.T.; Pei, Y.T.; Hosson, J.Th.M. De

    In this work, the influence of dry sliding between a steel counterpart ball and polytetrafluoroethylene (PTFE) plate sample on the transformation of PTFE molecular structure is investigated. With X-ray diffraction, differential scanning calorimetry, Fourier transform infrared (FT-IR) spectroscopy

  8. Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

    DEFF Research Database (Denmark)

    Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens

    1999-01-01

    2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v...

  9. Variational cellular model of the molecular and crystal electronic structure

    International Nuclear Information System (INIS)

    Ferreira, L.G.; Leite, J.R.

    1977-12-01

    A variational version of the cellular method is developed to calculate the electronic structure of molecules and crystals. Due to the simplicity of the secular equation, the method is easy to be implemented. Preliminary calculations on the hydrogen molecular ion suggest that it is also accurate and of fast convergence [pt

  10. Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

    DEFF Research Database (Denmark)

    Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens

    1999-01-01

    2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v anthr...

  11. Ultrafast THz saturable absorption in doped semiconductors at room temperature

    DEFF Research Database (Denmark)

    Turchinovich, Dmitry; Hoffmann, M. V.

    2011-01-01

    Ultrafast Phenomena XVII presents the latest advances in ultrafast science, including both ultrafast optical technology and the study of ultrafast phenomena. It covers picosecond, femtosecond and attosecond processes relevant to applications in physics, chemistry, biology, and engineering. Ultraf...

  12. Ultrafast scanning tunneling microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Botkin, D.A. [California Univ., Berkeley, CA (United States). Dept. of Physics]|[Lawrence Berkeley Lab., CA (United States)

    1995-09-01

    I have developed an ultrafast scanning tunneling microscope (USTM) based on uniting stroboscopic methods of ultrafast optics and scanned probe microscopy to obtain nanometer spatial resolution and sub-picosecond temporal resolution. USTM increases the achievable time resolution of a STM by more than 6 orders of magnitude; this should enable exploration of mesoscopic and nanometer size systems on time scales corresponding to the period or decay of fundamental excitations. USTM consists of a photoconductive switch with subpicosecond response time in series with the tip of a STM. An optical pulse from a modelocked laser activates the switch to create a gate for the tunneling current, while a second laser pulse on the sample initiates a dynamic process which affects the tunneling current. By sending a large sequence of identical pulse pairs and measuring the average tunnel current as a function of the relative time delay between the pulses in each pair, one can map the time evolution of the surface process. USTM was used to measure the broadband response of the STM`s atomic size tunnel barrier in frequencies from tens to hundreds of GHz. The USTM signal amplitude decays linearly with the tunnel junction conductance, so the spatial resolution of the time-resolved signal is comparable to that of a conventional STM. Geometrical capacitance of the junction does not appear to play an important role in the measurement, but a capacitive effect intimately related to tunneling contributes to the measured signals and may limit the ultimate resolution of the USTM.

  13. Ultrafast Graphene Photonics and Optoelectronics

    Science.gov (United States)

    2017-04-14

    AFRL-AFOSR-JP-TR-2017-0032 Ultrafast Graphene Photonics and Optoelectronics Kuang-Hsiung Wu National Chiao Tung University Final Report 04/14/2017...DATES COVERED (From - To) 18 Apr 2013 to 17 Apr 2016 4. TITLE AND SUBTITLE Ultrafast Graphene Photonics and Optoelectronics 5a.  CONTRACT NUMBER 5b...Prescribed by ANSI Std. Z39.18 Final Report for AOARD Grant FA2386-13-1-4022 “Ultrafast Graphene Photonics and Optoelectronics” Date May 23th, 2016

  14. Physiochemical Characteristics and Molecular Structures for Digestible Carbohydrates of Silages.

    Science.gov (United States)

    Refat, Basim; Prates, Luciana L; Khan, Nazir A; Lei, Yaogeng; Christensen, David A; McKinnon, John J; Yu, Peiqiang

    2017-10-18

    The main objectives of this study were (1) to assess the magnitude of differences among new barley silage varieties (BS) selected for varying rates of in vitro neutral detergent fiber (NDF) digestibility (ivNDFD; Cowboy BS with higher ivNDFD, Copeland BS with intermediate ivNDFD, and Xena BS with lower ivNDFD) with regard to their carbohydrate (CHO) molecular makeup, CHO chemical fractions, and rumen degradability in dairy cows in comparison with a new corn silage hybrid (Pioneer 7213R) and (2) to quantify the strength and pattern of association between the molecular structures and digestibility of carbohydrates. The carbohydrate-related molecular structure spectral data was measured using advanced vibrational molecular spectroscopy (FT/IR). In comparison to BS, corn silage showed a significantly (P carbohydrates were significantly (P carbohydrate content of the silages. In conclusion, the univariate approach with only one-factor consideration (ivNDFD) might not be a satisfactory method for evaluating and ranking BS quality. FT/IR molecular spectroscopy can be used to evaluate silage quality rapidly, particularly the digestible fiber content.

  15. Fast events in protein folding: structural volume changes accompanying the early events in the N-->I transition of apomyoglobin induced by ultrafast pH jump.

    OpenAIRE

    Abbruzzetti, S; Crema, E; Masino, L; Vecli, A; Viappiani, C; Small, J R; Libertini, L J; Small, E W

    2000-01-01

    Ultrafast, laser-induced pH jump with time-resolved photoacoustic detection has been used to investigate the early protonation steps leading to the formation of the compact acid intermediate (I) of apomyoglobin (ApoMb). When ApoMb is in its native state (N) at pH 7.0, rapid acidification induced by a laser pulse leads to two parallel protonation processes. One reaction can be attributed to the binding of protons to the imidazole rings of His24 and His119. Reaction with imidazole leads to an u...

  16. Molecular orientation and electronic structure at organic heterojunction interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Zhong, Shu [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Zhong, Jian Qiang; Wee, Andrew T.S. [Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); Chen, Wei, E-mail: phycw@nus.edu.sg [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); National University of Singapore (Suzhou) Research Institute, Suzhou (China)

    2015-10-01

    Highlights: • Molecular orientation at the organic heterojunction interfaces. • Energy level alignments at the organic heterojunction interfaces. • Gap-states mediated interfacial energy level alignment. - Abstract: Due to the highly anisotropic nature of π-conjugated molecules, the molecular orientation in organic thin films can significantly affect light absorption, charge transport, energy level alignment (ELA) and hence device performance. Synchrotron-based near-edge X-ray absorption fine structure (NEXAFS) spectroscopy represents a powerful technique for probing molecular orientation. The aim of this review paper is to provide a balanced assessment on the investigation of molecular orientation at the organic–organic heterojunction (OOH) interface by NEXAFS, as well as the gap-states mediated orientation dependent energy level alignment at OOH interfaces. We highlight recent progress in elucidating molecular orientation at OOH interfaces dominated by various interfacial interactions, gap-states controlled orientation dependent energy level alignments at OOH interfaces, and the manipulations of molecular orientation and ELA in OOH.

  17. Design of Carborane Molecular Architectures via Electronic Structure Computations

    International Nuclear Information System (INIS)

    Oliva, J.M.; Serrano-Andres, L.; Klein, D.J.; Schleyer, P.V.R.; Mich, J.

    2009-01-01

    Quantum-mechanical electronic structure computations were employed to explore initial steps towards a comprehensive design of poly carborane architectures through assembly of molecular units. Aspects considered were (i) the striking modification of geometrical parameters through substitution, (ii) endohedral carboranes and proposed ejection mechanisms for energy/ion/atom/energy storage/transport, (iii) the excited state character in single and dimeric molecular units, and (iv) higher architectural constructs. A goal of this work is to find optimal architectures where atom/ion/energy/spin transport within carborane superclusters is feasible in order to modernize and improve future photo energy processes.

  18. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

    Science.gov (United States)

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

  19. Building bridges between cellular and molecular structural biology.

    Science.gov (United States)

    Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

    2017-07-06

    The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

  20. Heat-induced changes to lipid molecular structure in Vimy flaxseed: Spectral intensity and molecular clustering

    Science.gov (United States)

    Yu, Peiqiang; Damiran, Daalkhaijav

    2011-06-01

    Autoclaving was used to manipulate nutrient utilization and availability. The objectives of this study were to characterize any changes of the functional groups mainly associated with lipid structure in flaxseed ( Linum usitatissimum, cv. Vimy), that occurred on a molecular level during the treatment process using infrared Fourier transform molecular spectroscopy. The parameters included lipid CH 3 asymmetric (ca. 2959 cm -1), CH 2 asymmetric (ca. 2928 cm -1), CH 3 symmetric (ca. 2871 cm -1) and CH 2 symmetric (ca. 2954 cm -1) functional groups, lipid carbonyl C dbnd O ester group (ca. 1745 cm -1), lipid unsaturation group (CH attached to C dbnd C) (ca. 3010 cm -1) as well as their ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify molecular spectral differences. Flaxseed samples were kept raw for the control or autoclaved in batches at 120 °C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. Molecular spectral analysis of lipid functional group ratios showed a significant decrease ( P 0.05) on lipid carbonyl C dbnd O ester group and lipid unsaturation group (CH attached to C dbnd C) (with average spectral peak area intensities of 138.3 and 68.8 IR intensity units, respectively). Multivariate molecular spectral analyses, CLA and PCA, were unable to make distinctions between the different treatment original spectra at the CH 3 and CH 2 asymmetric and symmetric region (ca. 2988-2790 cm -1). The results indicated that autoclaving had an impact to the mid-infrared molecular spectrum of flaxseed to identify heat-induced changes in lipid conformation. A future study is needed to quantify the relationship between lipid molecular structure changes and functionality/availability.

  1. Fourteenth International Conference on Ultrafast Phenomena

    CERN Document Server

    Kobayashi, Takayoshi; Kobayashi, Tetsuro; Nelson, Keith A; Silvestri, Sandro; Ultrafast Phenomena XIV

    2005-01-01

    Ultrafast Phenomena XIV presents the latest advances in ultrafast science, including ultrafast laser and measurement technology as well as studies of ultrafast phenomena. Pico-, femto-, and atosecond processes relevant in physics, chemistry, biology and engineering are presented. Ultrafast technology is now having a profound impact within a wide range of applications, among them imaging, material diagnostics, and transformation and high-speed optoelectronics. This book summarizes results presented at the 14th Ultrafast Phenomena Conference and reviews the state of the art in this important and rapidly advancing field.

  2. Sixteenth International Conference on Ultrafast Phenomena

    CERN Document Server

    Corkum, Paul; Nelson, Keith A; Riedle, Eberhard; Schoenlein, Robert W; Ultrafast Phenomena XVI

    2009-01-01

    Ultrafast Phenomena XVI presents the latest advances in ultrafast science, including both ultrafast optical technology and the study of ultrafast phenomena. It covers picosecond, femtosecond and attosecond processes relevant to applications in physics, chemistry, biology, and engineering. Ultrafast technology has a profound impact in a wide range of applications, amongst them biomedical imaging, chemical dynamics, frequency standards, material processing, and ultrahigh speed communications. This book summarizes the results presented at the 16th International Conference on Ultrafast Phenomena and provides an up-to-date view of this important and rapidly advancing field.

  3. Ab initio molecular crystal structures, spectra, and phase diagrams.

    Science.gov (United States)

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  4. Imaging Molecular Motion: Femtosecond X-Ray Scattering of an Electrocyclic Chemical Reaction

    Science.gov (United States)

    Minitti, M. P.; Budarz, J. M.; Kirrander, A.; Robinson, J. S.; Ratner, D.; Lane, T. J.; Zhu, D.; Glownia, J. M.; Kozina, M.; Lemke, H. T.; Sikorski, M.; Feng, Y.; Nelson, S.; Saita, K.; Stankus, B.; Northey, T.; Hastings, J. B.; Weber, P. M.

    2015-06-01

    Structural rearrangements within single molecules occur on ultrafast time scales. Many aspects of molecular dynamics, such as the energy flow through excited states, have been studied using spectroscopic techniques, yet the goal to watch molecules evolve their geometrical structure in real time remains challenging. By mapping nuclear motions using femtosecond x-ray pulses, we have created real-space representations of the evolving dynamics during a well-known chemical reaction and show a series of time-sorted structural snapshots produced by ultrafast time-resolved hard x-ray scattering. A computational analysis optimally matches the series of scattering patterns produced by the x rays to a multitude of potential reaction paths. In so doing, we have made a critical step toward the goal of viewing chemical reactions on femtosecond time scales, opening a new direction in studies of ultrafast chemical reactions in the gas phase.

  5. Molecular Cloud Structures and Massive Star Formation in N159

    Science.gov (United States)

    Nayak, O.; Meixner, M.; Fukui, Y.; Tachihara, K.; Onishi, T.; Saigo, K.; Tokuda, K.; Harada, R.

    2018-02-01

    The N159 star-forming region is one of the most massive giant molecular clouds (GMCs) in the Large Magellanic Cloud (LMC). We show the 12CO, 13CO, CS molecular gas lines observed with ALMA in N159 west (N159W) and N159 east (N159E). We relate the structure of the gas clumps to the properties of 24 massive young stellar objects (YSOs) that include 10 newly identified YSOs based on our search. We use dendrogram analysis to identify properties of the molecular clumps, such as flux, mass, linewidth, size, and virial parameter. We relate the YSO properties to the molecular gas properties. We find that the CS gas clumps have a steeper size–linewidth relation than the 12CO or 13CO gas clumps. This larger slope could potentially occur if the CS gas is tracing shocks. The virial parameters of the 13CO gas clumps in N159W and N159E are low (<1). The threshold for massive star formation in N159W is 501 M ⊙ pc‑2, and the threshold for massive star formation in N159E is 794 M ⊙ pc‑2. We find that 13CO is more photodissociated in N159E than N159W. The most massive YSO in N159E has cleared out a molecular gas hole in its vicinity. All the massive YSO candidates in N159E have a more evolved spectral energy distribution type in comparison to the YSO candidates in N159W. These differences lead us to conclude that the giant molecular cloud complex in N159E is more evolved than the giant molecular cloud complex in N159W.

  6. Structural and Molecular Modeling Features of P2X Receptors

    Directory of Open Access Journals (Sweden)

    Luiz Anastacio Alves

    2014-03-01

    Full Text Available Currently, adenosine 5'-triphosphate (ATP is recognized as the extracellular messenger that acts through P2 receptors. P2 receptors are divided into two subtypes: P2Y metabotropic receptors and P2X ionotropic receptors, both of which are found in virtually all mammalian cell types studied. Due to the difficulty in studying membrane protein structures by X-ray crystallography or NMR techniques, there is little information about these structures available in the literature. Two structures of the P2X4 receptor in truncated form have been solved by crystallography. Molecular modeling has proven to be an excellent tool for studying ionotropic receptors. Recently, modeling studies carried out on P2X receptors have advanced our knowledge of the P2X receptor structure-function relationships. This review presents a brief history of ion channel structural studies and shows how modeling approaches can be used to address relevant questions about P2X receptors.

  7. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    Science.gov (United States)

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

    2014-12-19

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Copyright © 2014 John Wiley & Sons, Inc.

  8. Calculation on uranium carbon oxygen system molecular structure by DFT

    International Nuclear Information System (INIS)

    Zhang Guangfeng; Wang Xiaolin; Zou Lexi; Sun Ying; Xue Weidong; Zhu Zhenghe; Wang Hongyan

    2001-01-01

    The authors study on the possible molecular structures U-C-O, U-O-C, C-U-O (angular structure C a nd linear structure C ∞υ ) of carbon monoxide interacting on uranium metal surface by Density functional theory (DFT). The uranium atom is used RECP (Relativistic Effective Core Potential) and contracted valence basis sets (6s5p2d4f)/[3s3p2d2f], and for carbon and oxygen atoms all are 6-311G basis sets. The author presents the results of energy optimum which shows that triple and quintuple state are more stable. The authors get the electronic state, geometry structure, energy, harmonic frequency, mechanical property, etc. of these twelve triple and quintuple state relative stable structures. The normal vibrational analytical figure of angular structure (C s ) and linear structure (C ∞υ ) is given at the same time. It is indicated that angular structure has lower energy than linear structure, moreover the angular structure of U-C-O( 3 A ) has the lowest energy. The bond strength between uranium atom and carbon monoxide is weak and between uranium atom and oxygen atom is slightly stronger than between uranium atom and carbon atom which the authors can know by superposition population and bond energy analysis among atoms

  9. Exponential Repulsion Improves Structural Predictability of Molecular Docking

    Czech Academy of Sciences Publication Activity Database

    Bazgier, Václav; Berka, K.; Otyepka, M.; Banáš, P.

    2016-01-01

    Roč. 37, č. 28 (2016), s. 2485-2494 ISSN 0192-8651 Institutional support: RVO:61389030 Keywords : cyclin-dependent kinases * structure-based design * scoring functions * cdk2 inhibitors * force-field * ligand interactions * drug discovery * purine * potent * protein-kinase-2 * molecular docking * dock 6.6 * drug design * cyclin-dependent kinase 2 * directory of decoys Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.229, year: 2016

  10. Invariant molecular-dynamics approach to structural phase transitions

    International Nuclear Information System (INIS)

    Wentzcovitch, R.M.

    1991-01-01

    Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

  11. VPAC receptors: structure, molecular pharmacology and interaction with accessory proteins.

    Science.gov (United States)

    Couvineau, Alain; Laburthe, Marc

    2012-05-01

    The vasoactive intestinal peptide (VIP) is a neuropeptide with wide distribution in both central and peripheral nervous systems, where it plays important regulatory role in many physiological processes. VIP displays a large biological functions including regulation of exocrine secretions, hormone release, fetal development, immune responses, etc. VIP appears to exert beneficial effect in neuro-degenerative and inflammatory diseases. The mechanism of action of VIP implicates two subtypes of receptors (VPAC1 and VPAC2), which are members of class B receptors belonging to the super-family of GPCR. This article reviews the current knowledge regarding the structure and molecular pharmacology of VPAC receptors. The structure-function relationship of VPAC1 receptor has been extensively studied, allowing to understand the molecular basis for receptor affinity, specificity, desensitization and coupling to adenylyl cyclase. Those studies have clearly demonstrated the crucial role of the N-terminal ectodomain (N-ted) of VPAC1 receptor in VIP recognition. By using different approaches including directed mutagenesis, photoaffinity labelling, NMR, molecular modelling and molecular dynamic simulation, it has been shown that the VIP molecule interacts with the N-ted of VPAC1 receptor, which is itself structured as a 'Sushi' domain. VPAC1 receptor also interacts with a few accessory proteins that play a role in cell signalling of receptors. Recent advances in the structural characterization of VPAC receptor and more generally of class B GPCRs will lead to the design of new molecules, which could have considerable interest for the treatment of inflammatory and neuro-degenerative diseases. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

  12. Isotope chemistry and molecular structure. The WINIMAX weighting factor

    International Nuclear Information System (INIS)

    Lee, M.W.; Bigeleisen, J.

    1979-01-01

    The modulating coefficients for the finite polynomial expansion of the logarithm of the reduced partition function, lnb (u), of a harmonic oscillator have been obtained for the range of 0 6 . It is shown that this weighting function is near optimum to insure minimum amplitudes of oscillation in the expansion of lnb (u) as a function of the order of the expansion and to include most of the important molecular structure information contained in the moments of the eigenvalues. Beyond Σu/sub i/ 6 , there is little new structural information

  13. Ultrafast dynamics of correlated electrons

    International Nuclear Information System (INIS)

    Rettig, Laurenz

    2012-01-01

    scattering along the d-wave gap and establishes the Cooper pair recombination in a strong bottleneck regime as dominating relaxation channel. Finally, spectroscopy of the occupied and unoccupied band structure of the prototypical CDW material RTe 3 (R = rare-earth element) using a position-sensitive time-of-flight (pTOF) spectrometer demonstrates the Fermi surface (FS) nesting driven CDW formation and reveals several details that go beyond a simple Tight-Binding description. The pTOF enables the observation of the ultrafast closing of the CDW gap and the reformation of a continuous, metallic FS within < 200 fs after optical excitation. The determination of the transient CDW order parameter reveals a momentum-dependent, asymmetric closing of the CDW gap, that is explained by a transient modification of the nesting condition. The temperature dependence of the CDW amplitude mode shows a characteristic frequency softening, and the collective nature of the amplitude mode is demonstrated by its coherent control.

  14. Ultrafast dynamics of correlated electrons

    Energy Technology Data Exchange (ETDEWEB)

    Rettig, Laurenz

    2012-07-09

    suppression of momentum scattering along the d-wave gap and establishes the Cooper pair recombination in a strong bottleneck regime as dominating relaxation channel. Finally, spectroscopy of the occupied and unoccupied band structure of the prototypical CDW material RTe{sub 3} (R = rare-earth element) using a position-sensitive time-of-flight (pTOF) spectrometer demonstrates the Fermi surface (FS) nesting driven CDW formation and reveals several details that go beyond a simple Tight-Binding description. The pTOF enables the observation of the ultrafast closing of the CDW gap and the reformation of a continuous, metallic FS within < 200 fs after optical excitation. The determination of the transient CDW order parameter reveals a momentum-dependent, asymmetric closing of the CDW gap, that is explained by a transient modification of the nesting condition. The temperature dependence of the CDW amplitude mode shows a characteristic frequency softening, and the collective nature of the amplitude mode is demonstrated by its coherent control.

  15. Using photoelectron diffraction to determine complex molecular adsorption structures

    International Nuclear Information System (INIS)

    Woodruff, D P

    2010-01-01

    Backscattering photoelectron diffraction, particularly in the energy-scan mode, is now an established technique for determining in a quantitative fashion the local structure of adsorbates on surfaces, and has been used successfully for ∼100 adsorbate phases. The elemental and chemical-state specificity afforded by the characteristic core level photoelectron binding energies means that it has particular advantages for molecular adsorbates, as the local geometry of inequivalent atoms in the molecule can be determined in a largely independent fashion. On the other hand, polyatomic molecules present a general problem for all methods of surface structure determination in that a mismatch of intramolecular distances with interatomic distances on the substrate surface means that the atoms in the adsorbed molecule are generally in low-symmetry sites. The quantities measured experimentally then represent an incoherent sum of the properties of each structural domain that is inequivalent with respect to the substrate point group symmetry. This typically leads to greater ambiguity or precision in the structural solutions. The basic principles of the method are described and illustrated with a simple example involving molecule/substrate bonding through only one constituent atom (TiO 2 -(110)/H 2 O). This example demonstrates the importance of obtaining quantitative local structural information. Further examples illustrate both the successes and the problems of this approach when applied to somewhat more complex molecular adsorbates.

  16. Carrier dynamics in graphene. Ultrafast many-particle phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Malic, E.; Brem, S.; Jago, R. [Department of Physics, Chalmers University of Technology, Goeteborg (Sweden); Winzer, T.; Wendler, F.; Knorr, A. [Institut fuer Theoretische Physik, Technische Universitaet Berlin (Germany); Mittendorff, M.; Koenig-Otto, J.C.; Schneider, H.; Helm, M.; Winnerl, S. [Helmholtz-Zentrum Dresden-Rossendorf, Dresden (Germany); Ploetzing, T.; Neumaier, D. [Advanced Microelectronic Center Aachen, AMO GmbH, Aachen (Germany)

    2017-11-15

    Graphene is an ideal material to study fundamental Coulomb- and phonon-induced carrier scattering processes. Its remarkable gapless and linear band structure opens up new carrier relaxation channels. In particular, Auger scattering bridging the valence and the conduction band changes the number of charge carriers and gives rise to a significant carrier multiplication - an ultrafast many-particle phenomenon that is promising for the design of highly efficient photodetectors. Furthermore, the vanishing density of states at the Dirac point combined with ultrafast phonon-induced intraband scattering results in an accumulation of carriers and a population inversion suggesting the design of graphene-based terahertz lasers. Here, we review our work on the ultrafast carrier dynamics in graphene and Landau-quantized graphene is presented providing a microscopic view on the appearance of carrier multiplication and population inversion. (copyright 2017 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  17. Ultrafast dynamics of hydrogen bond exchange in aqueous ionic solutions.

    Science.gov (United States)

    Park, Sungnam; Odelius, Michael; Gaffney, Kelly J

    2009-06-04

    The structural and dynamical properties of aqueous ionic solutions influence a wide range of natural and biological processes. In these solutions, water has the opportunity to form hydrogen bonds with other water molecules and anions. Knowing the time scale with which these configurations interconvert represents a key factor to understanding the influence of molecular scale heterogeneity on chemical events in aqueous ionic solutions. We have used ultrafast IR spectroscopy and Car-Parrinello molecular dynamics (CPMD) simulations to investigate the hydrogen bond (H-bond) structural dynamics in aqueous 6 M sodium perchlorate (NaClO4) solution. We have measured the H-bond exchange dynamics between spectrally distinct water-water and water-anion H-bond configurations with 2DIR spectroscopy and the orientational relaxation dynamics of water molecules in different H-bond configurations with polarization-selective IR pump-probe experiments. The experimental H-bond exchange time correlates strongly with the experimental orientational relaxation time of water molecules. This agrees with prior observations in water and aqueous halide solutions, and has been interpreted within the context of an orientational jump model for the H-bond exchange. The CPMD simulations performed on aqueous 6 M NaClO4 solution clearly demonstrate that water molecules organize into two radially and angularly distinct structural subshells within the first solvation shell of the perchlorate anion, with one subshell possessing the majority of the water molecules that donate H-bonds to perchlorate anions and the other subshell possessing predominantly water molecules that donate two H-bonds to other water molecules. Due to the high ionic concentration used in the simulations, essentially all water molecules reside in the first ionic solvation shells. The CPMD simulations also demonstrate that the molecular exchange between these two structurally distinct subshells proceeds more slowly than the H

  18. Molecular tailoring approach for exploring structures, energetics and ...

    Indian Academy of Sciences (India)

    Administrator

    Keywords. Molecular clusters; linear scaling methods; molecular tailoring approach (MTA); Hartree– ..... energy decomposition analysis also performed and which clearly ... through molecular dynamics simulation furnished by. Takeguchi,. 46.

  19. Tunneling and resonant conductance in one-dimensional molecular structures

    International Nuclear Information System (INIS)

    Kozhushner, M.A.; Posvyanskii, V.S.; Oleynik, I.I.

    2005-01-01

    We present a theory of tunneling and resonant transitions in one-dimensional molecular systems which is based on Green's function theory of electron sub-barrier scattering off the structural units (or functional groups) of a molecular chain. We show that the many-electron effects are of paramount importance in electron transport and they are effectively treated using a formalism of sub-barrier scattering operators. The method which calculates the total scattering amplitude of the bridge molecule not only predicts the enhancement of the amplitude of tunneling transitions in course of tunneling electron transfer through onedimensional molecular structures but also allows us to interpret conductance mechanisms by calculating the bound energy spectrum of the tunneling electron, the energies being obtained as poles of the total scattering amplitude of the bridge molecule. We found that the resonant tunneling via bound states of the tunneling electron is the major mechanism of electron conductivity in relatively long organic molecules. The sub-barrier scattering technique naturally includes a description of tunneling in applied electric fields which allows us to calculate I-V curves at finite bias. The developed theory is applied to explain experimental findings such as bridge effect due to tunneling through organic molecules, and threshold versus Ohmic behavior of the conductance due to resonant electron transfer

  20. Large Molecule Structures by Broadband Fourier Transform Molecular Rotational Spectroscopy

    Science.gov (United States)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

    2016-06-01

    Fourier transform molecular rotational resonance spectroscopy (FT-MRR) using pulsed jet molecular beam sources is a high-resolution spectroscopy technique that can be used for chiral analysis of molecules with multiple chiral centers. The sensitivity of the molecular rotational spectrum pattern to small changes in the three dimensional structure makes it possible to identify diastereomers without prior chemical separation. For larger molecules, there is the additional challenge that different conformations of each diastereomer may be present and these need to be differentiated from the diastereomers in the spectral analysis. Broadband rotational spectra of several larger molecules have been measured using a chirped-pulse FT-MRR spectrometer. Measurements of nootkatone (C15H22O), cedrol (C15H26O), ambroxide (C16H28O) and sclareolide (C16H26O2) are presented. These spectra are measured with high sensitivity (signal-to-noise ratio near 1,000:1) and permit structure determination of the most populated isomers using isotopic analysis of the 13C and 18O isotopologues in natural abundance. The accuracy of quantum chemistry calculations to identify diastereomers and conformers and to predict the dipole moment properties needed for three wave mixing measurements is examined.

  1. Ultrafast Digital Printing toward 4D Shape Changing Materials.

    Science.gov (United States)

    Huang, Limei; Jiang, Ruiqi; Wu, Jingjun; Song, Jizhou; Bai, Hao; Li, Bogeng; Zhao, Qian; Xie, Tao

    2017-02-01

    Ultrafast 4D printing (printing converts the structure into 3D. An additional dimension can be incorporated by choosing the printing precursors. The process overcomes the speed limiting steps of typical 3D (4D) printing. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Are water simulation models consistent with steady-state and ultrafast vibrational spectroscopy experiments?

    International Nuclear Information System (INIS)

    Schmidt, J.R.; Roberts, S.T.; Loparo, J.J.; Tokmakoff, A.; Fayer, M.D.; Skinner, J.L.

    2007-01-01

    Vibrational spectroscopy can provide important information about structure and dynamics in liquids. In the case of liquid water, this is particularly true for isotopically dilute HOD/D 2 O and HOD/H 2 O systems. Infrared and Raman line shapes for these systems were measured some time ago. Very recently, ultrafast three-pulse vibrational echo experiments have been performed on these systems, which provide new, exciting, and important dynamical benchmarks for liquid water. There has been tremendous theoretical effort expended on the development of classical simulation models for liquid water. These models have been parameterized from experimental structural and thermodynamic measurements. The goal of this paper is to determine if representative simulation models are consistent with steady-state, and especially with these new ultrafast, experiments. Such a comparison provides information about the accuracy of the dynamics of these simulation models. We perform this comparison using theoretical methods developed in previous papers, and calculate the experimental observables directly, without making the Condon and cumulant approximations, and taking into account molecular rotation, vibrational relaxation, and finite excitation pulses. On the whole, the simulation models do remarkably well; perhaps the best overall agreement with experiment comes from the SPC/E model

  3. Spatio-temporal imaging of voltage pulses with an ultrafast scanning tunneling microscope

    DEFF Research Database (Denmark)

    Jensen, Jacob Riis; Keil, Ulrich Dieter Felix; Hvam, Jørn Märcher

    1997-01-01

    Measurements on an ultrafast scanning tunneling microscope with simultaneous spatial and temporal resolution are presented. We show images of picosecond pulses propagating on a coplanar waveguide and resolve their mode structures. The influence of transmission line discontinuities on the mode...

  4. Molecular Diagnostics of the Internal Structure of Starspots and Sunspots

    Science.gov (United States)

    Afram, N.; Berdyugina, S. V.; Fluri, D. M.; Solanki, S. K.; Lagg, A.; Petit, P.; Arnaud, J.

    2006-12-01

    We have analyzed the usefulness of molecules as a diagnostic tool for studying solar and stellar magnetism with the molecular Zeeman and Paschen-Back effects. In the first part we concentrate on molecules that are observed in sunspots such as MgH and TiO. We present calculated molecular line profiles obtained by assuming magnetic fields of 2-3 kG and compare these synthetic Stokes profiles with spectro-polarimetric observations in sunspots. The good agreement between the theory and observations allows us to turn our attention in the second part to starspots to gain insight into their internal structure. We investigate the temperature range in which the selected molecules can serve as indicators for magnetic fields on highly active cool stars and compare synthetic Stokes profiles with our recent observations.

  5. Towards structural models of molecular recognition in olfactory receptors.

    Science.gov (United States)

    Afshar, M; Hubbard, R E; Demaille, J

    1998-02-01

    The G protein coupled receptors (GPCR) are an important class of proteins that act as signal transducers through the cytoplasmic membrane. Understanding the structure and activation mechanism of these proteins is crucial for understanding many different aspects of cellular signalling. The olfactory receptors correspond to the largest family of GPCRs. Very little is known about how the structures of the receptors govern the specificity of interaction which enables identification of particular odorant molecules. In this paper, we review recent developments in two areas of molecular modelling: methods for modelling the configuration of trans-membrane helices and methods for automatic docking of ligands into receptor structures. We then show how a subset of these methods can be combined to construct a model of a rat odorant receptor interacting with lyral for which experimental data are available. This modelling can help us make progress towards elucidating the specificity of interactions between receptors and odorant molecules.

  6. Structure of a molecular liquid GeI4

    International Nuclear Information System (INIS)

    Fuchizaki, Kazuhiro; Sakagami, Takahiro; Kohara, Shinji; Mizuno, Akitoshi; Asano, Yuta; Hamaya, Nozomu

    2016-01-01

    A molecular liquid GeI 4 is a candidate that undergoes a pressure-induced liquid-to-liquid phase transition. This study establishes the reference structure of the low-pressure liquid phase. Synchrotron x-ray diffraction measurements were carried out at several temperatures between the melting and the boiling points under ambient pressure. The molecule has regular tetrahedral symmetry, and the intramolecular Ge–I length of 2.51 Å is almost temperature-independent within the measured range. A reverse Monte Carlo (RMC) analysis is employed to find that the distribution of molecular centers remains self-similar against heating, and thus justifying the length-scaling method adopted in determining the density. The RMC analysis also reveals that the vertex-to-face orientation of the nearest molecules are not straightly aligned, but are inclined at about 20 degrees, thereby making the closest intermolecular I–I distance definitely shorter than the intramolecular one. The prepeak observed at  ∼1 Å −1 in the structural factor slightly shifts and increases in height with increasing temperature. The origin of the prepeak is clearly identified to be traces of the 111 diffraction peak in the crystalline state. The prepeak, assuming the residual spatial correlation between germanium sites in the densest direction, thus shifts toward lower wavenumbers with thermal expansion. The aspect that a relative reduction in molecular size associated with the volume expansion is responsible for the increase in the prepeak’s height is confirmed by a simulation, in which the molecular size is changed. (paper)

  7. Interpreting closed-loop learning control of molecular fragmentation in terms of wave-packet dynamics and enhanced molecular ionization

    International Nuclear Information System (INIS)

    Cardoza, David; Baertschy, Mark; Weinacht, Thomas

    2005-01-01

    We interpret a molecular fragmentation experiment using shaped, ultrafast laser pulses in terms of enhanced molecular ionization during dissociation. A closed-loop learning control experiment was performed to maximize the CF 3 + /CH 3 + production ratio in the dissociative ionization of CH 3 COCF 3 . Using ab inito molecular structure calculations and quasistatic molecular ionization calculations along with data from pump-probe experiments, we identify the primary control mechanism which is quite general and should be applicable to a broad class of molecules

  8. III - V semiconductor structures for biosensor and molecular electronics applications

    Energy Technology Data Exchange (ETDEWEB)

    Luber, S M

    2007-01-15

    The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed by a

  9. III - V semiconductor structures for biosensor and molecular electronics applications

    Energy Technology Data Exchange (ETDEWEB)

    Luber, S.M.

    2007-01-15

    The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed

  10. Progress in Ultrafast Intense Laser Science Volume V

    CERN Document Server

    Yamanouchi, Kaoru; Ledingham, Kenneth

    2010-01-01

    The PUILS series delivers up-to-date reviews of progress in Ultrafast Intense Laser Science, a newly emerging interdisciplinary research field spanning atomic and molecular physics, molecular science, and optical science, which has been stimulated by the recent developments in ultrafast laser technologies. Each volume compiles peer-reviewed articles authored by researchers at the forefront of each their own subfields of UILS. Every chapter opens with an overview of the topics to be discussed, so that researchers unfamiliar to the subfield, as well as graduate students, can grasp the importance and attractions of the research topic at hand; these are followed by reports of cutting-edge discoveries. This fifth volume covers a broad range of topics from this interdisciplinary research field, focusing on coherent responses of gaseous and condensed matter to ultrashort intense laser pulses, propagation of intense laser pulses, and laser-plasma interaction and its applications.

  11. The interface of protein structure, protein biophysics, and molecular evolution

    Science.gov (United States)

    Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

    2012-01-01

    Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

  12. Contributions to advances in blend pellet products (BPP) research on molecular structure and molecular nutrition interaction by advanced synchrotron and globar molecular (Micro)spectroscopy.

    Science.gov (United States)

    Guevara-Oquendo, Víctor H; Zhang, Huihua; Yu, Peiqiang

    2018-04-13

    To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

  13. Free radicals. High-resolution spectroscopy and molecular structure

    International Nuclear Information System (INIS)

    Hirota, E.

    1983-01-01

    High-resolution, high-sensitivity spectroscopy using CW laser and microwave sources has been applied to free radicals and transient molecules to establish their existence and to explore their properties in detail. The radicals studied were mainly generated by discharge-induced reactions. A few molecules are used as typical examples to illustrate the results so far obtained. The molecular and electronic structures of free radicals, intramolecular motions of large amplitudes in some labile molecules, and metastable electronic states of carbenes are given special emphasis. The significance of the present spectroscopic results in other related fields such as astronomy and atmospheric chemistry is stressed. 4 figures, 3 tables

  14. Coalescence of silver unidimensional structures by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G.; Arenas, J.

    2007-01-01

    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  15. Nonlinear excitations in two-dimensional molecular structures with impurities

    DEFF Research Database (Denmark)

    Gaididei, Yuri Borisovich; Rasmussen, Kim; Christiansen, Peter Leth

    1995-01-01

    We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence...... of the impurity. Transforming the equation to the noninertial frame of reference coupled with the center of mass we investigate the soliton behavior in the close vicinity of the impurity. With the help of the lens transformation we show that the soliton width is governed by an Ermakov-Pinney equation. We also...... excitations. Analytical results are in good agreement with numerical simulations of the nonlinear Schrodinger equation....

  16. The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Bianchi, L.

    2000-05-01

    Neutron diffraction (ND) measurements on liquid methanol (CD 3 OD, CD 3 O(H/D), CD 3 OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), G dist (r) and inter-molecular, G inter (r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, G XHo (r) (X=C, O, and H - a methyl hydrogen) and G XX (r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, G XHo (r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct G XX (r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular G XX (r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), g HoHo (r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular G XHo (r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial

  17. Cooperative photo-induced effects: from photo-magnetism under continuous irradiation to ultra-fast phenomena - study through optical spectroscopy and X-ray diffraction

    International Nuclear Information System (INIS)

    Glijer, D.

    2006-12-01

    The control with ultra-short laser pulses of the collective and concerted transformation of molecules driving a macroscopic state switching on an ultra-fast time scale in solid state opens new prospects in materials science. The goal is to realize at the material level what happens at the molecular level in femto-chemistry. These processes are highly cooperative and highly non-linear, leading to self-amplification and self-organization within the material, a so-called photo-induced phase transition with a new long range order (structural, magnetic, ferroelectric,...). Two families of molecular compounds have been studied here: first of all, spin transition materials changing from a diamagnetic state over to a paramagnetic state under the effect of temperature or under continuous laser excitation. It concerns photo-active molecular bi-stability prototype materials in solid state, whose switching has been studied during X-ray diffraction, optical reflectivity and magnetism experiments. Then we have studied charge-transfer molecular systems, prototype compounds for ultrafast photo-induced phase transitions: insulator-metal, neutral-ionic....As well as ultrafast optical experiments, time-resolved X ray crystallography is a key technique in order to follow at the atomic level the different steps of the photo-induced transformation and thus to observe the involved mechanisms. We have underlined a process of photo-formation of one-dimensional nano-domains of lattice-relaxed charge-transfer excitations, governing the photo-induced phase transition of the molecular charge-transfer complex TTF-CA by the first time-resolved diffuse scattering measurements. Moreover, a new femtosecond laser-plasma source and a optical pump-probe spectroscopy set-up with a highly sensitive detecting system have been developed in this work. The results presented here will be an illustration of the present scientific challenges existing on the one hand with the development of projects of major

  18. Molecular simulations of hydrated proton exchange membranes. The structure

    Energy Technology Data Exchange (ETDEWEB)

    Marcharnd, Gabriel [Duisburg-Essen Univ., Essen (Germany). Lehrstuhl fuer Theoretische Chemie; Bordeaux Univ., Talence (France). Dept. of Chemistry; Bopp, Philippe A. [Bordeaux Univ., Talence (France). Dept. of Chemistry; Spohr, Eckhard [Duisburg-Essen Univ., Essen (Germany). Lehrstuhl fuer Theoretische Chemie

    2013-01-15

    The structure of two hydrated proton exchange membranes for fuel cells (PEMFC), Nafion {sup registered} (Dupont) and Hyflon {sup registered} (Solvay), is studied by all-atom molecular dynamics (MD) computer simulations. Since the characteristic times of these systems are long compared to the times for which they can be simulated, several different, but equivalent, initial configurations with a large degree of randomness are generated for different water contents and then equilibrated and simulated in parallel. A more constrained structure, analog to the newest model proposed in the literature based on scattering experiments, is investigated in the same way. One might speculate that a limited degree of entanglement of the polymer chains is a key feature of the structures showing the best agreement with experiment. Nevertheless, the overall conclusion remains that the scattering experiments cannot distinguish between the several, in our view equally plausible, structural models. We thus find that the characteristic features of experimental scattering curves are, after equilibration, fairly well reproduced by all systems prepared with our method. We thus study in more detail some structural details. We attempt to characterize the spatial and size distribution of the water rich domains, which is where the proton diffusion mostly takes place, using several clustering algorithms. (orig.)

  19. CRYSTAL AND MOLECULAR STRUCTURE OF 5-NITROPIRIDINE PIPERIDINE-SULFENAMIDE

    OpenAIRE

    Brito, Iván; León, Yasna; Arias, Mauricio; Vargas, Danitza; Carmona, Francisco; Ramírez, Eduardo; Restovic, Ambrosio; Cárdenas, Alejandro; Wittke, Oscar; López-Rodríguez, Matías

    2002-01-01

    The crystal and molecular structure of 5-nitropiridine piperidine-sulfenamide, C10H13N3O2 S is described and compared with other sulfenamides and with other similar compounds. This structure belongs to a type of divalent sulphur compound and crystallizes in the orthorhombic space group Pnma with a= 27.810(4), b=6.797(1), c=6.110(1)Å, and Dx =1.376 g cm-3 with Z=4. The S-N bond distance of 1.699(4) Å is shorter than a single S-N bond [1.74 Å]. The NO2-(C6H3N)-S-N(C 5H10) molecule lies on a cry...

  20. Chemical structure and properties of low-molecular furin inhibitors

    Directory of Open Access Journals (Sweden)

    T. V. Osadchuk

    2016-12-01

    Full Text Available The review is devoted to the analysis of the relationship between a chemical structure and properties of low-molecular weight inhibitors of furin, the most studied proprotein convertase, which is involved in the development of some pathologies, such as oncologic diseases, viral and bacterial infections, etc. The latest data concerning the influence of peptides, pseudo-peptides, aromatic and heterocyclic compounds, some natural ones such as flavonoids, coumarins, and others on enzyme inactivation are considered. The power of furin inhibition is shown to rise with the increasing number of positively charged groups in the structure of these compounds. Peptidomimetics (Ki = 5-8 pM are shown to be the most effective furin inhibitors. The synthesized substances, however, have not been used in practical application yet. Nowadays it is very important to find more selective inhibitors, improve their stability, bioavailability and safety for the human organism.

  1. Surfaces of Microparticles in Colloids: Structure and Molecular Adsorption Kinetics

    Science.gov (United States)

    Dai, Hai-Lung

    2002-03-01

    Surfaces of micron and sub-micron size particles in liquid solution are probed by second harmonic generation (SHG) facilitated with femtosecond laser pulses. The particles probed include inorganic objects such as carbon black and color pigments, polymeric species like polystyrene beads, and biological systems such as blood cells and ecoli. In the experiments, dye molecules are first adsorbed onto the particle surface to allow generation of second harmonics upon light irradiation. Competition for adsorption between these surface dye molecules and the molecules of interest in the solution is then monitored by the SHG signal to reveal the molecular adsorption kinetics and surface structure. Specifically, surfactant adsorption on polymer surfaces, the structure of carbon black surface, and protein adsorption on biological surfaces, monitored by this technique, will be discussed.

  2. Structures and physicochemical properties of molecular aggregates of lipids

    International Nuclear Information System (INIS)

    Iwahashi, Makio

    2005-01-01

    Structures and physicochemical properties of lipids such as fatty acids, alcohols, acylglycerols and steroids in their two- or three-dimensional states were studied through the measurements of surface pressure (π), surface-molecular area (A), vapor-pressure osmosis, radioactivity (R), self-diffusion coefficient (D), density, viscosity, near-infrared spectroscopy (NIR), 13 C-NMR spin-lattice relaxation time (T 1 ), ESR, SEM, DSC, X-ray diffraction and small-angle neutron scattering (SANS). Following results are obtained: (1) π-A and R-A relationships indicate that the explanation, being widely believed, of the reaction occurred in the oleic acid or the trioleylglycerol monolayer on the aqueous KMnO 4 solution is incorrect. (2) By using the LB film of 3 H-labelled fatty acid, the upper limit of the neutrino mass was determined. In addition, by using the LB film of 14 C-labelled fatty acid, a new type of crystal-transformation process was found, in which fatty-acid crystal transforms from its unstable state to its stable one by the transfer of the fatty acid molecules through the vapor phase. (3) Fatty acids always exist as their dimers in their liquid state and mostly in non-polar solvents; the dimers are the units of the molecular movements in the molten liquid and in solvents. T 1 results clearly showed the internal molecular movements of the dimers. In addition, D and SANS results indicated that two different kinds of fatty acids in their binary mixture make only each homodimers. (4) Furthermore, the study on the liquid structure of fatty acids such as cis-6-, cis-9-, cis-11-, trans-9-octadecenoic acids and stearic acid indicated that these fatty-acid dimers construct the clusters resemble to the smectic-liquid crystal in the liquid state. The clusters determine the physicochemical properties of the liquid of the fatty acid. (author)

  3. Micro structure processing on plastics by accelerated hydrogen molecular ions

    Science.gov (United States)

    Hayashi, H.; Hayakawa, S.; Nishikawa, H.

    2017-08-01

    A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

  4. Influence of thickness-dependent structural evolution on ultrafast magnetization dynamics in C o2F e0.4M n0.6Si Heusler alloy thin films

    Science.gov (United States)

    Pan, Santanu; Mondal, Sucheta; Seki, Takeshi; Takanashi, Koki; Barman, Anjan

    2016-11-01

    We experimentally investigate thickness (t )-dependent evolution of structural and magnetic properties in C o2F e0.4M n0.6Si (CFMS) thin films and correlate them with ultrafast demagnetization time (τd) and relaxation time (τ1) as well as the Gilbert damping coefficient (α ). Structural ordering and magnetic parameters, including α , exhibit a nonmonotonic variation with increasing t . A remarkably low value of α of 0.009 is obtained for the CFMS film with t =20 nm without any buffer layers, which helps to avoid possible diffusion of the buffer layer into CFMS. Highest saturation magnetization, lowest coercivity, and the α value imply CFMS film with t =20 nm is most suitable for integrated spintronics devices, viz. low-current switched spin transfer torque, and magnetic tunnel junction with a high tunnel magnetoresistance ratio at room temperature. Despite the presence of strain, a lower degree of chemical ordering in the low-t regime, and increased defect density in the high-t regime, we obtained a reasonably low value of damping. In addition to the intrinsic fourfold magnetocrystalline anisotropy, an induced uniaxial anisotropy is found, which also varies nonmonotonically with t . Finally, unique band structure controlled demagnetization and fast relaxation in half-metallic CFMS is correlated to α .

  5. X-RAY HIGH-RESOLUTION SPECTROSCOPY REVEALS FEEDBACK IN A SEYFERT GALAXY FROM AN ULTRA-FAST WIND WITH COMPLEX IONIZATION AND VELOCITY STRUCTURE

    International Nuclear Information System (INIS)

    Longinotti, A. L.; Krongold, Y.; Guainazzi, M.; Santos-Lleo, M.; Rodriguez-Pascual, P.; Giroletti, M.; Panessa, F.; Costantini, E.

    2015-01-01

    Winds outflowing from active galactic nuclei (AGNs) may carry significant amounts of mass and energy out to their host galaxies. In this paper we report the detection of a sub-relativistic outflow observed in the narrow line Seyfert 1 galaxy IRAS 17020+4544 as a series of absorption lines corresponding to at least five absorption components with an unprecedented wide range of associated column densities and ionization levels and velocities in the range of 23,000–33,000 km s −1 , detected at X-ray high spectral resolution (E/ΔE ∼ 1000) with the ESA's observatory XMM-Newton. The charge states of the material constituting the wind clearly indicate a range of low to moderate ionization states in the outflowing gas and column densities that are significantly lower than observed in highly ionized ultra-fast outflows. We estimate that at least one of the outflow components may carry sufficient energy to substantially suppress star formation and heat the gas in the host galaxy. IRAS 17020+4544 therefore provides an interesting example of feedback by a moderately luminous AGN that is hosted in a spiral galaxy, a case barely envisaged in most evolution models, which often predict that feedback processes take place in massive elliptical galaxies hosting luminous quasars in a post-merger phase

  6. X-RAY HIGH-RESOLUTION SPECTROSCOPY REVEALS FEEDBACK IN A SEYFERT GALAXY FROM AN ULTRA-FAST WIND WITH COMPLEX IONIZATION AND VELOCITY STRUCTURE

    Energy Technology Data Exchange (ETDEWEB)

    Longinotti, A. L. [Catedrática CONACYT—Instituto Nacional de Astrofísica, Óptica y Electrónica, Luis E. Erro 1, Tonantzintla, Puebla, C.P. 72840, México (Mexico); Krongold, Y. [Instituto de Astronomia, Universidad Nacional Autonoma de Mexico, Apartado Postal 70264, 04510 Mexico D.F. (Mexico); Guainazzi, M.; Santos-Lleo, M.; Rodriguez-Pascual, P. [ESAC, P.O. Box, 78 E-28691 Villanueva de la Cañada, Madrid (Spain); Giroletti, M. [INAF Osservatorio di Radioastronomia, via Gobetti 101, I-40129 Bologna (Italy); Panessa, F. [INAF—Istituto di Astrofisica e Planetologia Spaziali di Roma (IAPS), Via del Fosso del Cavaliere 100, I-00133 Roma (Italy); Costantini, E. [SRON Netherlands Institute for Space Research, Sorbonnelaan 2, 3584 CA Utrecht (Netherlands)

    2015-11-10

    Winds outflowing from active galactic nuclei (AGNs) may carry significant amounts of mass and energy out to their host galaxies. In this paper we report the detection of a sub-relativistic outflow observed in the narrow line Seyfert 1 galaxy IRAS 17020+4544 as a series of absorption lines corresponding to at least five absorption components with an unprecedented wide range of associated column densities and ionization levels and velocities in the range of 23,000–33,000 km s{sup −1}, detected at X-ray high spectral resolution (E/ΔE ∼ 1000) with the ESA's observatory XMM-Newton. The charge states of the material constituting the wind clearly indicate a range of low to moderate ionization states in the outflowing gas and column densities that are significantly lower than observed in highly ionized ultra-fast outflows. We estimate that at least one of the outflow components may carry sufficient energy to substantially suppress star formation and heat the gas in the host galaxy. IRAS 17020+4544 therefore provides an interesting example of feedback by a moderately luminous AGN that is hosted in a spiral galaxy, a case barely envisaged in most evolution models, which often predict that feedback processes take place in massive elliptical galaxies hosting luminous quasars in a post-merger phase.

  7. Teaching Structure-Property Relationships: Investigating Molecular Structure and Boiling Point

    Science.gov (United States)

    Murphy, Peter M.

    2007-01-01

    A concise, well-organized table of the boiling points of 392 organic compounds has facilitated inquiry-based instruction in multiple scientific principles. Many individual or group learning activities can be derived from the tabulated data of molecular structure and boiling point based on the instructor's education objectives and the students'…

  8. Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data

    Science.gov (United States)

    Wang, Yongcui; Chen, Shilong; Deng, Naiyang; Wang, Yong

    2013-01-01

    Computational inference of novel therapeutic values for existing drugs, i.e., drug repositioning, offers the great prospect for faster and low-risk drug development. Previous researches have indicated that chemical structures, target proteins, and side-effects could provide rich information in drug similarity assessment and further disease similarity. However, each single data source is important in its own way and data integration holds the great promise to reposition drug more accurately. Here, we propose a new method for drug repositioning, PreDR (Predict Drug Repositioning), to integrate molecular structure, molecular activity, and phenotype data. Specifically, we characterize drug by profiling in chemical structure, target protein, and side-effects space, and define a kernel function to correlate drugs with diseases. Then we train a support vector machine (SVM) to computationally predict novel drug-disease interactions. PreDR is validated on a well-established drug-disease network with 1,933 interactions among 593 drugs and 313 diseases. By cross-validation, we find that chemical structure, drug target, and side-effects information are all predictive for drug-disease relationships. More experimentally observed drug-disease interactions can be revealed by integrating these three data sources. Comparison with existing methods demonstrates that PreDR is competitive both in accuracy and coverage. Follow-up database search and pathway analysis indicate that our new predictions are worthy of further experimental validation. Particularly several novel predictions are supported by clinical trials databases and this shows the significant prospects of PreDR in future drug treatment. In conclusion, our new method, PreDR, can serve as a useful tool in drug discovery to efficiently identify novel drug-disease interactions. In addition, our heterogeneous data integration framework can be applied to other problems. PMID:24244318

  9. Chemistry and structure of giant molecular clouds in energetic environments

    Science.gov (United States)

    Anderson, Crystal Nicole

    2016-09-01

    Throughout the years many studies on Galactic star formation have been conducted. This resulted in the idea that giant molecular clouds (GMCs) are hierarchical in nature with substructures spanning a large range of sizes. The physical processes that determine how molecular clouds fragment, form clumps/cores and then stars depends strongly on both recent radiative and mechanical feed- back from massive stars and, on longer term, from enhanced cooling due to the buildup of metals. Radiative and mechanical energy input from stellar populations can alter subsequent star formation over a large part of a galaxy and hence is relevant to the evolution of galaxies. Much of our knowledge of star formation on galaxy wide scales is based on scaling laws and other parametric descriptions. But to understand the overall evolution of star formation in galaxies we need to watch the feedback processes at work on giant molecular cloud (GMC) scales. By doing this we can begin to answer how strong feedback environments change the properties of the substructure in GMCs. Tests of Galactic star formation theory to other galaxies has been a challenging process due to the lack of resolution with current instruments. Thus, only the nearest galaxies allow us to resolve GMCs and their substructures. The Large Magellanic Cloud (LMC), is one of the closest low metallicity dwarf galaxies (D˜ 50 kpc) and is close enough that current instruments can resolve the sub- structure of its GMCs to molecular gas tracers (e.g. HCO+, HCN, HNC, CS, C2H, N2H+) detected in the LMC at 1.5-40 pc scales and in NGC 5253 at 40 pc scales. I then compare the molecular gas detections to the Central Molecular Zone in our Galaxy. Dense molecular gas was detected in all of the sources. For the regions in the LMC, molecular lines of CS, N2H+, C 2H, HNC, HCO+ and HCN were all detected in N159W and N113 while only HCN, HCO+, HNC, and C2H were detected in 30Dor-10. Toward NGC 5253 only HCO+, HCN, C2H and CS were detected. I

  10. Functional Annotation of Ion Channel Structures by Molecular Simulation.

    Science.gov (United States)

    Trick, Jemma L; Chelvaniththilan, Sivapalan; Klesse, Gianni; Aryal, Prafulla; Wallace, E Jayne; Tucker, Stephen J; Sansom, Mark S P

    2016-12-06

    Ion channels play key roles in cell membranes, and recent advances are yielding an increasing number of structures. However, their functional relevance is often unclear and better tools are required for their functional annotation. In sub-nanometer pores such as ion channels, hydrophobic gating has been shown to promote dewetting to produce a functionally closed (i.e., non-conductive) state. Using the serotonin receptor (5-HT 3 R) structure as an example, we demonstrate the use of molecular dynamics to aid the functional annotation of channel structures via simulation of the behavior of water within the pore. Three increasingly complex simulation analyses are described: water equilibrium densities; single-ion free-energy profiles; and computational electrophysiology. All three approaches correctly predict the 5-HT 3 R crystal structure to represent a functionally closed (i.e., non-conductive) state. We also illustrate the application of water equilibrium density simulations to annotate different conformational states of a glycine receptor. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. Dynamics of liquids, molecules, and proteins measured with ultrafast 2D IR vibrational echo chemical exchange spectroscopy.

    Science.gov (United States)

    Fayer, M D

    2009-01-01

    A wide variety of molecular systems undergo fast structural changes under thermal equilibrium conditions. Such transformations are involved in a vast array of chemical problems. Experimentally measuring equilibrium dynamics is a challenging problem that is at the forefront of chemical research. This review describes ultrafast 2D IR vibrational echo chemical exchange experiments and applies them to several types of molecular systems. The formation and dissociation of organic solute-solvent complexes are directly observed. The dissociation times of 13 complexes, ranging from 4 ps to 140 ps, are shown to obey a relationship that depends on the complex's formation enthalpy. The rate of rotational gauche-trans isomerization around a carbon-carbon single bond is determined for a substituted ethane at room temperature in a low viscosity solvent. The results are used to obtain an approximate isomerization rate for ethane. Finally, the time dependence of a well-defined single structural transformation of a protein is measured.

  12. Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

    Directory of Open Access Journals (Sweden)

    Aparecido R. Silva

    2008-05-01

    Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

  13. Molecular structures from density functional calculations with simulated annealing

    International Nuclear Information System (INIS)

    Jones, R.O.

    1991-01-01

    The geometrical structure of any aggregate of atoms is one of its basic properties and, in principle, straightforward to predict. One chooses a structure, determines the total energy E of the system of electrons and ions, and repeats the calculation for all possible geometries. The ground state structure is that with the lowest energy. A quantum mechanical calculation of the exact wave function Ψ would lead to the total energy, but this is practicable only in very small molecules. Furthermore, the number of local minima in the energy surface increases dramatically with increasing molecular size. While traditional ab initio methods have had many impressive successes, the difficulties have meant that they have focused on systems with relatively few local minima, or have used experiments or experience to limit the range of geometries studied. On the other hand, calculations for much larger molecules and extended systems are often forced to use simplifying assumptions about the interatomic forces that limit their predictive capability. The approach described here avoids both of these extremes: Total energies of predictive value are calculated without using semi-empirical force laws, and the problem of multiple minima in the energy surface is addressed. The density functional formalism, with a local density approximation for the exchange-correlation energy, allows one to calculate the total energy for a given geometry in an efficient, if approximate, manner. Calculations for heavier elements are not significantly more difficult than for those in the first row and provide an ideal way to study bonding trends. When coupled with finite-temperature molecular dynamics, this formalism can avoid many of the energetically unfavorable minima in the energy surface. We show here that the method leads to surprising and exciting results. (orig.)

  14. Mathematical analysis of compressive/tensile molecular and nuclear structures

    Science.gov (United States)

    Wang, Dayu

    Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

  15. Ultrafast vibrations of gold nanorings

    DEFF Research Database (Denmark)

    Kelf, T; Tanaka, Y; Matsuda, O

    2011-01-01

    We investigate the vibrational modes of gold nanorings on a silica substrate with an ultrafast optical technique. By comparison with numerical simulations, we identify several resonances in the gigahertz range associated with axially symmetric deformations of the nanoring and substrate. We...

  16. Ultrafast spectroscopy of biological photoreceptors

    NARCIS (Netherlands)

    Kennis, J.T.M.; Groot, M.L.

    2007-01-01

    We review recent new insights on reaction dynamics of photoreceptors proteins gained from ultrafast spectroscopy. In Blue Light sensing Using FAD (BLUF) domains, a hydrogen-bond rearrangement around the flavin chromophore proceeds through a radical-pair mechanism, by which light-induced electron and

  17. Ultrafast Spectroscopy of Semiconductor Devices

    DEFF Research Database (Denmark)

    Borri, Paola; Langbein, Wolfgang; Hvam, Jørn Marcher

    1999-01-01

    In this work we present an experimental technique for investigating ultrafast carrier dynamics in semiconductor optical amplifiers at room temperature. These dynamics, influenced by carrier heating, spectral hole-burning and two-photon absorption, are very important for device applications in inf...

  18. Ultrafast vibrations of gold nanorings

    DEFF Research Database (Denmark)

    Kelf, T; Tanaka, Y; Matsuda, O

    2011-01-01

    We investigate the vibrational modes of gold nanorings on a silica substrate with an ultrafast optical technique. By comparison with numerical simulations, we identify several resonances in the gigahertz range associated with axially symmetric deformations of the nanoring and substrate. We elucid...

  19. Catecholaminergic systems in stress: structural and molecular genetic approaches.

    Science.gov (United States)

    Kvetnansky, Richard; Sabban, Esther L; Palkovits, Miklos

    2009-04-01

    Stressful stimuli evoke complex endocrine, autonomic, and behavioral responses that are extremely variable and specific depending on the type and nature of the stressors. We first provide a short overview of physiology, biochemistry, and molecular genetics of sympatho-adrenomedullary, sympatho-neural, and brain catecholaminergic systems. Important processes of catecholamine biosynthesis, storage, release, secretion, uptake, reuptake, degradation, and transporters in acutely or chronically stressed organisms are described. We emphasize the structural variability of catecholamine systems and the molecular genetics of enzymes involved in biosynthesis and degradation of catecholamines and transporters. Characterization of enzyme gene promoters, transcriptional and posttranscriptional mechanisms, transcription factors, gene expression and protein translation, as well as different phases of stress-activated transcription and quantitative determination of mRNA levels in stressed organisms are discussed. Data from catecholamine enzyme gene knockout mice are shown. Interaction of catecholaminergic systems with other neurotransmitter and hormonal systems are discussed. We describe the effects of homotypic and heterotypic stressors, adaptation and maladaptation of the organism, and the specificity of stressors (physical, emotional, metabolic, etc.) on activation of catecholaminergic systems at all levels from plasma catecholamines to gene expression of catecholamine enzymes. We also discuss cross-adaptation and the effect of novel heterotypic stressors on organisms adapted to long-term monotypic stressors. The extra-adrenal nonneuronal adrenergic system is described. Stress-related central neuronal regulatory circuits and central organization of responses to various stressors are presented with selected examples of regulatory molecular mechanisms. Data summarized here indicate that catecholaminergic systems are activated in different ways following exposure to distinct

  20. Ultrafast Microscopy of Energy and Charge Transport

    Science.gov (United States)

    Huang, Libai

    The frontier in solar energy research now lies in learning how to integrate functional entities across multiple length scales to create optimal devices. Advancing the field requires transformative experimental tools that probe energy transfer processes from the nano to the meso lengthscales. To address this challenge, we aim to understand multi-scale energy transport across both multiple length and time scales, coupling simultaneous high spatial, structural, and temporal resolution. In my talk, I will focus on our recent progress on visualization of exciton and charge transport in solar energy harvesting materials from the nano to mesoscale employing ultrafast optical nanoscopy. With approaches that combine spatial and temporal resolutions, we have recently revealed a new singlet-mediated triplet transport mechanism in certain singlet fission materials. This work demonstrates a new triplet exciton transport mechanism leading to favorable long-range triplet exciton diffusion on the picosecond and nanosecond timescales for solar cell applications. We have also performed a direct measurement of carrier transport in space and in time by mapping carrier density with simultaneous ultrafast time resolution and 50 nm spatial precision in perovskite thin films using transient absorption microscopy. These results directly visualize long-range carrier transport of 220nm in 2 ns for solution-processed polycrystalline CH3NH3PbI3 thin films. The spatially and temporally resolved measurements reported here underscore the importance of the local morphology and establish an important first step towards discerning the underlying transport properties of perovskite materials.

  1. A US Based Ultrafast Interdisciplinary Research Facility

    Science.gov (United States)

    Gueye, Paul; Hill, Wendell; Johnson, Anthony

    2006-10-01

    The US scientific competitiveness on the world arena has substantially decreased due to the lack of funding and training of qualified personnel. Most of the potential workforce found in higher education is composed of foreign students and post-docs. In the specific field of low- and high-field science, the European and Asian communities are rapidly catching-up with the US, even leading in some areas. To remain the leader in ultrafast science and technology, new visions and commitment must be embraced. For that reason, an international effort of more than 70 countries for a US-based interdisciplinary research facility using ultrafast laser technology is under development. It will provide research and educational training, as well as new venues for a strong collaboration between the fields of astrophysics, nuclear/high energy physics, plasma physics, optical sciences, biological and medical physics. This facility will consist of a uniquely designed high contrast multi-lines concept housing twenty experimental rooms shared between four beams:[0.1 TW, 1 kHz], [10 TW, 9 kHz], [100-200 TW, 10 Hz] and [500 TW, 10 Hz]. The detail schematic of this multi-laser system, foreseen research and educational programs, and organizational structure of this facility will be presented.

  2. Solving structures of protein complexes by molecular replacement with Phaser

    International Nuclear Information System (INIS)

    McCoy, Airlie J.

    2006-01-01

    Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described. Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ‘tree search with pruning’ approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ‘automated MR’ mode and two case studies are used to show how to modify the automated search strategy for problematic cases

  3. Introductory group theory and its application to molecular structure

    CERN Document Server

    Ferraro, John R

    1975-01-01

    The success of the first edition of this book has encouraged us to revise and update it. In the second edition we have attempted to further clarify por­ tions of the text in reference to point symmetry, keeping certain sections and removing others. The ever-expanding interest in solids necessitates some discussion on space symmetry. In this edition we have expanded the discus­ sion on point symmetry to include space symmetry. The selection rules in­ clude space group selection rules (for k = 0). Numerous examples are pro­ vided to acquaint the reader with the procedure necessary to accomplish this. Recent examples from the literature are given to illustrate the use of group theory in the interpretation of molecular spectra and in the determination of molecular structure. The text is intended for scientists and students with only a limited theoretical background in spectroscopy. For this reason we have presented detailed procedures for carrying out the selection rules and normal coor­ dinate treatment of ...

  4. Molecular Origin of the Vibrational Structure of Ice Ih.

    Science.gov (United States)

    Moberg, Daniel R; Straight, Shelby C; Knight, Christopher; Paesani, Francesco

    2017-06-15

    An unambiguous assignment of the vibrational spectra of ice I h remains a matter of debate. This study demonstrates that an accurate representation of many-body interactions between water molecules, combined with an explicit treatment of nuclear quantum effects through many-body molecular dynamics (MB-MD), leads to a unified interpretation of the vibrational spectra of ice I h in terms of the structure and dynamics of the underlying hydrogen-bond network. All features of the infrared and Raman spectra in the OH stretching region can be unambiguously assigned by taking into account both the symmetry and the delocalized nature of the lattice vibrations as well as the local electrostatic environment experienced by each water molecule within the crystal. The high level of agreement with experiment raises prospects for predictive MB-MD simulations that, complementing analogous measurements, will provide molecular-level insights into fundamental processes taking place in bulk ice and on ice surfaces under different thermodynamic conditions.

  5. Effect of processing on carbon molecular sieve structure and performance

    KAUST Repository

    Das, Mita; Perry, John D.; Koros, William J.

    2010-01-01

    Sub-micron sized carbon molecular sieve (CMS) materials were produced via ball milling for subsequent use in hybrid material formation. A detailed analysis of the effects of the milling process in the presence of different milling environments is reported. The milling process apparently alters the molecular scale structure and properties of the carbon material. Three cases: unmilled, air milled and nitrogen milled, were analyzed in this work. The property changes were probed using equilibrium sorption experiments with different gases. Furthermore, WAXD and BET results also showed differences between milling processes. Finally in order to improve the interfacial polymer-sieve region of hybrid membranes, the CMS surface was chemically modified with a linkage unit capable of covalently bonding the polymer to the sieve. A published single-wall carbon nanotube (SWCNTs) modification method was adopted to attach a primary aromatic amine to the surface. Several aspects including rigidity, chemical composition, bulky groups and length were considered in selecting the preferred linkage unit. Fortunately kinetic and equilibrium sorption properties of the modified sieves showed very little difference from unmodified samples, suggesting that the linkage unit is not excessively filling or obstructing access to the pores of the CMSs during the modification process. © 2010 Elsevier Ltd. All rights reserved.

  6. Effect of processing on carbon molecular sieve structure and performance

    KAUST Repository

    Das, Mita

    2010-11-01

    Sub-micron sized carbon molecular sieve (CMS) materials were produced via ball milling for subsequent use in hybrid material formation. A detailed analysis of the effects of the milling process in the presence of different milling environments is reported. The milling process apparently alters the molecular scale structure and properties of the carbon material. Three cases: unmilled, air milled and nitrogen milled, were analyzed in this work. The property changes were probed using equilibrium sorption experiments with different gases. Furthermore, WAXD and BET results also showed differences between milling processes. Finally in order to improve the interfacial polymer-sieve region of hybrid membranes, the CMS surface was chemically modified with a linkage unit capable of covalently bonding the polymer to the sieve. A published single-wall carbon nanotube (SWCNTs) modification method was adopted to attach a primary aromatic amine to the surface. Several aspects including rigidity, chemical composition, bulky groups and length were considered in selecting the preferred linkage unit. Fortunately kinetic and equilibrium sorption properties of the modified sieves showed very little difference from unmodified samples, suggesting that the linkage unit is not excessively filling or obstructing access to the pores of the CMSs during the modification process. © 2010 Elsevier Ltd. All rights reserved.

  7. Electronic structure and molecular dynamics of Na2Li

    Science.gov (United States)

    Malcolm, Nathaniel O. J.; McDouall, Joseph J. W.

    Following the first report (Mile, B., Sillman, P. D., Yacob, A. R. and Howard, J. A., 1996, J. chem. Soc. Dalton Trans , 653) of the EPR spectrum of the mixed alkali-metal trimer Na2Li a detailed study has been made of the electronic structure and structural dynamics of this species. Two isomeric forms have been found: one of the type, Na-Li-Na, of C , symmetry and another, Li-Na-Na, of C symmetry. Also, there are two linear saddle points which correspond to 'inversion' transition structures, and a saddle point of C symmetry which connects the two minima. A molecular dynamics investigation of these species shows that, at the temperature of the reported experiments (170 K), the C minimum is not 'static', but undergoes quite rapid inversion. At higher temperatures the C minimum converts to the C form, but by a mechanism very different from that suggested by minimum energy path considerations. 2 2v s s 2v 2v s

  8. Transmission electron microscopy in molecular structural biology: A historical survey.

    Science.gov (United States)

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Coding considerations for standalone molecular dynamics simulations of atomistic structures

    Science.gov (United States)

    Ocaya, R. O.; Terblans, J. J.

    2017-10-01

    The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

  10. On the nodal structure of atomic and molecular Wigner functions

    International Nuclear Information System (INIS)

    Dahl, J.P.; Schmider, H.

    1996-01-01

    In previous work on the phase-space representation of quantum mechanics, we have presented detailed pictures of the electronic one-particle reduced Wigner function for atoms and small molecules. In this communication, we focus upon the nodal structure of the function. On the basis of the simplest systems, we present an expression which relates the oscillatory decay of the Wigner function solely to the dot product of the position and momentum vector, if both arguments are large. We then demonstrate the regular behavior of nodal patterns for the larger systems. For the molecular systems, an argument analogous to the open-quotes bond-oscillatory principleclose quotes for momentum densities links the nuclear framework to an additional oscillatory term in momenta parallel to bonds. It is shown that these are visible in the Wigner function in terms of characteristic nodes

  11. Influence of the molecular structure on hydrolyzability of epoxy resins

    International Nuclear Information System (INIS)

    Pays, M.F.

    1996-01-01

    EDF has decided to use glass reinforced composites for certain pipework in Pressurized Water Reactors (service water, emergency-supplied service water, fine pipe works, etc...) as a replacement for traditional materials. In practice, steel is prone to rapid corrosion in these circuits; introducing composites could prove economically viable if their long term behaviour can be demonstrated. However, composite materials can undergo deterioration in service through hydrolysis of the resin or the fibre-matrix interface. Different resins can be chosen depending on the programmed use. A first study has covered the hydrolyzability of polyester and vinyl ester resins. The present document undertakes the resistance to hydrolysis of epoxy resins, concentrating on those reputed to withstand high temperatures. This research uses model monomer, linking the molecular structure of the materials to their resistance to hydrolysis. (author)

  12. Calculations of optical rotation: Influence of molecular structure

    Directory of Open Access Journals (Sweden)

    Yu Jia

    2012-01-01

    Full Text Available Ab initio Hartree-Fock (HF method and Density Functional Theory (DFT were used to calculate the optical rotation of 26 chiral compounds. The effects of theory and basis sets used for calculation, solvents influence on the geometry and values of calculated optical rotation were all discussed. The polarizable continuum model, included in the calculation, did not improve the accuracy effectively, but it was superior to γs. Optical rotation of five or sixmembered of cyclic compound has been calculated and 17 pyrrolidine or piperidine derivatives which were calculated by HF and DFT methods gave acceptable predictions. The nitrogen atom affects the calculation results dramatically, and it is necessary in the molecular structure in order to get an accurate computation result. Namely, when the nitrogen atom was substituted by oxygen atom in the ring, the calculation result deteriorated.

  13. Hamiltonian flow over saddles for exploring molecular phase space structures

    Science.gov (United States)

    Farantos, Stavros C.

    2018-03-01

    Despite using potential energy surfaces, multivariable functions on molecular configuration space, to comprehend chemical dynamics for decades, the real happenings in molecules occur in phase space, in which the states of a classical dynamical system are completely determined by the coordinates and their conjugate momenta. Theoretical and numerical results are presented, employing alanine dipeptide as a model system, to support the view that geometrical structures in phase space dictate the dynamics of molecules, the fingerprints of which are traced by following the Hamiltonian flow above saddles. By properly selecting initial conditions in alanine dipeptide, we have found internally free rotor trajectories the existence of which can only be justified in a phase space perspective. This article is part of the theme issue `Modern theoretical chemistry'.

  14. Mode-dependent dispersion in Raman line shapes: Observation and implications from ultrafast Raman loss spectroscopy

    International Nuclear Information System (INIS)

    Umapathy, S.; Mallick, B.; Lakshmanna, A.

    2010-01-01

    Ultrafast Raman loss spectroscopy (URLS) enables one to obtain the vibrational structural information of molecular systems including fluorescent materials. URLS, a nonlinear process analog to stimulated Raman gain, involves a narrow bandwidth picosecond Raman pump pulse and a femtosecond broadband white light continuum. Under nonresonant condition, the Raman response appears as a negative (loss) signal, whereas, on resonance with the electronic transition the line shape changes from a negative to a positive through a dispersive form. The intensities observed and thus, the Franck-Condon activity (coordinate dependent), are sensitive to the wavelength of the white light corresponding to a particular Raman frequency with respect to the Raman pump pulse wavelength, i.e., there is a mode-dependent response in URLS.

  15. Ultrafast dynamics of colloidal semiconductor nanocrystals relevant to solar fuels production

    Science.gov (United States)

    Cogan, Nicole M. B.; Liu, Cunming; Qiu, Fen; Burke, Rebeckah; Krauss, Todd D.

    2017-05-01

    Artificial conversion of sunlight to chemical fuels has attracted attention for several decades as a potential source of clean, renewable energy. We recently found that CdSe quantum dots (QDs) and simple aqueous Ni2+ salts in the presence of a sacrificial electron donor form a highly efficient, active, and robust system for photochemical reduction of protons to molecular hydrogen. Ultrafast transient absorption spectroscopy studies of electron transfer (ET) processes from the QDs to the Ni catalysts reveal extremely fast ET, and provide a fundamental explanation for the exceptional photocatalytic H2 activity. Additionally, by studying H2 production of the Ni catalyst with CdSe/CdS nanoparticles of various structures, it was determined that surface charge density plays an important role in charge transfer and ultimately H2 production activity.

  16. Determining the stereochemical structures of molecular ions by ''Coulomb-explosion'' techniques with fast (MeV) molecular ion beams

    International Nuclear Information System (INIS)

    Gemmell, D.S.

    1980-01-01

    Recent studies on the dissociation of fast (MeV) molecular ion beams in thin foils suggest a novel alternative approach to the determination of molecular ion structures. In this article we review some recent high-resolution studies on the interactions of fast molecular ion beams with solid and gaseous targets and indicate how such studies may be applied to the problem of determining molecular ion structures. The main features of the Coulomb explosion of fast-moving molecular ion projectiles and the manner in which Coulomb-explosion techniques may be applied to the problem (difficult to attack by more conventional means) of determining the stereochemical structures of molecular ions has been described in this paper. Examples have been given of early experiments designed to elicit structure information. The techniques are still in their infancy, and it is to be expected that as both the technology and the analysis are refined, the method will make valuable contributions to the determination of molecular ion structures

  17. Ultrafast dynamics and laser action of organic semiconductors

    CERN Document Server

    Vardeny, Zeev Valy

    2009-01-01

    Spurred on by extensive research in recent years, organic semiconductors are now used in an array of areas, such as organic light emitting diodes (OLEDs), photovoltaics, and other optoelectronics. In all of these novel applications, the photoexcitations in organic semiconductors play a vital role. Exploring the early stages of photoexcitations that follow photon absorption, Ultrafast Dynamics and Laser Action of Organic Semiconductors presents the latest research investigations on photoexcitation ultrafast dynamics and laser action in pi-conjugated polymer films, solutions, and microcavities.In the first few chapters, the book examines the interplay of charge (polarons) and neutral (excitons) photoexcitations in pi-conjugated polymers, oligomers, and molecular crystals in the time domain of 100 fs-2 ns. Summarizing the state of the art in lasing, the final chapters introduce the phenomenon of laser action in organics and cover the latest optoelectronic applications that use lasing based on a variety of caviti...

  18. Physical chemistry: Molecular motion watched

    Science.gov (United States)

    Siwick, Bradley; Collet, Eric

    2013-04-01

    A laser pulse can switch certain crystals from an insulating phase to a highly conducting phase. The ultrafast molecular motions that drive the transition have been directly observed using electron diffraction. See Letter p.343

  19. Ultrafast Librational Relaxation of H2O in Liquid Water

    DEFF Research Database (Denmark)

    Petersen, Jakob; Møller, Klaus Braagaard; Rey, Rossend

    2013-01-01

    The ultrafast librational (hindered rotational) relaxation of a rotationally excited H2O molecule in pure liquid water is investigated by means of classical nonequilibrium molecular dynamics simulations and a power and work analysis. This analysis allows the mechanism of the energy transfer from...... the excited H2O to its water neighbors, which occurs on a sub-100 fs time scale, to be followed in molecular detail, i.e., to determine which water molecules receive the energy and in which degrees of freedom. It is found that the dominant energy flow is to the four hydrogen-bonded water partners in the first...

  20. Coherent structural trapping through wave packet dispersion during photoinduced spin state switching

    DEFF Research Database (Denmark)

    Lemke, Henrik T.; Kjær, Kasper Skov; Hartsock, Robert

    2017-01-01

    The description of ultrafast nonadiabatic chemical dynamics during molecular photo-transformations remains challenging because electronic and nuclear configurations impact each other and cannot be treated independently. Here we gain experimental insights, beyond the Born-Oppenheimer approximation...... is distinguished from the structural trapping dynamics, which launches a coherent oscillating wave packet (265 fs period), clearly identified as molecular breathing. Throughout the structural trapping, the dispersion of the wave packet along the reaction coordinate reveals details of intramolecular vibronic...

  1. Structural and molecular basis of starch viscosity in hexaploid wheat.

    Science.gov (United States)

    Ral, J-P; Cavanagh, C R; Larroque, O; Regina, A; Morell, M K

    2008-06-11

    Wheat starch is considered to have a low paste viscosity relative to other starches. Consequently, wheat starch is not preferred for many applications as compared to other high paste viscosity starches. Increasing the viscosity of wheat starch is expected to increase the functionality of a range of wheat flour-based products in which the texture is an important aspect of consumer acceptance (e.g., pasta, and instant and yellow alkaline noodles). To understand the molecular basis of starch viscosity, we have undertaken a comprehensive structural and rheological analysis of starches from a genetically diverse set of wheat genotypes, which revealed significant variation in starch traits including starch granule protein content, starch-associated lipid content and composition, phosphate content, and the structures of the amylose and amylopectin fractions. Statistical analysis highlighted the association between amylopectin chains of 18-25 glucose residues and starch pasting properties. Principal component analysis also identified an association between monoesterified phosphate and starch pasting properties in wheat despite the low starch-phosphate level in wheat as compared to tuber starches. We also found a strong negative correlation between the phosphate ester content and the starch content in flour. Previously observed associations between internal starch granule fatty acids and the swelling peak time and pasting temperature have been confirmed. This study has highlighted a range of parameters associated with increased starch viscosity that could be used in prebreeding/breeding programs to modify wheat starch pasting properties.

  2. Fast electronic structure methods for strongly correlated molecular systems

    International Nuclear Information System (INIS)

    Head-Gordon, Martin; Beran, Gregory J O; Sodt, Alex; Jung, Yousung

    2005-01-01

    A short review is given of newly developed fast electronic structure methods that are designed to treat molecular systems with strong electron correlations, such as diradicaloid molecules, for which standard electronic structure methods such as density functional theory are inadequate. These new local correlation methods are based on coupled cluster theory within a perfect pairing active space, containing either a linear or quadratic number of pair correlation amplitudes, to yield the perfect pairing (PP) and imperfect pairing (IP) models. This reduces the scaling of the coupled cluster iterations to no worse than cubic, relative to the sixth power dependence of the usual (untruncated) coupled cluster doubles model. A second order perturbation correction, PP(2), to treat the neglected (weaker) correlations is formulated for the PP model. To ensure minimal prefactors, in addition to favorable size-scaling, highly efficient implementations of PP, IP and PP(2) have been completed, using auxiliary basis expansions. This yields speedups of almost an order of magnitude over the best alternatives using 4-center 2-electron integrals. A short discussion of the scope of accessible chemical applications is given

  3. Molecular structure-adsorption study on current textile dyes.

    Science.gov (United States)

    Örücü, E; Tugcu, G; Saçan, M T

    2014-01-01

    This study was performed to investigate the adsorption of a diverse set of textile dyes onto granulated activated carbon (GAC). The adsorption experiments were carried out in a batch system. The Langmuir and Freundlich isotherm models were applied to experimental data and the isotherm constants were calculated for 33 anthraquinone and azo dyes. The adsorption equilibrium data fitted more adequately to the Langmuir isotherm model than the Freundlich isotherm model. Added to a qualitative analysis of experimental results, multiple linear regression (MLR), support vector regression (SVR) and back propagation neural network (BPNN) methods were used to develop quantitative structure-property relationship (QSPR) models with the novel adsorption data. The data were divided randomly into training and test sets. The predictive ability of all models was evaluated using the test set. Descriptors were selected with a genetic algorithm (GA) using QSARINS software. Results related to QSPR models on the adsorption capacity of GAC showed that molecular structure of dyes was represented by ionization potential based on two-dimensional topological distances, chromophoric features and a property filter index. Comparison of the performance of the models demonstrated the superiority of the BPNN over GA-MLR and SVR models.

  4. Molecular structure of tetramethylgermane from gas electron diffraction

    Science.gov (United States)

    Csákvári, Éva; Rozsondai, Béla; Hargittai, István

    1991-05-01

    The molecular structure of Ge(CH 3) 4 has been determined from gas-phase electron diffraction augmented by a normal coordinate analysis. Assuming tetrahedral symmetry for the germanium bond configuration, the following structural parameters are found: rg(GeC) = 1.958 ± 0.004 Å, rg(CH) = 1.111 ± 0.003 Å and ∠(GeCH) = 110.7 ± 0.2° ( R=4.0%). The methyl torsional barrier V 0 is estimated to be 1.3 kJ mol -1 on the basis of an effective angle of torsion 23.0 ± 1.5°, from the staggered form, yielded directly by the analysis. The GeC bond length of Ge(CH 3) 4 is the same, within experimental error, as that of Ge(C 6H 5) 4 and is in agreement with the prediction of a modified Schomaker-Stevenson relationship.

  5. Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

    Science.gov (United States)

    Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2012-06-01

    The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

  6. Bonding and structure in dense multi-component molecular mixtures.

    Science.gov (United States)

    Meyer, Edmund R; Ticknor, Christopher; Bethkenhagen, Mandy; Hamel, Sebastien; Redmer, Ronald; Kress, Joel D; Collins, Lee A

    2015-10-28

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10,000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systems engendered by variations in the concentration ratios. A basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.

  7. Molecular clouds in the North American and Pelican Nebulae: structures

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shaobo; Xu, Ye; Yang, Ji, E-mail: shbzhang@pmo.ac.cn [Purple Mountain Observatory, and Key Laboratory for Radio Astronomy, Chinese Academy of Sciences, Nanjing 210008 (China)

    2014-03-01

    We present observations of a 4.25 deg{sup 2} area toward the North American and Pelican Nebulae in the J = 1-0 transitions of {sup 12}CO, {sup 13}CO, and C{sup 18}O. Three molecules show different emission areas with their own distinct structures. These different density tracers reveal several dense clouds with a surface density of over 500 M {sub ☉} pc{sup –2} and a mean H{sub 2} column density of 5.8, 3.4, and 11.9 × 10{sup 21} cm{sup –2} for {sup 12}CO, {sup 13}CO, and C{sup 18}O, respectively. We obtain a total mass of 5.4 × 10{sup 4} M {sub ☉} ({sup 12}CO), 2.0 × 10{sup 4} M {sub ☉} ({sup 13}CO), and 6.1 × 10{sup 3} M {sub ☉} (C{sup 18}O) in the complex. The distribution of excitation temperature shows two phases of gas: cold gas (∼10 K) spreads across the whole cloud; warm gas (>20 K) outlines the edge of the cloud heated by the W80 H II region. The kinetic structure of the cloud indicates an expanding shell surrounding the ionized gas produced by the H II region. There are six discernible regions in the cloud: the Gulf of Mexico, Caribbean Islands and Sea, and Pelican's Beak, Hat, and Neck. The areas of {sup 13}CO emission range within 2-10 pc{sup 2} with mass of (1-5) × 10{sup 3} M {sub ☉} and line width of a few km s{sup –1}. The different line properties and signs of star-forming activity indicate they are in different evolutionary stages. Four filamentary structures with complicated velocity features are detected along the dark lane in LDN 935. Furthermore, a total of 611 molecular clumps within the {sup 13}CO tracing cloud are identified using the ClumpFind algorithm. The properties of the clumps suggest that most of the clumps are gravitationally bound and at an early stage of evolution with cold and dense molecular gas.

  8. Ultrafast proton shuttling in Psammocora cyan fluorescent protein.

    Science.gov (United States)

    Kennis, John T M; van Stokkum, Ivo H M; Peterson, Dayna S; Pandit, Anjali; Wachter, Rebekka M

    2013-09-26

    Cyan, green, yellow, and red fluorescent proteins (FPs) homologous to green fluorescent protein (GFP) are used extensively as model systems to study fundamental processes in photobiology, such as the capture of light energy by protein-embedded chromophores, color tuning by the protein matrix, energy conversion by Förster resonance energy transfer (FRET), and excited-state proton transfer (ESPT) reactions. Recently, a novel cyan fluorescent protein (CFP) termed psamFP488 was isolated from the genus Psammocora of reef building corals. Within the cyan color class, psamFP488 is unusual because it exhibits a significantly extended Stokes shift. Here, we applied ultrafast transient absorption and pump-dump-probe spectroscopy to investigate the mechanistic basis of psamFP488 fluorescence, complemented with fluorescence quantum yield and dynamic light scattering measurements. Transient absorption spectroscopy indicated that, upon excitation at 410 nm, the stimulated cyan emission rises in 170 fs. With pump-dump-probe spectroscopy, we observe a very short-lived (110 fs) ground-state intermediate that we assign to the deprotonated, anionic chromophore. In addition, a minor fraction (14%) decays with 3.5 ps to the ground state. Structural analysis of homologous proteins indicates that Glu-167 is likely positioned in sufficiently close vicinity to the chromophore to act as a proton acceptor. Our findings support a model where unusually fast ESPT from the neutral chromophore to Glu-167 with a time constant of 170 fs and resulting emission from the anionic chromophore forms the basis of the large psamFP488 Stokes shift. When dumped to the ground state, the proton on neutral Glu is very rapidly shuttled back to the anionic chromophore in 110 fs. Proton shuttling in excited and ground states is a factor of 20-4000 faster than in GFP, which probably results from a favorable hydrogen-bonding geometry between the chromophore phenolic oxygen and the glutamate acceptor, possibly

  9. Real-time control of ultrafast laser micromachining by laser-induced breakdown spectroscopy

    International Nuclear Information System (INIS)

    Tong Tao; Li Jinggao; Longtin, Jon P.

    2004-01-01

    Ultrafast laser micromachining provides many advantages for precision micromachining. One challenging problem, however, particularly for multilayer and heterogeneous materials, is how to prevent a given material from being ablated, as ultrafast laser micromachining is generally material insensitive. We present a real-time feedback control system for an ultrafast laser micromachining system based on laser-induced breakdown spectroscopy (LIBS). The characteristics of ultrafast LIBS are reviewed and discussed so as to demonstrate the feasibility of the technique. Comparison methods to identify the material emission patterns are developed, and several of the resulting algorithms were implemented into a real-time computer control system. LIBS-controlled micromachining is demonstrated for the fabrication of microheater structures on thermal sprayed materials. Compared with a strictly passive machining process without any such feedback control, the LIBS-based system provides several advantages including less damage to the substrate layer, reduced machining time, and more-uniform machining features

  10. Mega-electron-volt ultrafast electron diffraction at SLAC National Accelerator Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Weathersby, S. P.; Brown, G.; Chase, T. F.; Coffee, R.; Corbett, J.; Eichner, J. P.; Frisch, J. C.; Fry, A. R.; Gühr, M.; Hartmann, N.; Hast, C.; Hettel, R.; Jobe, R. K.; Jongewaard, E. N.; Lewandowski, J. R.; Li, R. K., E-mail: lrk@slac.stanford.edu; Lindenberg, A. M.; Makasyuk, I.; May, J. E.; McCormick, D. [SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025 (United States); and others

    2015-07-15

    Ultrafast electron probes are powerful tools, complementary to x-ray free-electron lasers, used to study structural dynamics in material, chemical, and biological sciences. High brightness, relativistic electron beams with femtosecond pulse duration can resolve details of the dynamic processes on atomic time and length scales. SLAC National Accelerator Laboratory recently launched the Ultrafast Electron Diffraction (UED) and microscopy Initiative aiming at developing the next generation ultrafast electron scattering instruments. As the first stage of the Initiative, a mega-electron-volt (MeV) UED system has been constructed and commissioned to serve ultrafast science experiments and instrumentation development. The system operates at 120-Hz repetition rate with outstanding performance. In this paper, we report on the SLAC MeV UED system and its performance, including the reciprocal space resolution, temporal resolution, and machine stability.

  11. Fast events in protein folding: structural volume changes accompanying the early events in the N-->I transition of apomyoglobin induced by ultrafast pH jump.

    Science.gov (United States)

    Abbruzzetti, S; Crema, E; Masino, L; Vecli, A; Viappiani, C; Small, J R; Libertini, L J; Small, E W

    2000-01-01

    Ultrafast, laser-induced pH jump with time-resolved photoacoustic detection has been used to investigate the early protonation steps leading to the formation of the compact acid intermediate (I) of apomyoglobin (ApoMb). When ApoMb is in its native state (N) at pH 7.0, rapid acidification induced by a laser pulse leads to two parallel protonation processes. One reaction can be attributed to the binding of protons to the imidazole rings of His24 and His119. Reaction with imidazole leads to an unusually large contraction of -82 +/- 3 ml/mol, an enthalpy change of 8 +/- 1 kcal/mol, and an apparent bimolecular rate constant of (0.77 +/- 0.03) x 10(10) M(-1) s(-1). Our experiments evidence a rate-limiting step for this process at high ApoMb concentrations, characterized by a value of (0. 60 +/- 0.07) x 10(6) s(-1). The second protonation reaction at pH 7. 0 can be attributed to neutralization of carboxylate groups and is accompanied by an apparent expansion of 3.4 +/- 0.2 ml/mol, occurring with an apparent bimolecular rate constant of (1.25 +/- 0.02) x 10(11) M(-1) s(-1), and a reaction enthalpy of about 2 kcal/mol. The activation energy for the processes associated with the protonation of His24 and His119 is 16.2 +/- 0.9 kcal/mol, whereas that for the neutralization of carboxylates is 9.2 +/- 0.9 kcal/mol. At pH 4.5 ApoMb is in a partially unfolded state (I) and rapid acidification experiments evidence only the process assigned to carboxylate protonation. The unusually large contraction and the high energetic barrier observed at pH 7.0 for the protonation of the His residues suggests that the formation of the compact acid intermediate involves a rate-limiting step after protonation.

  12. Ultrafast MR Imaging in Pediatric Neuroradiology

    International Nuclear Information System (INIS)

    Singh, R.K.; Smith, J.T.; Wilkinson, I.D.; Griffiths, P.D.

    2003-01-01

    Purpose: To compare the diagnostic information obtained from ultrafast MR imaging with standard MR imaging techniques in pediatric neuroradiology. The goal was to judge whether ultrafast methods can be used to replace standard methods and reduce the need for sedation or general anesthesia as a result of the considerably shorter scan times. Material and Methods: Our prospective study involved 125 patients. Routine clinical imaging was performed along with two ultrafast methods. Single shot fast spin echo (SSFSE) was used to give T2-weighted images and an echo planar imaging (EPI) sequence to provide a T1-weighted images. The ultrafast images were presented to an experienced neuro radiologist who was also given the information present on the initial referral card. These reports based on the ultrafast images were then compared with the formal radiologic report made solely on the basis of the standard imaging. Results: The overall sensitivity and specificity for ultrafast imaging when compared to the reference standard were 78% and 98% with positive and negative predictive values of 98% and 76%. Pathologies characterized by small areas of subtle T2 prolongation were difficult or impossible to see on the ultrafast images but otherwise they provided reliable information. Conclusions: This paper demonstrates that ultrafast MR imaging can diagnose many pediatric intracranial abnormalities as well as standard methods. Anatomic resolution limits its capacity to define subtle developmental anomalies and contrast resolution limitations of the ultrafast methods reduce the detection of pathology characterized by subtle T2 prolongation

  13. Ab initio study of structural and mechanical property of solid molecular hydrogens

    Science.gov (United States)

    Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

    2015-06-01

    Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

  14. Ultrafast Thermal Transport at Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Cahill, David [Univ. of Illinois, Champaign, IL (United States); Murphy, Catherine [Univ. of Illinois, Champaign, IL (United States); Martin, Lane [Univ. of Illinois, Champaign, IL (United States)

    2014-10-21

    Our research program on Ultrafast Thermal Transport at Interfaces advanced understanding of the mesoscale science of heat conduction. At the length and time scales of atoms and atomic motions, energy is transported by interactions between single-particle and collective excitations. At macroscopic scales, entropy, temperature, and heat are the governing concepts. Key gaps in fundamental knowledge appear at the transitions between these two regimes. The transport of thermal energy at interfaces plays a pivotal role in these scientific issues. Measurements of heat transport with ultrafast time resolution are needed because picoseconds are the fundamental scales where the lack of equilibrium between various thermal excitations becomes a important factor in the transport physics. A critical aspect of our work has been the development of experimental methods and model systems that enabled more precise and sensitive investigations of nanoscale thermal transport.

  15. Light-operated machines based on threaded molecular structures.

    Science.gov (United States)

    Credi, Alberto; Silvi, Serena; Venturi, Margherita

    2014-01-01

    Rotaxanes and related species represent the most common implementation of the concept of artificial molecular machines, because the supramolecular nature of the interactions between the components and their interlocked architecture allow a precise control on the position and movement of the molecular units. The use of light to power artificial molecular machines is particularly valuable because it can play the dual role of "writing" and "reading" the system. Moreover, light-driven machines can operate without accumulation of waste products, and photons are the ideal inputs to enable autonomous operation mechanisms. In appropriately designed molecular machines, light can be used to control not only the stability of the system, which affects the relative position of the molecular components but also the kinetics of the mechanical processes, thereby enabling control on the direction of the movements. This step forward is necessary in order to make a leap from molecular machines to molecular motors.

  16. Ultrafast comparison of personal genomes

    OpenAIRE

    Mauldin, Denise; Hood, Leroy; Robinson, Max; Glusman, Gustavo

    2017-01-01

    We present an ultra-fast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into 'genome fingerprints' that can be readily compared across sequencing technologies and reference versions. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. This enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative s...

  17. Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems.

    Science.gov (United States)

    DiMaio, Frank

    2017-01-01

    Molecular replacement (MR), a method for solving the crystallographic phase problem using phases derived from a model of the target structure, has proven extremely valuable, accounting for the vast majority of structures solved by X-ray crystallography. However, when the resolution of data is low, or the starting model is very dissimilar to the target protein, solving structures via molecular replacement may be very challenging. In recent years, protein structure prediction methodology has emerged as a powerful tool in model building and model refinement for difficult molecular replacement problems. This chapter describes some of the tools available in Rosetta for model building and model refinement specifically geared toward difficult molecular replacement cases.

  18. Molecular structures of fructans from Agave tequilana Weber var. azul.

    Science.gov (United States)

    Lopez, Mercedes G; Mancilla-Margalli, Norma A; Mendoza-Diaz, Guillermo

    2003-12-31

    Agave plants utilize crassulacean acid metabolism (CAM) for CO(2) fixation. Fructans are the principal photosynthetic products generated by agave plants. These carbohydrates are fructose-bound polymers frequently with a single glucose moiety. Agave tequilana Weber var. azul is an economically important CAM species not only because it is the sole plant allowed for tequila production but because it is a potential source of prebiotics. Because of the large amounts of carbohydrates in A. tequilana, in this study the molecular structures of its fructans were determined by fructan derivatization for linkage analysis coupled with gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Fructans were extracted from 8-year-old A. tequilana plants. The linkage types present in fructans from A. tequilana were determined by permethylation followed by reductive cleavage, acetylation, and finally GC-MS analysis. Analysis of the degree of polymerization (DP) estimated by (1)H NMR integration and (13)C NMR and confirmed by MALDI-TOF-MS showed a wide DP ranging from 3 to 29 units. All of the analyses performed demonstrated that fructans from A. tequilana consist of a complex mixture of fructooligosaccharides containing principally beta(2 --> 1) linkages, but also beta(2 --> 6) and branch moieties were observed. Finally, it can be stated that fructans from A. tequilana Weber var. azul are not an inulin type as previously thought.

  19. Molecular structures of some 8-isoanalogues of steroid estrogens

    International Nuclear Information System (INIS)

    Starova, G.L.; Eliseev, I.I.; Abusalimov, Sh.N.; Tsogoeva, S.B.; Shavva, A.G.

    2001-01-01

    The molecular structures of three steroids, namely, 17β-acetoxy-3-methoxy-8-isoestra-1,3,5(10)-triene (I), 17β-acetoxy-3-methoxy-7α-methyl-8-isoestra-1,3,5(10)-triene (II), and 17β-acetoxy-3-methoxy-1-methyl-8-isoestra-1,3,5(10)-triene (III), are determined by X-ray diffraction analysis. It is shown that the substituents in the A and B rings of the compounds of the 8-iso series have a slight effect on the conformation of the steroid skeleton as a whole, which manifests itself only in insignificant distortions of the B and D rings. The methyl group in the 1-position (compound III) affects the geometric parameters of the steroid nucleus less than the same substituent in the 7-position (compound II). A sharp decrease in the uterotropic activity of compounds II and III (compared to compound I) revealed in biological studies can be attributed to unfavorable steric interactions of the substituents in the A and B rings with the estradiol receptor

  20. A study of the molecular structure in CR-39

    International Nuclear Information System (INIS)

    Stejny, J.; Portwood, T.

    1986-01-01

    A technique is presented for examining the molecular structure of CR-39 by analysis of the etch products from hydrolysis of the polymer network. The CR-39 network consists of polyallyl chains jointed by diethyleneglycol dicarbonate links. The etching cuts the carbonate links and liberates the polyallyl chains which makes them amenable to common analytical methods. Gel Permeation Chromatography was used to characterize the chain lengths and their distribution. It was found that the average length is rather short and that it decreases with increasing concentration of the initiator. This technique has been also used to identify the radiation sensitive link in the CR-39 network. It was found that the length of polyallyl chain is not changed in 60 Co γ-irradiated plastic while the etch rate significantly increases. This shows that the polyallyl chains are relatively inert and not responsible for the radiation sensitivity of CR-39 and that it is the diethyleneglycol dicarbonate links which are damaged by radiation. (author)

  1. An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates

    International Nuclear Information System (INIS)

    Gal, Maayan; Kern, Thomas; Schanda, Paul; Frydman, Lucio; Brutscher, Bernhard

    2009-01-01

    Multidimensional NMR spectroscopy is a well-established technique for the characterization of structure and fast-time-scale dynamics of highly populated ground states of biological macromolecules. The investigation of short-lived excited states that are important for molecular folding, misfolding and function, however, remains a challenge for modern biomolecular NMR techniques. Off-equilibrium real-time kinetic NMR methods allow direct observation of conformational or chemical changes by following peak positions and intensities in a series of spectra recorded during a kinetic event. Because standard multidimensional NMR methods required to yield sufficient atom-resolution are intrinsically time-consuming, many interesting phenomena are excluded from real-time NMR analysis. Recently, spatially encoded ultrafast 2D NMR techniques have been proposed that allow one to acquire a 2D NMR experiment within a single transient. In addition, when combined with the SOFAST technique, such ultrafast experiments can be repeated at high rates. One of the problems detected for such ultrafast protein NMR experiments is related to the heteronuclear decoupling during detection with interferences between the pulses and the oscillatory magnetic field gradients arising in this scheme. Here we present a method for improved ultrafast data acquisition yielding higher signal to noise and sharper lines in single-scan 2D NMR spectra. In combination with a fast-mixing device, the recording of 1 H- 15 N correlation spectra with repetition rates of up to a few Hertz becomes feasible, enabling real-time studies of protein kinetics occurring on time scales down to a few seconds

  2. Ultrafast chiroptical spectroscopy: Monitoring optical activity in quick time

    Directory of Open Access Journals (Sweden)

    Hanju Rhee

    2011-12-01

    Full Text Available Optical activity spectroscopy provides rich structural information of biologically important molecules in condensed phases. However, a few intrinsic problems of conventional method based on electric field intensity measurement scheme prohibited its extension to time domain technique. We have recently developed new types of optical activity spectroscopic methods capable of measuring chiroptical signals with femtosecond pulses. It is believed that these novel approaches will be applied to a variety of ultrafast chiroptical studies.

  3. High speed fluorescence imaging with compressed ultrafast photography

    Science.gov (United States)

    Thompson, J. V.; Mason, J. D.; Beier, H. T.; Bixler, J. N.

    2017-02-01

    Fluorescent lifetime imaging is an optical technique that facilitates imaging molecular interactions and cellular functions. Because the excited lifetime of a fluorophore is sensitive to its local microenvironment,1, 2 measurement of fluorescent lifetimes can be used to accurately detect regional changes in temperature, pH, and ion concentration. However, typical state of the art fluorescent lifetime methods are severely limited when it comes to acquisition time (on the order of seconds to minutes) and video rate imaging. Here we show that compressed ultrafast photography (CUP) can be used in conjunction with fluorescent lifetime imaging to overcome these acquisition rate limitations. Frame rates up to one hundred billion frames per second have been demonstrated with compressed ultrafast photography using a streak camera.3 These rates are achieved by encoding time in the spatial direction with a pseudo-random binary pattern. The time domain information is then reconstructed using a compressed sensing algorithm, resulting in a cube of data (x,y,t) for each readout image. Thus, application of compressed ultrafast photography will allow us to acquire an entire fluorescent lifetime image with a single laser pulse. Using a streak camera with a high-speed CMOS camera, acquisition rates of 100 frames per second can be achieved, which will significantly enhance our ability to quantitatively measure complex biological events with high spatial and temporal resolution. In particular, we will demonstrate the ability of this technique to do single-shot fluorescent lifetime imaging of cells and microspheres.

  4. Direct observation of ultrafast long-range charge separation at polymer–fullerene heterojunctions

    KAUST Repository

    Provencher, Franç oise; Bé rubé , Nicolas; Parker, Anthony W.; Greetham, Gregory M.; Towrie, Michael; Hellmann, Christoph; Cô té , Michel; Stingelin, Natalie; Silva, Carlos; Hayes, Sophia C.

    2014-01-01

    In polymeric semiconductors, charge carriers are polarons, which means that the excess charge deforms the molecular structure of the polymer chain that hosts it. This results in distinctive signatures in the vibrational modes of the polymer. Here, we probe polaron photogeneration dynamics at polymer:fullerene heterojunctions by monitoring its time-resolved resonance-Raman spectrum following ultrafast photoexcitation. We conclude that polarons emerge within 300 fs. Surprisingly, further structural evolution on ≤50-ps timescales is modest, indicating that the polymer conformation hosting nascent polarons is not significantly different from that near equilibrium. We interpret this as suggestive that charges are free from their mutual Coulomb potential because we would expect rich vibrational dynamics associated with charge-pair relaxation. We address current debates on the photocarrier generation mechanism at molecular heterojunctions, and our work is, to our knowledge, the first direct probe of molecular conformation dynamics during this fundamentally important process in these materials. © 2014 Macmillan Publishers Limited. All rights reserved.

  5. Direct observation of ultrafast long-range charge separation at polymer–fullerene heterojunctions

    KAUST Repository

    Provencher, Françoise

    2014-07-01

    In polymeric semiconductors, charge carriers are polarons, which means that the excess charge deforms the molecular structure of the polymer chain that hosts it. This results in distinctive signatures in the vibrational modes of the polymer. Here, we probe polaron photogeneration dynamics at polymer:fullerene heterojunctions by monitoring its time-resolved resonance-Raman spectrum following ultrafast photoexcitation. We conclude that polarons emerge within 300 fs. Surprisingly, further structural evolution on ≤50-ps timescales is modest, indicating that the polymer conformation hosting nascent polarons is not significantly different from that near equilibrium. We interpret this as suggestive that charges are free from their mutual Coulomb potential because we would expect rich vibrational dynamics associated with charge-pair relaxation. We address current debates on the photocarrier generation mechanism at molecular heterojunctions, and our work is, to our knowledge, the first direct probe of molecular conformation dynamics during this fundamentally important process in these materials. © 2014 Macmillan Publishers Limited. All rights reserved.

  6. Pathways to Structure-Property Relationships of Peptide-Materials Interfaces: Challenges in Predicting Molecular Structures.

    Science.gov (United States)

    Walsh, Tiffany R

    2017-07-18

    An in-depth appreciation of how to manipulate the molecular-level recognition between peptides and aqueous materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomolecules is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomolecule onto one materials composition over another, one surface facet over another, or one crystalline polymorph over another. Deeper knowledge of the aqueous abiotic-biotic interface, to establish clear structure-property relationships in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relationships but can often be challenging to accomplish via experimental approaches alone. In addition to myriad existing challenges associated with determining the detailed molecular structure of any molecule adsorbed at an aqueous interface, experimental characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to experimental techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with experiment, molecular simulations at the atomistic level can bring complementary and critical insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, molecular simulation approaches also face

  7. Ultrafast Hierarchical OTDM/WDM Network

    Directory of Open Access Journals (Sweden)

    Hideyuki Sotobayashi

    2003-12-01

    Full Text Available Ultrafast hierarchical OTDM/WDM network is proposed for the future core-network. We review its enabling technologies: C- and L-wavelength-band generation, OTDM-WDM mutual multiplexing format conversions, and ultrafast OTDM wavelengthband conversions.

  8. Avant-Garde Ultrafast Laser Writing

    Directory of Open Access Journals (Sweden)

    Kazansky P. G.

    2013-11-01

    Full Text Available Ultrafast laser processing of transparent materials reveals new phenomena. Reviewed, are recent demonstrations of 5D optical memory, vortex polarization and Airy beam converters employing self-assembled nanostructuring, ultrafast laser calligraphy and polarization writing control using pulses with tilted front.

  9. Ultrafast phosphate hydration dynamics in bulk H2O

    International Nuclear Information System (INIS)

    Costard, Rene; Tyborski, Tobias; Fingerhut, Benjamin P.; Elsaesser, Thomas

    2015-01-01

    Phosphate vibrations serve as local probes of hydrogen bonding and structural fluctuations of hydration shells around ions. Interactions of H 2 PO 4 − ions and their aqueous environment are studied combining femtosecond 2D infrared spectroscopy, ab-initio calculations, and hybrid quantum-classical molecular dynamics (MD) simulations. Two-dimensional infrared spectra of the symmetric (ν S (PO 2 − )) and asymmetric (ν AS (PO 2 − )) PO 2 − stretching vibrations display nearly homogeneous lineshapes and pronounced anharmonic couplings between the two modes and with the δ(P-(OH) 2 ) bending modes. The frequency-time correlation function derived from the 2D spectra consists of a predominant 50 fs decay and a weak constant component accounting for a residual inhomogeneous broadening. MD simulations show that the fluctuating electric field of the aqueous environment induces strong fluctuations of the ν S (PO 2 − ) and ν AS (PO 2 − ) transition frequencies with larger frequency excursions for ν AS (PO 2 − ). The calculated frequency-time correlation function is in good agreement with the experiment. The ν(PO 2 − ) frequencies are mainly determined by polarization contributions induced by electrostatic phosphate-water interactions. H 2 PO 4 − /H 2 O cluster calculations reveal substantial frequency shifts and mode mixing with increasing hydration. Predicted phosphate-water hydrogen bond (HB) lifetimes have values on the order of 10 ps, substantially longer than water-water HB lifetimes. The ultrafast phosphate-water interactions observed here are in marked contrast to hydration dynamics of phospholipids where a quasi-static inhomogeneous broadening of phosphate vibrations suggests minor structural fluctuations of interfacial water

  10. Ultrafast phosphate hydration dynamics in bulk H2O

    Science.gov (United States)

    Costard, Rene; Tyborski, Tobias; Fingerhut, Benjamin P.; Elsaesser, Thomas

    2015-06-01

    Phosphate vibrations serve as local probes of hydrogen bonding and structural fluctuations of hydration shells around ions. Interactions of H2PO4- ions and their aqueous environment are studied combining femtosecond 2D infrared spectroscopy, ab-initio calculations, and hybrid quantum-classical molecular dynamics (MD) simulations. Two-dimensional infrared spectra of the symmetric ( ν S ( PO2 - ) ) and asymmetric ( ν A S ( PO2 - ) ) PO 2- stretching vibrations display nearly homogeneous lineshapes and pronounced anharmonic couplings between the two modes and with the δ(P-(OH)2) bending modes. The frequency-time correlation function derived from the 2D spectra consists of a predominant 50 fs decay and a weak constant component accounting for a residual inhomogeneous broadening. MD simulations show that the fluctuating electric field of the aqueous environment induces strong fluctuations of the ν S ( PO2 - ) and ν A S ( PO2 - ) transition frequencies with larger frequency excursions for ν A S ( PO2 - ) . The calculated frequency-time correlation function is in good agreement with the experiment. The ν ( PO2 - ) frequencies are mainly determined by polarization contributions induced by electrostatic phosphate-water interactions. H2PO4-/H2O cluster calculations reveal substantial frequency shifts and mode mixing with increasing hydration. Predicted phosphate-water hydrogen bond (HB) lifetimes have values on the order of 10 ps, substantially longer than water-water HB lifetimes. The ultrafast phosphate-water interactions observed here are in marked contrast to hydration dynamics of phospholipids where a quasi-static inhomogeneous broadening of phosphate vibrations suggests minor structural fluctuations of interfacial water.

  11. Structural studies on Mycobacterium tuberculosis RecA: Molecular ...

    Indian Academy of Sciences (India)

    2015-01-11

    Jan 11, 2015 ... The molecular geometry of RecA and the location of the nucleotide binding site ...... the residue in all the glycerol complexes clusters together along with the two ..... an X-ray and molecular dynamics investigation on banana.

  12. Oxygen Activated, Palladium Nanoparticle Catalyzed, Ultrafast Cross-Coupling of Organolithium Reagents

    NARCIS (Netherlands)

    Heijnen, Dorus; Tosi, Filippo; Vila, Carlos; Stuart, Marc C. A.; Elsinga, Philip H.; Szymanski, Wiktor; Feringa, Ben L.

    2017-01-01

    The discovery of an ultrafast cross-coupling of alkyland aryllithium reagents with a range of aryl bromides is presented. The essential role of molecular oxygen to form the active palladium catalyst was established; palladium nanoparticles that are highly active in cross-coupling reactions with

  13. Ultrafast Science Opportunities with Electron Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    DURR, HERMANN; Wang, X.J., ed.

    2016-04-28

    X-rays and electrons are two of the most fundamental probes of matter. When the Linac Coherent Light Source (LCLS), the world’s first x-ray free electron laser, began operation in 2009, it transformed ultrafast science with the ability to generate laser-like x-ray pulses from the manipulation of relativistic electron beams. This document describes a similar future transformation. In Transmission Electron Microscopy, ultrafast relativistic (MeV energy) electron pulses can achieve unsurpassed spatial and temporal resolution. Ultrafast temporal resolution will be the next frontier in electron microscopy and can ideally complement ultrafast x-ray science done with free electron lasers. This document describes the Grand Challenge science opportunities in chemistry, material science, physics and biology that arise from an MeV ultrafast electron diffraction & microscopy facility, especially when coupled with linac-based intense THz and X-ray pump capabilities.

  14. Ultrafast photoelectron spectroscopy of small molecule organic films

    Science.gov (United States)

    Read, Kendall Laine

    As research in the field of ultrafast optics has produced shorter and shorter pulses, at an ever-widening range of frequencies, ultrafast spectroscopy has grown correspondingly. In particular, ultrafast photoelectron spectroscopy allows direct observation of electrons in transient or excited states, regardless of the eventual relaxation mechanisms. High-harmonic conversion of 800nm, femtosecond, Ti:sapphire laser pulses allows excite/probe spectroscopy down into atomic core level states. To this end, an ultrafast, X-UV photoelectron spectroscopic system is described, including design considerations for the high-harmonic generation line, the time of flight detector, and the subsequent data collection electronics. Using a similar experimental setup, I have performed several ultrafast, photoelectron excited state decay studies at the IBM, T. J. Watson Research Center. All of the observed materials were electroluminescent thin film organics, which have applications as the emitter layer in organic light emitting devices. The specific materials discussed are: Alq, BAlq, DPVBi, and Alq doped with DCM or DMQA. Alq:DCM is also known to lase at low photoexcitation thresholds. A detailed understanding of the involved relaxation mechanisms is beneficial to both applications. Using 3.14 eV excite, and 26.7 eV probe, 90 fs laser pulses, we have observed the lowest unoccupied molecular orbital (LUMO) decay rate over the first 200 picoseconds. During this time, diffusion is insignificant, and all dynamics occur in the absence of electron transport. With excitation intensities in the range of 100μJ/cm2, we have modeled the Alq, BAlq, and DPVBi decays via bimolecular singlet-singlet annihilation. At similar excitations, we have modeled the Alq:DCM decay via Förster transfer, stimulated emission, and excimeric formation. Furthermore, the Alq:DCM occupied to unoccupied molecular orbital energy gap was seen to shrink as a function of excite-to-probe delay, in accordance with the

  15. Influence of the molecular structure on hydrolysability of unsaturated polyesters

    International Nuclear Information System (INIS)

    Pays, M.F.; Denis, V.

    1993-09-01

    EDF has decided to replace conventional materials by glass reinforced plastics for certain PWR water distribution systems (raw water system, essential service water system, firefighting water distribution system, etc...). Since steel corrodes rapidly in these pipings, introducing composite materials will be economically beneficial if the long-term resistance of these materials can be guaranteed. However, due to hydrolysis of the resin or of the fiber-matrix interface, composite materials deteriorations may occur during service life. This paper reports on the hydrolysis resistance of polyester and vinylester resins. - Model monomers were studied to relate the molecular structure to the hydrolysis resistance. Two ester categories were determined, the diacids and the diols. For the diacids, we obtained the following classification in increasing order of resistance: < maleates < ethoxysuccinates < succinates < fumerates < terephtalates < orthophtalates < isophtalates and for the diols: trioxyethylene glycol << butane diol ∼ ethylene glycol < neopentyl glycol < bisphenol A. The positions obtained for neopentyl glycol and isophtalic acid on this scale justify their inclusion in the formulation of hydrolysis-resistant resins. Since aliphatic unsaturated esters are highly sensitive to hydrolysis, the cross linking procedures for these materials, notably the post-cure stages, must be the subject of particular care. - The hydrolytic degradation of cross linked materials was studied. It was shown that hydrolysis could be monitored by a simple gravimetric method. Used in association with accelerated aging tests, it predicts the time lapse to initiation of the phenomenon. The better hydrolysis resistance of vinylester resins as compared with unsaturated polyesters has been demonstrated. However, forecasting over a 30-year life span is difficult to guarantee in that this involves indicating in the resin specifications the in-service stress which it will be required to

  16. Geometric and electronic structures of molecular ions from high energy collisions

    International Nuclear Information System (INIS)

    Groeneveld, K.O.

    1983-01-01

    This chapter examines the characteristics of heavy ion collision and of beam foil spectroscopy. It discusses the kinematic consequences of the high energies and presents results from ''Coulomb explosion'' and structure determination of molecular ions. It demonstrates that studies of molecular ions with accelerators can provide electronic and geometric structure information of molecules or molecular ions and points out that the understanding of the microscopic processes at such high energies is incomplete and needs further experimental and theoretical efforts

  17. Molecular structure determination of cyclootane by ab initio and electron diffraction methods in the gas phase

    OpenAIRE

    De Almeida, Wagner B.

    2000-01-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can ma...

  18. Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques.

    Science.gov (United States)

    Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M; Prates, Luciana L; Yu, Peiqiang

    2017-08-05

    The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HED N/OM ), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. An Insight towards Conceptual Understanding: Looking into the Molecular Structures of Compounds

    Science.gov (United States)

    Uyulgan, Melis Arzu; Akkuzu, Nalan

    2016-01-01

    The subject of molecular structures is one of the most important and complex subject in chemistry which a majority of the undergraduate students have difficulties to understand its concepts and characteristics correctly. To comprehend the molecular structures and their characteristics the students need to understand related subjects such as Lewis…

  20. Fast and ultrafast MR-imaging of the heart

    International Nuclear Information System (INIS)

    Schulthess, G.K. von; Davis, C.P.; Debatin, J.F.; McKinnon, G.C.

    1995-01-01

    MRI has been hampered by long image acquisition times. This combined with its non-realtime nature and the limited spatial resolution has made it difficult to extend MRT to the study of small cardiac structures. Recent technical improvements have made breath-held or realtime MRI feasible and thus laid the foundations for further applications in the field of cardiovascular imaging, notably MR coronary angiography, imaging of cardiac valve leaflets, as well as firstpass perfusion studies. Moreover ultrafast MR techniques may eventually replace conventional data acquisition strategies and thus drastically increase patient throughput by shortening acquisition time. This article provides an overview of the technical advances in MRI and their application to the cardiovascular system and discusses possibilities of combined ultrafast and interventional strategies. (orig.) [de

  1. A spectroelectrochemical cell for ultrafast two-dimensional infrared spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    El Khoury, Youssef; Van Wilderen, Luuk J. G. W.; Vogt, Tim; Winter, Ernst; Bredenbeck, Jens, E-mail: bredenbeck@biophysik.uni-frankfurt.org, E-mail: bredenbeck@biophysik.uni-frankfurt.de [Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 1, 60438 Frankfurt (Germany)

    2015-08-15

    A spectroelectrochemical cell has been designed to combine electrochemistry and ultrafast two-dimensional infrared (2D-IR) spectroscopy, which is a powerful tool to extract structure and dynamics information on the femtosecond to picosecond time scale. Our design is based on a gold mirror with the dual role of performing electrochemistry and reflecting IR light. To provide the high optical surface quality required for laser spectroscopy, the gold surface is made by electron beam evaporation on a glass substrate. Electrochemical cycling facilitates in situ collection of ultrafast dynamics of redox-active molecules by means of 2D-IR. The IR beams are operated in reflection mode so that they travel twice through the sample, i.e., the signal size is doubled. This methodology is optimal for small sample volumes and successfully tested with the ferricyanide/ferrocyanide redox system of which the corresponding electrochemically induced 2D-IR difference spectrum is reported.

  2. rf streak camera based ultrafast relativistic electron diffraction.

    Science.gov (United States)

    Musumeci, P; Moody, J T; Scoby, C M; Gutierrez, M S; Tran, T

    2009-01-01

    We theoretically and experimentally investigate the possibility of using a rf streak camera to time resolve in a single shot structural changes at the sub-100 fs time scale via relativistic electron diffraction. We experimentally tested this novel concept at the UCLA Pegasus rf photoinjector. Time-resolved diffraction patterns from thin Al foil are recorded. Averaging over 50 shots is required in order to get statistics sufficient to uncover a variation in time of the diffraction patterns. In the absence of an external pump laser, this is explained as due to the energy chirp on the beam out of the electron gun. With further improvements to the electron source, rf streak camera based ultrafast electron diffraction has the potential to yield truly single shot measurements of ultrafast processes.

  3. A spectroelectrochemical cell for ultrafast two-dimensional infrared spectroscopy

    International Nuclear Information System (INIS)

    El Khoury, Youssef; Van Wilderen, Luuk J. G. W.; Vogt, Tim; Winter, Ernst; Bredenbeck, Jens

    2015-01-01

    A spectroelectrochemical cell has been designed to combine electrochemistry and ultrafast two-dimensional infrared (2D-IR) spectroscopy, which is a powerful tool to extract structure and dynamics information on the femtosecond to picosecond time scale. Our design is based on a gold mirror with the dual role of performing electrochemistry and reflecting IR light. To provide the high optical surface quality required for laser spectroscopy, the gold surface is made by electron beam evaporation on a glass substrate. Electrochemical cycling facilitates in situ collection of ultrafast dynamics of redox-active molecules by means of 2D-IR. The IR beams are operated in reflection mode so that they travel twice through the sample, i.e., the signal size is doubled. This methodology is optimal for small sample volumes and successfully tested with the ferricyanide/ferrocyanide redox system of which the corresponding electrochemically induced 2D-IR difference spectrum is reported

  4. Ultrafast terahertz electrodynamics of photonic and electronic nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Liang [Iowa State Univ., Ames, IA (United States)

    2015-01-01

    This thesis summarizes my work on using ultrafast laser pulses to study Terahertz (THz) electrodynamics of photonic and electronic nanostructures and microstructures. Ultrafast timeresolved (optical, NIR, MIR, THz) pump-probe spectroscopy setup has been successfully built, which enables me to perform a series of relevant experiments. Firstly, a novel high e ciency and compact THz wave emitter based on split-ring-resonators has been developed and characterized. The emitter can be pumped at any wavelength by tailoring the magnetic resonance and could generate gapless THz waves covering the entire THz band. Secondly, two kinds of new photonic structures for THz wave manipulation have been successfully designed and characterized. One is based on the 1D and 2D photo-imprinted di ractive elements. The other is based on the photoexcited double-split-ring-resonator metamaterials. Both structures are exible and can modulate THz waves with large tunability. Thirdly, the dark excitons in semiconducting singlewalled carbon nanotubes are studied by optical pump and THz probe spectroscopy, which provides the rst insights into the THz responses of nonequilibrium excitonic correlations and dynamics from the dark ground states in carbon nanotubes. Next, several on-going projects are brie y presented such as the study of ultrafast THz dynamics of Dirac fermions in topological insulator Bi2Se3 with Mid-infrared excitation. Finally, the thesis ends with a summary of the completed experiments and an outlook of the future plan.

  5. Molecular evolution, intracellular organization, and the quinary structure of proteins.

    OpenAIRE

    McConkey, E H

    1982-01-01

    High-resolution two-dimensional polyacrylamide gel electrophoresis shows that at least half of 370 denatured polypeptides from hamster cells and human cells are indistinguishable in terms of isoelectric points and molecular weights. Molecular evolution may have been more conservative for this set of proteins than sequence studies on soluble proteins have implied. This may be a consequence of complexities of intracellular organization and the numerous macromolecular interactions in which most ...

  6. Desolvation of polymers by ultrafast heating: Influence of hydrophilicity

    Science.gov (United States)

    Sun, Si Neng; Urbassek, Herbert M.

    2010-10-01

    Using molecular-dynamics simulation, we investigate the consequences of ultrafast laser-induced heating of a small water droplet containing a solvated polymer. Two polymers are studied: polyethylene as an example of a hydrophobic, and polyketone as an example of a hydrophilic polymer. In both cases, when the droplet is heated below the critical temperature of water, strong water evaporation is started, but the polymer remains in contact with a central water cluster. However, upon heating beyond the critical temperature, the hydrophilic polyethylene becomes completely desolvated, while polyketone still remains solvated. We analyze this behavior in terms of the intermolecular interactions and of the expansion dynamics of the heated droplet.

  7. Ultrafast Laser-Based Spectroscopy and Sensing: Applications in LIBS, CARS, and THz Spectroscopy

    Science.gov (United States)

    Leahy-Hoppa, Megan R.; Miragliotta, Joseph; Osiander, Robert; Burnett, Jennifer; Dikmelik, Yamac; McEnnis, Caroline; Spicer, James B.

    2010-01-01

    Ultrafast pulsed lasers find application in a range of spectroscopy and sensing techniques including laser induced breakdown spectroscopy (LIBS), coherent Raman spectroscopy, and terahertz (THz) spectroscopy. Whether based on absorption or emission processes, the characteristics of these techniques are heavily influenced by the use of ultrafast pulses in the signal generation process. Depending on the energy of the pulses used, the essential laser interaction process can primarily involve lattice vibrations, molecular rotations, or a combination of excited states produced by laser heating. While some of these techniques are currently confined to sensing at close ranges, others can be implemented for remote spectroscopic sensing owing principally to the laser pulse duration. We present a review of ultrafast laser-based spectroscopy techniques and discuss the use of these techniques to current and potential chemical and environmental sensing applications. PMID:22399883

  8. Ultrafast Laser-Based Spectroscopy and Sensing: Applications in LIBS, CARS, and THz Spectroscopy

    Directory of Open Access Journals (Sweden)

    Megan R. Leahy-Hoppa

    2010-04-01

    Full Text Available Ultrafast pulsed lasers find application in a range of spectroscopy and sensing techniques including laser induced breakdown spectroscopy (LIBS, coherent Raman spectroscopy, and terahertz (THz spectroscopy. Whether based on absorption or emission processes, the characteristics of these techniques are heavily influenced by the use of ultrafast pulses in the signal generation process. Depending on the energy of the pulses used, the essential laser interaction process can primarily involve lattice vibrations, molecular rotations, or a combination of excited states produced by laser heating. While some of these techniques are currently confined to sensing at close ranges, others can be implemented for remote spectroscopic sensing owing principally to the laser pulse duration. We present a review of ultrafast laser-based spectroscopy techniques and discuss the use of these techniques to current and potential chemical and environmental sensing applications.

  9. Intensified CCD for ultrafast diagnostics

    International Nuclear Information System (INIS)

    Cheng, J.; Tripp, G.; Coleman, L.

    1978-01-01

    Many of the present laser fusion diagnostics are recorded on either ultrafast streak cameras or on oscilloscopes. For those experiments in which a large volume of data is accumulated, direct computer processing of the information becomes important. We describe an approach which uses a RCA 52501 back-thinned CCD sensor to obtain direct electron readouts for both the streak camera and the CRT. Performance of the 100 GHz streak camera and the 4 GHz CRT are presented. Design parameters and computer interfacing for both systems are described in detail

  10. Compression of Ultrafast Laser Beams

    Science.gov (United States)

    2016-03-01

    Copyright 2003, AIP Publishing LLC. DOI: http://dx.doi.org/10.1063/1.1611998.) When designing the pulse shaper, the laser beam must completely fill the...for the design of future versions of this device. The easiest way to align the pulse shaper is to use the laser beam that will be shaped, without...Afterward, an ultrafast thin beam splitter is placed into the system after the diameter of the laser beam is reduced; this is done to monitor the beam

  11. 16O+16O molecular nature of the superdeformed band of 32S and the evolution of the molecular structure

    International Nuclear Information System (INIS)

    Kimura, Masaaki; Horiuchi, Hisashi

    2004-01-01

    The relation between the superdeformed band of 32 S and 16 O+ 16 O molecular bands is studied by the deformed-basis antisymmetrized molecular dynamics with the Gogny D1S force. It is found that the obtained superdeformed band members of S have a considerable amount of the 16 O+ 16 O component. Above the superdeformed band, we have obtained two excited rotational bands which have more prominent character of the 16 O+ 16 O molecular band. These three rotational bands are regarded as a series of 16 O+ 16 O molecular bands which were predicted by using the unique 16 O- 16 O optical potential. As the excitation energy and principal quantum number of the relative motion increase, the 16 O+ 16 O cluster structure becomes more prominent but at the same time, the band members are fragmented into several states

  12. Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking.

    Science.gov (United States)

    Sixto-López, Yudibeth; Bello, Martiniano; Correa-Basurto, José

    2018-03-06

    Histone deacetylases (HDACs) are a family of proteins whose main function is the removal of acetyl groups from lysine residues located on histone and non-histone substrates, which regulates gene transcription and other activities in cells. HDAC1 dysfunction has been implicated in cancer development and progression; thus, its inhibition has emerged as a new therapeutic strategy. Two additional metal binding sites (Site 1 and Site 2) in HDACs have been described that are primarily occupied by potassium ions, suggesting a possible structural role that affects HDAC activity. In this work, we explored the structural role of potassium ions in Site 1 and Site 2 and how they affect the interactions of compounds with high affinities for HDAC1 (AC1OCG0B, Chlamydocin, Dacinostat and Quisinostat) and SAHA (a pan-inhibitor) using molecular docking and molecular dynamics (MD) simulations in concert with a Molecular-Mechanics-Generalized-Born-Surface-Area (MMGBSA) approach. Four models were generated: one with a potassium ion (K + ) in both sites (HDAC1 k ), a second with K + only at site 1 (HDAC1 ks1 ), a third with K + only at site 2 (HDAC1 ks2 ) and a fourth with no K + (HDAC1 wk ). We found that the presence or absence of K + not only impacted the structural flexibility of HDAC1, but also its molecular recognition, consistent with experimental findings. These results could therefore be useful for further structure-based drug design studies addressing new HDAC1 inhibitors.

  13. Molecular structure and correlations in liquid D-2-propanol through neutron diffraction

    International Nuclear Information System (INIS)

    Sahoo, A.; Sarkar, S.; Joarder, R.N.; Krishna, P.S.R.

    2003-01-01

    Like t-butanol, 2-propanol molecules are quite big with substantial amount of asymmetry in the structure and so the analysis of the neutron diffraction data is tricky. A modified method of analysis, similar to one for liquid t-butanol, enables extraction of the detailed molecular conformation and intermolecular correlations through neutron diffraction. The pre-peak in the structure function, a signature of chain molecular association together with partially identified inter-molecular correlations yield some information about the nature of possible H-bonded molecular clusters in the liquid state. (author)

  14. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  15. Ultra-fast analog-to-digital converter based on a nonlinear triplexer and an optical coder with a photonic crystal structure.

    Science.gov (United States)

    Mehdizadeh, Farhad; Soroosh, Mohammad; Alipour-Banaei, Hamed; Farshidi, Ebrahim

    2017-03-01

    In this paper, we propose what we believe is a novel all-optical analog-to-digital converter (ADC) based on photonic crystals. The proposed structure is composed of a nonlinear triplexer and an optical coder. The nonlinear triplexer is for creating discrete levels in the continuous optical input signal, and the optical coder is for generating a 2-bit standard binary code out of the discrete levels coming from the nonlinear triplexer. Controlling the resonant mode of the resonant rings through optical intensity is the main objective and working mechanism of the proposed structure. The maximum delay time obtained for the proposed structure was about 5 ps and the total footprint is about 1520  μm2.

  16. Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters using Density Functional Theory

    Science.gov (United States)

    2017-05-05

    Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6390--17-9724 Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters...TELEPHONE NUMBER (include area code) b. ABSTRACT c. THIS PAGE 18. NUMBER OF PAGES 17. LIMITATION OF ABSTRACT Equilibrium Structures and Absorption...and electronic excited-state absorption spectra for eqilibrium structures of SixOy molecular clusters using density function theory (DFT) and time

  17. Spatial and mass distributions of molecular clouds and spiral structure

    International Nuclear Information System (INIS)

    Kwan, J.; Valdes, F.; National Optical Astronomy Observatories, Tucson, AZ)

    1987-01-01

    The growth of molecular clouds resulting from cloud-cloud collisions and coalescence in the Galactic ring between 4 and 8 kpc are modeled, taking into account the presence of a spiral potential and the mutual cloud-cloud gravitational attraction. The mean lifetime of molecular clouds is determined to be about 200 million years. The clouds are present in both spiral arm and interarm regions, but a spiral pattern in their spatial distribution is clearly discernible, with the more massive clouds showing a stronger correlation with the spiral arms. As viewed from within the Galactic disk, however, it is very difficult to ascertain that the molecular cloud distribution in longitude-velocity space has a spiral pattern. 19 references

  18. Ultrafast Electron Dynamics in Solar Energy Conversion.

    Science.gov (United States)

    Ponseca, Carlito S; Chábera, Pavel; Uhlig, Jens; Persson, Petter; Sundström, Villy

    2017-08-23

    Electrons are the workhorses of solar energy conversion. Conversion of the energy of light to electricity in photovoltaics, or to energy-rich molecules (solar fuel) through photocatalytic processes, invariably starts with photoinduced generation of energy-rich electrons. The harvesting of these electrons in practical devices rests on a series of electron transfer processes whose dynamics and efficiencies determine the function of materials and devices. To capture the energy of a photogenerated electron-hole pair in a solar cell material, charges of opposite sign have to be separated against electrostatic attractions, prevented from recombining and being transported through the active material to electrodes where they can be extracted. In photocatalytic solar fuel production, these electron processes are coupled to chemical reactions leading to storage of the energy of light in chemical bonds. With the focus on the ultrafast time scale, we here discuss the light-induced electron processes underlying the function of several molecular and hybrid materials currently under development for solar energy applications in dye or quantum dot-sensitized solar cells, polymer-fullerene polymer solar cells, organometal halide perovskite solar cells, and finally some photocatalytic systems.

  19. Molecular cloning, structural analysis and expression of a zinc ...

    African Journals Online (AJOL)

    The results of prokaryotic expression of ZnBP and overexpression of the ZnBP gene in A. thaliana improve our understanding of the function of this gene. Future studies should investigate the molecular mechanisms involved in gland morphogenesis in cotton. Key words: Gossypium hirsutum, pigment gland, zinc binding ...

  20. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

    We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...

  1. Theoretical study on the molecular and crystal structures of nitrogen ...

    Indian Academy of Sciences (India)

    By analyzing the simulation trajectory of molecular packing within ... The total charges of NF3 and BF3 are nearly zero. (0.075e and ... ity due to the charge density distribution. After hav- .... sity distributions are not discrete like a spectral density.

  2. Molecular structure descriptors in the computer-aided design of biologically active compounds

    International Nuclear Information System (INIS)

    Raevsky, Oleg A

    1999-01-01

    The current state of description of molecular structure in computer-aided molecular design of biologically active compounds by means of descriptors is analysed. The information contents of descriptors increases in the following sequence: element-level descriptors-structural formulae descriptors-electronic structure descriptors-molecular shape descriptors-intermolecular interaction descriptors. Each subsequent class of descriptors normally covers information contained in the previous-level ones. It is emphasised that it is practically impossible to describe all the features of a molecular structure in terms of any single class of descriptors. It is recommended to optimise the number of descriptors used by means of appropriate statistical procedures and characteristics of structure-property models based on these descriptors. The bibliography includes 371 references.

  3. The Atom in a Molecule: Implications for Molecular Structure and Properties

    Science.gov (United States)

    2016-05-23

    Briefing Charts 3. DATES COVERED (From - To) 01 February 2016 – 23 May 2016 4. TITLE AND SUBTITLE The atom in a molecule: Implications for molecular...For presentation at American Physical Society - Division of Atomic , Molecular, and Optical Physics (May 2016) PA Case Number: #16075; Clearance Date...10 Energy (eV) R C--H (au) R C--H(au) The Atom in a Molecule: Implications for Molecular Structures and Properties P. W. Langhoff, Chemistry

  4. Thermodynamic Stability of Structure H Hydrates Based on the Molecular Properties of Large Guest Molecules

    OpenAIRE

    Tezuka, Kyoichi; Taguchi, Tatsuhiko; Alavi, Saman; Sum, Amadeu K.; Ohmura, Ryo

    2012-01-01

    This paper report analyses of thermodynamic stability of structure-H clathrate hydrates formed with methane and large guest molecules in terms of their gas phase molecular sizes and molar masses for the selection of a large guest molecule providing better hydrate stability. We investigated the correlation among the gas phase molecular sizes, the molar masses of large molecule guest substances, and the equilibrium pressures. The results suggest that there exists a molecular-size value for the ...

  5. Molecular structures and metabolic characteristics of protein in brown and yellow flaxseed with altered nutrient traits.

    Science.gov (United States)

    Khan, Nazir Ahmad; Booker, Helen; Yu, Peiqiang

    2014-07-16

    The objectives of this study were to investigate the chemical profiles; crude protein (CP) subfractions; ruminal CP degradation characteristics and intestinal digestibility of rumen undegraded protein (RUP); and protein molecular structures using molecular spectroscopy of newly developed yellow-seeded flax (Linum usitatissimum L.). Seeds from two yellow flaxseed breeding lines and two brown flaxseed varieties were evaluated. The yellow-seeded lines had higher (P RUP (29.2 vs 35.1% CP) than that in the brown-seeded varieties. However, the total supply of digestible RUP was not significantly different between the two seed types. Regression equations based on protein molecular structural features gave relatively good estimation for the contents of CP (R(2) = 0.87), soluble CP (R(2) = 0.92), RUP (R(2) = 0.97), and intestinal digestibility of RUP (R(2) = 0.71). In conclusion, molecular spectroscopy can be used to rapidly characterize feed protein molecular structures and predict their nutritive value.

  6. Classification of proteins: available structural space for molecular modeling.

    Science.gov (United States)

    Andreeva, Antonina

    2012-01-01

    The wealth of available protein structural data provides unprecedented opportunity to study and better understand the underlying principles of protein folding and protein structure evolution. A key to achieving this lies in the ability to analyse these data and to organize them in a coherent classification scheme. Over the past years several protein classifications have been developed that aim to group proteins based on their structural relationships. Some of these classification schemes explore the concept of structural neighbourhood (structural continuum), whereas other utilize the notion of protein evolution and thus provide a discrete rather than continuum view of protein structure space. This chapter presents a strategy for classification of proteins with known three-dimensional structure. Steps in the classification process along with basic definitions are introduced. Examples illustrating some fundamental concepts of protein folding and evolution with a special focus on the exceptions to them are presented.

  7. Ultrafast coherence transfer in DNA-templated silver nanoclusters

    DEFF Research Database (Denmark)

    Thyrhaug, Erling; Bogh, Sidsel Ammitzbøll; Carro, Miguel

    2017-01-01

    DNA-templated silver nanoclusters of a few tens of atoms or less have come into prominence over the last several years due to very strong absorption and efficient emission. Applications in microscopy and sensing have already been realized, however little is known about the excited-state structure...... and dynamics in these clusters. Here we report on a multidimensional spectroscopy investigation of the energy-level structure and the early-time relaxation cascade, which eventually results in the population of an emitting state. We find that the ultrafast intramolecular relaxation is strongly coupled...

  8. Effect of steam explosion pre-treatment on molecular structure of ...

    African Journals Online (AJOL)

    Purpose: To examine the effect of steam-explosion (SE) strength on the molecular ... pressure-holding time on the molecular structure of the sweet potato starch were ... overheated liquid and then their pores are filled ... expands and exerts pressure on the cell walls, ... oscillation using distilled water as the dispersing agent.

  9. Laser-induced blurring of molecular structure information in high harmonic spectroscopy

    DEFF Research Database (Denmark)

    Risoud, Francois; Leveque, Camille; Labeye, Marie

    2017-01-01

    High harmonic spectroscopy gives access to molecular structure with Angstrom resolution. Such information is encoded in the destructive interferences occurring between the harmonic emissions from the different parts of the molecule. By solving the time-dependent Schrodinger equation, either....... These findings have important consequences for molecular imaging and orbital tomography using high harmonic spectroscopy....

  10. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    Energy Technology Data Exchange (ETDEWEB)

    Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche

    1997-09-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.

  11. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    International Nuclear Information System (INIS)

    Swygenhoven, H. van; Caro, A.

    1997-01-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young's modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs

  12. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    Energy Technology Data Exchange (ETDEWEB)

    Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J., E-mail: fwilliams@qi.fcen.uba.ar [INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química-Física, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EHA (Argentina)

    2015-11-14

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  13. Ultrafast THz Saturable Absorption in Doped Semiconductors

    DEFF Research Database (Denmark)

    Turchinovich, Dmitry; Hoffmann, Matthias C.

    2011-01-01

    We demonstrate ultrafast THz saturable absorption in n-doped semiconductors by nonlinear THz time-domain spectroscopy. This effect is caused by the semiconductor conductivity modulation due to electron heating and satellite-valley scattering in strong THz fields.......We demonstrate ultrafast THz saturable absorption in n-doped semiconductors by nonlinear THz time-domain spectroscopy. This effect is caused by the semiconductor conductivity modulation due to electron heating and satellite-valley scattering in strong THz fields....

  14. Molecular structures and functional relationships in clostridial neurotoxins.

    Science.gov (United States)

    Swaminathan, Subramanyam

    2011-12-01

    The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here. Journal compilation © 2011 FEBS. No claim to original US government works.

  15. Representation of molecular structure using quantum topology with inductive logic programming in structure-activity relationships.

    Science.gov (United States)

    Buttingsrud, Bård; Ryeng, Einar; King, Ross D; Alsberg, Bjørn K

    2006-06-01

    The requirement of aligning each individual molecule in a data set severely limits the type of molecules which can be analysed with traditional structure activity relationship (SAR) methods. A method which solves this problem by using relations between objects is inductive logic programming (ILP). Another advantage of this methodology is its ability to include background knowledge as 1st-order logic. However, previous molecular ILP representations have not been effective in describing the electronic structure of molecules. We present a more unified and comprehensive representation based on Richard Bader's quantum topological atoms in molecules (AIM) theory where critical points in the electron density are connected through a network. AIM theory provides a wealth of chemical information about individual atoms and their bond connections enabling a more flexible and chemically relevant representation. To obtain even more relevant rules with higher coverage, we apply manual postprocessing and interpretation of ILP rules. We have tested the usefulness of the new representation in SAR modelling on classifying compounds of low/high mutagenicity and on a set of factor Xa inhibitors of high and low affinity.

  16. Structure and Interface Properties of Nanophase Ceramics: Multimillion Particle Molecular-Dynamics Simulations on Parallel Computer

    National Research Council Canada - National Science Library

    Kalia, Rajiv

    1997-01-01

    Large-scale molecular-dynamics (MD) simulations were performed to investigate: (1) sintering process, structural correlations, and mechanical behavior including dynamic fracture in microporous and nanophase Si3N4...

  17. Structural Molecular Biology-A Personal Reflection on the Occasion of John Kendrew's 100th Birthday.

    Science.gov (United States)

    Cramer, Patrick

    2017-08-18

    Here, I discuss the development and future of structural molecular biology, concentrating on the eukaryotic transcription machinery and reflecting on John Kendrew's legacy from a personal perspective. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Density functional study of molecular interactions in secondary structures of proteins.

    Science.gov (United States)

    Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

    2016-01-01

    Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

  19. Adsorption and double layer charging in molecular sieve carbons in relation to molecular dimensions and pore structures

    International Nuclear Information System (INIS)

    Koresh, J.

    1982-09-01

    The pore structure of a fibrous carbon molecular sieve was studied by adsorption of molecular probes. Mild activation steps enabled the graduated opening of critical pore dimensions in the range 3.1-5.0 A, which keeps adsorption selectivity between molecules differing by 0.2 A in cross section diameter, to be considerably greater than 100/1. High adsorption stereospecificity over a wide pore dimension range enabled the studied adsorbates to be ordered in a sequence of increasing critical molecular dimension. Estimation of molecular dimensions by various experimental methods was discussed and their relevance to nonspherical molecules was evaluated. Polar molecules assume different dimensions depending on whether the carbon surface was polar (oxidized) or not. Hydrogen acquires, surprisingly, large width in accordance with its high liquid molar volume. Adsorbent-adsorbate interactions play a crucial role in determining molecular dimensions. Adsorption of ions from aqueous solutions into the developed ultramicropores of fibrous carbon electrodes was also studied. The dependence of the double layer capacitance and the charging rate on the pore critical dimension and on surface oxidation was studied using linear potential sweep voltametry. (Author)

  20. Application of molecular spectroscopy to the determination of organic structures

    International Nuclear Information System (INIS)

    Leicknam, J.P.

    1976-01-01

    Some brief accounts are presented followed by a discussion about various physico-chemical techniques: Raman spectrometry, infrared spectrometry, resonance Raman spectrometry, conformational analysis and polarized Rayleigh diffusion. Applications of the Nuclear Magnetic Resonance to nucleotide structure in aqueous solution are described as well as some applications of neutron scattering to the study of organic structures [fr

  1. Using vibrational molecular spectroscopy to reveal association of steam-flaking induced carbohydrates molecular structural changes with grain fractionation, biodigestion and biodegradation

    Science.gov (United States)

    Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

    2018-04-01

    Advanced vibrational molecular spectroscopy has been developed as a rapid and non-destructive tool to reveal intrinsic molecular structure conformation of biological tissues. However, this technique has not been used to systematically study flaking induced structure changes at a molecular level. The objective of this study was to use vibrational molecular spectroscopy to reveal association between steam flaking induced CHO molecular structural changes in relation to grain CHO fractionation, predicted CHO biodegradation and biodigestion in ruminant system. The Attenuate Total Reflectance Fourier-transform Vibrational Molecular Spectroscopy (ATR-Ft/VMS) at SRP Key Lab of Molecular Structure and Molecular Nutrition, Ministry of Agriculture Strategic Research Chair Program (SRP, University of Saskatchewan) was applied in this study. The fractionation, predicted biodegradation and biodigestion were evaluated using the Cornell Net Carbohydrate Protein System. The results show that: (1) The steam flaking induced significant changes in CHO subfractions, CHO biodegradation and biodigestion in ruminant system. There were significant differences between non-processed (raw) and steam flaked grain corn (P R2 = 0.87, RSD = 0.74, P R2 = 0.87, RSD = 0.24, P < .01). In summary, the processing induced molecular CHO structure changes in grain corn could be revealed by the ATR-Ft/VMS vibrational molecular spectroscopy. These molecular structure changes in grain were potentially associated with CHO biodegradation and biodigestion.

  2. Simple and robust generation of ultrafast laser pulse trains using polarization-independent parallel-aligned thin films

    Science.gov (United States)

    Wang, Andong; Jiang, Lan; Li, Xiaowei; Wang, Zhi; Du, Kun; Lu, Yongfeng

    2018-05-01

    Ultrafast laser pulse temporal shaping has been widely applied in various important applications such as laser materials processing, coherent control of chemical reactions, and ultrafast imaging. However, temporal pulse shaping has been limited to only-in-lab technique due to the high cost, low damage threshold, and polarization dependence. Herein we propose a novel design of ultrafast laser pulse train generation device, which consists of multiple polarization-independent parallel-aligned thin films. Various pulse trains with controllable temporal profile can be generated flexibly by multi-reflections within the splitting films. Compared with other pulse train generation techniques, this method has advantages of compact structure, low cost, high damage threshold and polarization independence. These advantages endow it with high potential for broad utilization in ultrafast applications.

  3. Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

    Directory of Open Access Journals (Sweden)

    Catherine L Worth

    Full Text Available BACKGROUND: Up until recently the only available experimental (high resolution structure of a G-protein-coupled receptor (GPCR was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY: We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s for building a comparative molecular model. CONCLUSIONS: The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying

  4. Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

    Science.gov (United States)

    Worth, Catherine L; Kleinau, Gunnar; Krause, Gerd

    2009-09-16

    Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will

  5. A parity function for studying the molecular electronic structure

    DEFF Research Database (Denmark)

    Schmider, Hartmut

    1996-01-01

    Sections through the molecular Wigner function with zero momentum variable are shown to provide important information about the off-diagonal regions of the spinless one-particle reduced density matrix. Since these regions are characteristic for the bonding situation in molecules, the sections...... are qualitatively even more affected by the presence of chemical bonds than a complementary projection, the reciprocal form factor. In this paper we discuss, on the grounds of a variety of examples, how this rather simple function may aid the understanding of the chemical bond on a one-particle level. (C) 1996...

  6. Molecular-Field Calculation of the Magnetic Structure in Erbium

    DEFF Research Database (Denmark)

    Jensen, J.

    1976-01-01

    A molecular-field calculation of the magnetic configurations in Er is found to reproduce the neutron diffraction results of the three different magnetic phases and to give a reasonable fit to the magnetization data at 4.2K. The two-ion coupling is considered to be described by the inter......-planar coupling parameters deduced from the dispersion of the spin waves in the low temperature conical phases. The four (effective) crystal-field parameters are determined by the fit to the experimental data. Projecting the magnetic moments present in the intermediate phase of Er (18-52.4K) to a common origin...

  7. Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Bibby, Jaclyn [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Keegan, Ronan M. [Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom)

    2013-11-01

    Processing of NMR structures for molecular replacement by AMPLE works well. AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

  8. Molecular Structural Transformation of 2:1 Clay Minerals by a Constant-Pressure Molecular Dynamics Simulation Method

    International Nuclear Information System (INIS)

    Wang, J.; Gutierre, M.S.

    2010-01-01

    This paper presents results of a molecular dynamics simulation study of dehydrated 2:1 clay minerals using the Parrinello-Rahman constant-pressure molecular dynamics method. The method is capable of simulating a system under the most general applied stress conditions by considering the changes of MD cell size and shape. Given the advantage of the method, it is the major goal of the paper to investigate the influence of imposed cell boundary conditions on the molecular structural transformation of 2:1 clay minerals under different normal pressures. Simulation results show that the degrees of freedom of the simulation cell (i.e., whether the cell size or shape change is allowed) determines the final equilibrated crystal structure of clay minerals. Both the MD method and the static method have successfully revealed unforeseen structural transformations of clay minerals upon relaxation under different normal pressures. It is found that large shear distortions of clay minerals occur when full allowance is given to the cell size and shape change. A complete elimination of the interlayer spacing is observed in a static simulation. However, when only the cell size change is allowed, interlayer spacing is retained, but large internal shear stresses also exist.

  9. Structures of water molecular nanotube induced by axial tensile strains

    Energy Technology Data Exchange (ETDEWEB)

    Li, H. [Key Laboratory of Liquid Structures and Heredity of Materials, Ministry of Education, School of Materials Science and Engineering, Shandong University (China)], E-mail: lihuilmy@hotmail.com; Zhang, X.Q. [Physics Department, Ocean University of China, Qingdao (China); Liew, K.M. [Department of Building and Constructions, City University of Hong Kong, Kowloon (Hong Kong); Liu, X.F. [Key Laboratory of Liquid Structures and Heredity of Materials, Ministry of Education, School of Materials Science and Engineering, Shandong University (China)

    2008-10-06

    Five well-ordered nano-ice structures embedded in carbon nanotubes are obtained in this study. These five nano-ice phases all exhibit single walled tubular morphologies, including the pentagon, hexagon ice nanotubes whose structures are quite different from bulk ice. Our simulation results indicate that water molecules tend to rearrange into surface ring structures to reduce the number of free OH groups. The structural behavior of these ice nanotubes inside CNTs subject to axial stress is also investigated. The ice nanotubes tend to be drawn to ice nanorings or ice nanospring during the mechanical stretching. The distribution function exhibits typical order-to-disorder transition of the water network confined in carbon nanotube during the stretching. By analysis, we suggest that it is unlikely that additional water molecules will enter the tubes because of the increased volume available if the tubes are stretched at contact with a water reservoir.

  10. Ultrafast probing of core hole localization in N2.

    Science.gov (United States)

    Schöffler, M S; Titze, J; Petridis, N; Jahnke, T; Cole, K; Schmidt, L Ph H; Czasch, A; Akoury, D; Jagutzki, O; Williams, J B; Cherepkov, N A; Semenov, S K; McCurdy, C W; Rescigno, T N; Cocke, C L; Osipov, T; Lee, S; Prior, M H; Belkacem, A; Landers, A L; Schmidt-Böcking, H; Weber, Th; Dörner, R

    2008-05-16

    Although valence electrons are clearly delocalized in molecular bonding frameworks, chemists and physicists have long debated the question of whether the core vacancy created in a homonuclear diatomic molecule by absorption of a single x-ray photon is localized on one atom or delocalized over both. We have been able to clarify this question with an experiment that uses Auger electron angular emission patterns from molecular nitrogen after inner-shell ionization as an ultrafast probe of hole localization. The experiment, along with the accompanying theory, shows that observation of symmetry breaking (localization) or preservation (delocalization) depends on how the quantum entangled Bell state created by Auger decay is detected by the measurement.

  11. Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth

    Energy Technology Data Exchange (ETDEWEB)

    Bernstein, Hans C.; McClure, Ryan S.; Hill, Eric A.; Markillie, Lye Meng; Chrisler, William B.; Romine, Margie F.; McDermott, Jason E.; Posewitz, Matthew C.; Bryant, Donald A.; Konopka, Allan E.; Fredrickson, James K.; Beliaev, Alexander S.

    2016-07-26

    ABSTRACT

    Harnessing the metabolic potential of photosynthetic microbes for next-generation biotechnology objectives requires detailed scientific understanding of the physiological constraints and regulatory controls affecting carbon partitioning between biomass, metabolite storage pools, and bioproduct synthesis. We dissected the cellular mechanisms underlying the remarkable physiological robustness of the euryhaline unicellular cyanobacteriumSynechococcussp. strain PCC 7002 (Synechococcus7002) and identify key mechanisms that allow cyanobacteria to achieve unprecedented photoautotrophic productivities (~2.5-h doubling time). Ultrafast growth ofSynechococcus7002 was supported by high rates of photosynthetic electron transfer and linked to significantly elevated transcription of precursor biosynthesis and protein translation machinery. Notably, no growth or photosynthesis inhibition signatures were observed under any of the tested experimental conditions. Finally, the ultrafast growth inSynechococcus7002 was also linked to a 300% expansion of average cell volume. We hypothesize that this cellular adaptation is required at high irradiances to support higher cell division rates and reduce deleterious effects, corresponding to high light, through increased carbon and reductant sequestration.

    IMPORTANCEEfficient coupling between photosynthesis and productivity is central to the development of biotechnology based on solar energy. Therefore, understanding the factors constraining maximum rates of carbon processing is necessary to identify regulatory mechanisms and devise strategies to overcome productivity constraints. Here, we interrogate the molecular mechanisms that operate at a systems level to allow cyanobacteria to achieve ultrafast growth. This was done by considering growth and photosynthetic kinetics with global transcription patterns. We have delineated

  12. Advanced understanding on electronic structure of molecular semiconductors and their interfaces

    Science.gov (United States)

    Akaike, Kouki

    2018-03-01

    Understanding the electronic structure of organic semiconductors and their interfaces is critical to optimizing functionalities for electronics applications, by rational chemical design and appropriate combination of device constituents. The unique electronic structure of a molecular solid is characterized as (i) anisotropic electrostatic fields that originate from molecular quadrupoles, (ii) interfacial energy-level lineup governed by simple electrostatics, and (iii) weak intermolecular interactions that make not only structural order but also energy distributions of the frontier orbitals sensitive to atmosphere and interface growth. This article shows an overview on these features with reference to the improved understanding of the orientation-dependent electronic structure, comprehensive mechanisms of molecular doping, and energy-level alignment. Furthermore, the engineering of ionization energy by the control of the electrostatic fields and work function of practical electrodes by contact-induced doping is briefly described for the purpose of highlighting how the electronic structure impacts the performance of organic devices.

  13. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    International Nuclear Information System (INIS)

    Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

    2013-01-01

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts

  14. Molecular structure determination of cyclooctane by Ab Initio and electron diffraction methods in the gas phase

    International Nuclear Information System (INIS)

    Almeida, Wagner B. de

    2000-01-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase an initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions. (author)

  15. Molecular structure, functionality and applications of oxidized starches: A review.

    Science.gov (United States)

    Vanier, Nathan Levien; El Halal, Shanise Lisie Mello; Dias, Alvaro Renato Guerra; da Rosa Zavareze, Elessandra

    2017-04-15

    During oxidation, the hydroxyl groups of starch molecules are first oxidized to carbonyl groups, then to carboxyl groups. The contents of the carbonyl and carboxyl groups in a starch molecule therefore indicate the extent of starch oxidation. The mechanisms of starch oxidation with different oxidizing agents, including sodium hypochlorite, hydrogen peroxide, ozone and sodium periodate, are described in this review. The effects of these oxidizing agents on the molecular, physicochemical, thermal, pasting and morphological properties of starch are described as well. In addition, the main industrial applications of oxidized starches are presented. The present review is important for understanding the effects of oxidation on starch properties, and this information may facilitate the development of novel oxidized starches for both food and non-food applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Introductory group theory and its application to molecular structure

    CERN Document Server

    Ferraro, John R

    1969-01-01

    This volume is a consequence of a series of seminars presented by the authors at the Infrared Spectroscopy Institute, Canisius College, Buffalo, New York, over the last nine years. Many participants on an intermediate level lacked a sufficient background in mathematics and quantum mechan­ ics, and it became evident that a non mathematical or nearly nonmathe­ matical approach would be necessary. The lectures were designed to fill this need and proved very successful. As a result of the interest that was developed in this approach, it was decided to write this book. The text is intended for scientists and students with only limited theore­ tical background in spectroscopy, but who are sincerely interested in the interpretation of molecular spectra. The book develops the detailed selection rules for fundamentals, combinations, and overtones for molecules in several point groups. Detailed procedures used in carrying out the normal coordinate treatment for several molecules are also presented. Numerous examples...

  17. Electronic structure, transport, and collective effects in molecular layered systems

    Directory of Open Access Journals (Sweden)

    Torsten Hahn

    2017-10-01

    Full Text Available The great potential of organic heterostructures for organic device applications is exemplified by the targeted engineering of the electronic properties of phthalocyanine-based systems. The transport properties of two different phthalocyanine systems, a pure copper phthalocyanine (CoPc and a flourinated copper phthalocyanine–manganese phthalocyanine (F16CoPc/MnPc heterostructure, are investigated by means of density functional theory (DFT and the non-equilibrium Green’s function (NEGF approach. Furthermore, a master-equation-based approach is used to include electronic correlations beyond the mean-field-type approximation of DFT. We describe the essential theoretical tools to obtain the parameters needed for the master equation from DFT results. Finally, an interacting molecular monolayer is considered within a master-equation approach.

  18. The Structural, Functional and Molecular Organization of the Brainstem

    Directory of Open Access Journals (Sweden)

    Rudolf eNieuwenhuys

    2011-06-01

    Full Text Available According to Wilhelm His (1891, 1893 the brainstem consists of two longitudinal zones, the dorsal alar plate (sensory in nature and the ventral basal plate (motor in nature. Johnston and Herrick indicated that both plates can be subdivided into separate somatic and visceral zones, distinguishing somatosensory and viscerosensory zones within the alar plate, and visceromotor and somatomotor zones within the basal plate. To test the validity of this ‘four-functional-zones’ concept, I developed a topological procedure, surveying the spatial relationships of the various cell masses in the brainstem in a single figure. Brainstems of 16 different anamniote species were analyzed, and revealed that the brainstems are clearly divisible into four morphological zones, which correspond largely with the functional zones of Johnston and Herrick. Exceptions include (1 the magnocellular vestibular nucleus situated in the viscerosensory zone; (2 the basal plate containing a number of evidently non-motor centres (superior and inferior olives. Nevertheless the ‘functional zonal model’ has explanatory value. Thus, it is possible to interpret certain brain specializations related to particular behavioural profiles, as ‘local hypertrophies’ of one or two functional columns. Recent developmental molecular studies on brains of birds and mammals confirmed the presence of longitudinal zones, and also showed molecularly defined transverse bands or neuromeres throughout development. The intersecting boundaries of the longitudinal zones and the transverse bands appeared to delimit radially arranged histogenetic domains. Because neuromeres have been observed in embryonic and larval stages of numerous anamniote species, it may be hypothesized that the brainstems of all vertebrates share a basic organizational plan, in which intersecting longitudinal and transverse zones form fundamental histogenetic and genoarchitectonic units.

  19. Molecular dynamics simulations of single siloxane dendrimers: Molecular structure and intramolecular mobility of terminal groups

    Science.gov (United States)

    Kurbatov, A. O.; Balabaev, N. K.; Mazo, M. A.; Kramarenko, E. Yu.

    2018-01-01

    Molecular dynamics simulations of two types of isolated siloxane dendrimers of various generations (from the 2nd to the 8th) have been performed for temperatures ranging from 150 K to 600 K. The first type of dendrimer molecules has short spacers consisting of a single oxygen atom. In the dendrimers of the second type, spacers are longer and comprised of two oxygen atoms separated by a single silicon atom. A comparative analysis of molecular macroscopic parameters such as the gyration radius and the shape factor as well as atom distributions within dendrimer interior has been performed for varying generation number, temperature, and spacer length. It has been found that the short-spacer dendrimers of the 7th and 8th generations have a stressed central part with elongated bonds and deformed valence angles. Investigation of the time evolution of radial displacements of the terminal Si atoms has shown that a fraction of the Si groups have a reduced mobility. Therefore, rather long time trajectories (of the order of tens of nanoseconds) are required to study dendrimer intramolecular dynamics.

  20. Magnetic structure of molecular magnet Fe[Fe(CN) 6

    Indian Academy of Sciences (India)

    We have studied the magnetic structure of Fe[Fe(CN)6]·4H2O, prepared by precipitation method, using neutron diffraction technique. Temperature dependent DC magnetization study down to 4.2 K shows that the compound undergoes from a high temperature disordered (paramagnetic) to an ordered magnetic phase ...

  1. Energy-related atomic and molecular structure and scattering studies: Final report

    International Nuclear Information System (INIS)

    1987-01-01

    The general goals of the DOE research concerned the use of molecular beams techniques in the study of atomic and molecular polarizabilities and the study of the interactions between electrons and highly polar molecules. Both of these goals are directly relevant to the general problem of the role played by long-range forces in atomic and molecular physics. Details related to this motivation can be found in the published literature. Here we will describe in general terms the work performed under DOE sponsorship in the atomic beams laboratory at NYU. Our original intent was to exploit techniques developed at NYU, mainly in the study of simple atomic systems, to the more complex atomic and molecular systems that are related to DOE interests. These included the developing understanding of the structure of molecular systems, particularly of alkali halide molecules, and the study of the interactions of electrons with such molecules. The structure experiments would serve as critical experimental benchmarks for computational techniques on molecular properties, including both molecular wave functions and derivative properties of them, such as vibrational and rotational constants, but in particular of molecular electric dipole polarizabilities. We believe that we have at least to some extent fulfilled these goals. 16 refs., 1 fig

  2. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    International Nuclear Information System (INIS)

    Eisenberg, David S.

    2008-01-01

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  3. Structural insights of Staphylococcus aureus FtsZ inhibitors through molecular docking, 3D-QSAR and molecular dynamics simulations.

    Science.gov (United States)

    Ballu, Srilata; Itteboina, Ramesh; Sivan, Sree Kanth; Manga, Vijjulatha

    2018-02-01

    Filamentous temperature-sensitive protein Z (FtsZ) is a protein encoded by the FtsZ gene that assembles into a Z-ring at the future site of the septum of bacterial cell division. Structurally, FtsZ is a homolog of eukaryotic tubulin but has low sequence similarity; this makes it possible to obtain FtsZ inhibitors without affecting the eukaryotic cell division. Computational studies were performed on a series of substituted 3-arylalkoxybenzamide derivatives reported as inhibitors of FtsZ activity in Staphylococcus aureus. Quantitative structure-activity relationship models (QSAR) models generated showed good statistical reliability, which is evident from r 2 ncv and r 2 loo values. The predictive ability of these models was determined and an acceptable predictive correlation (r 2 Pred ) values were obtained. Finally, we performed molecular dynamics simulations in order to examine the stability of protein-ligand interactions. This facilitated us to compare free binding energies of cocrystal ligand and newly designed molecule B1. The good concordance between the docking results and comparative molecular field analysis (CoMFA)/comparative molecular similarity indices analysis (CoMSIA) contour maps afforded obliging clues for the rational modification of molecules to design more potent FtsZ inhibitors.

  4. Spectroscopic Investigation of the Ultrafast Photoinduced Dynamics in pi-Conjugated Terpyridines

    NARCIS (Netherlands)

    Siebert, R.; Akimov, D.; Schmitt, M.; Winter, A.; Schubert, U.S.; Dietzek, B.; Popp, J.

    2009-01-01

    Time-resolved spectroscopy is applied to investigate the ultrafast relaxation dynamics of several pi-conjugated mono-, bis-, tris- and tetrakis(terpyridine) derivs. This particular series of structurally closely related systems was prepd. applying efficient synthetic strategies and resembles key

  5. Low damage electrical modification of 4H-SiC via ultrafast laser irradiation

    Science.gov (United States)

    Ahn, Minhyung; Cahyadi, Rico; Wendorf, Joseph; Bowen, Willie; Torralva, Ben; Yalisove, Steven; Phillips, Jamie

    2018-04-01

    The electrical properties of 4H-SiC under ultrafast laser irradiation in the low fluence regime (engineering spatially localized structural and electronic modification of wide bandgap materials such as 4H-SiC with relatively low surface damage via low temperature processing.

  6. Hot-electrons-induced ultrafast demagnitization in Co/Pt multilayers

    NARCIS (Netherlands)

    Bergeard, N.; Hehn, M.; Mangin, S.; Lengaigne, G.; Montaigne, F.; Lalieu, M. L. M.; Koopmans, B.; Malinowski, G.

    2016-01-01

    Using specially engineered structures to tailor the optical absorption in a metallic multilayer, we analyze the magnetization dynamics of a Co/Pt multilayer buried below a thick Cu layer. We demonstrate that hot electrons alone can very efficiently induce ultrafast demagnetization. Simulations based

  7. The Scent of Roses and beyond: Molecular Structures, Analysis, and Practical Applications of Odorants

    Science.gov (United States)

    Mannschreck, Albrecht; von Angerer, Erwin

    2011-01-01

    A few odorous compounds found in roses are chosen to arouse the reader's interest in their molecular structures. This article differs from some similar reports on odorants mainly by combining the structural description with the presentation of the following types of isomers: constitutional isomers, enantiomers, and diastereomers. The preparation…

  8. Structure and properties of sodium aluminosilicate glasses from molecular dynamics simulations

    DEFF Research Database (Denmark)

    Xiang, Ye; Du, Jincheng; Smedskjær, Morten Mattrup

    2013-01-01

    the recent Corning® Gorilla® Glass. In this paper, the structures of sodium aluminosilicate glasses with a wide range of Al/Na ratios (from 1.5 to 0.6) have been studied using classical molecular dynamics simulations in a system containing around 3000 atoms, with the aim to understand the structural role...

  9. Ultrafast laser spectroscopy in complex solid state materials

    Energy Technology Data Exchange (ETDEWEB)

    Li, Tianqi [Iowa State Univ., Ames, IA (United States)

    2014-12-01

    This thesis summarizes my work on applying the ultrafast laser spectroscopy to the complex solid state materials. It shows that the ultrafast laser pulse can coherently control the material properties in the femtosecond time scale. And the ultrafast laser spectroscopy can be employed as a dynamical method for revealing the fundamental physical problems in the complex material systems.

  10. The structure of the Orion A molecular cloud

    International Nuclear Information System (INIS)

    Gerola, H.; Sofia, S.

    1975-01-01

    A consistent model of the Orion A molecular cloud is obtained by making use of the observed brightness temperature distributions of the J=2→1 and the J=1→0 transitions of the CO molecule, and the central component (F=2→1) of the J=1→0 transition of HCN, as well as the observed line profiles of the J=2→1 transition of CO, and the J=1→0 transition of HCN. The modeling is accomplished by fitting simultaneously all of these observations through solutions of the coupled equations of statistical equilibrium and radiative transfer for a spherical cloud having a kinetic temperature gradient, and different density and velocity distributions. We find that Orion A is strongly gravitationally bound and contracting, and that it can maintain the observed temperature distribution only by virtue of internal energy sources other than the contraction. This last conclusion is reached by computing the radiative losses due to the CO and HD cooling, as well as the losses due to the CO and HD cooling, as well as the losses due to inelastic collisions between the gas and the dust. Our results show that while the contraction rate is just about sufficient to balance the rate of radiation by CO, it is less than one-tenth of the rate at which energy is radiated by HD, and less than 0.001 of that at which energy could be lost to cool grains through totally inelastic collisions

  11. Structure-Function Based Molecular Relationships in Ewing's Sarcoma

    Science.gov (United States)

    2015-01-01

    Ewing's Sarcoma Oncogene (ews) on chromosome 22q12 is encoding a ubiquitously expressed RNA-binding protein (EWS) with unknown function that is target of tumor-specific chromosomal translocations in Ewing's sarcoma family of tumors. A model of transcription complex was proposed in which the heterodimer Rpb4/7 binds to EAD, connecting it to Core RNA Pol II. The DNA-binding domain, provided by EFP, is bound to the promoter. Rpb4/7 binds RNA, stabilizing the transcription complex. The complex Rpb4/7 can stabilize the preinitiation complexes by converting the conformation of RNA Pol II. EWS may change its conformation, so that NTD becomes accessible. Two different mechanisms of interaction between EWS and RNA Pol II are proposed: (I) an intermolecular EWS-EWS interaction between two molecules, pushing conformation from “closed” to “open” state, or (II) an intramolecular interaction inside the molecule of EWS, pushing conformation of the molecule from “closed” to “open” state. The modified forms of EWS may interact with Pol II subunits hsRpb5 and hsRpb7. The EWS and EFPs binding partners are described schematically in a model, an attempt to link the transcription with the splicing. The proposed model helps to understand the functional molecular interactions in cancer, to find new partners and ways to treat cancer. PMID:25688366

  12. Molecular Descriptors Family on Structure Activity Relationships 1. Review of the Methodology

    Directory of Open Access Journals (Sweden)

    Lorentz JÄNTSCHI

    2005-01-01

    Full Text Available This review cumulates the knowledge about the use of Molecular Descriptors Family usage on Structure Activity Relationships. The methodology is augmented through the general Structure Activity Relationships methodology. The obtained models in a series of five papers are quantitatively analyzed by comparing with previous reported results by using of the correlated correlations tests. The scores for a series of 13 data sets unpublished yet results are presented. Two unrestricted online access portals to the Molecular Descriptors Family Structure Activity Relationship models results are given.

  13. NATO Advanced Study Institute on Electronic Structure of Polymers and Molecular Crystals

    CERN Document Server

    Ladik, János

    1975-01-01

    The NATO Advanced Study Institute on "Electronic Structure of Polymers and Molecular Crystals" was held at the Facultes Universi­ taires de Namur (F.U.N.) from September 1st till September 14th, 1974. We wish to express our appreciation to the NATO Scientific Affairs Division whose generous support made this Institute possible and to the Facultes Universitaires de Namur and the Societe Chimique de Belgique which provided fellowships and travel grants to a number of students. This volume contains the main lectures about the basic principles of the field and about different recent developments of the theory of the electronic structure of polymers and molecular crystals. The school started with the presentation of the basic SCF-LCAO theory of the electronic structure of periodic polymers and molecular crystals (contributions by Ladik, Andre & Delhalle) showing how a combination of quantum chemical and solid state physical methods can provide band structures for these systems. The numerical aspects of these ...

  14. Relation between molecular electronic structure and nuclear spin-induced circular dichroism

    DEFF Research Database (Denmark)

    Štěpánek, Petr; Coriani, Sonia; Sundholm, Dage

    2017-01-01

    with spatially localized, high-resolution information. To survey the factors relating the molecular and electronic structure to the NSCD signal, we theoretically investigate NSCD of twenty structures of the four most common nucleic acid bases (adenine, guanine, thymine, cytosine). The NSCD signal correlates...... with the spatial distribution of the excited states and couplings between them, reflecting changes in molecular structure and conformation. This constitutes a marked difference to the nuclear magnetic resonance (NMR) chemical shift, which only reflects the local molecular structure in the ground electronic state....... The calculated NSCD spectra are rationalized by means of changes in the electronic density and by a sum-over-states approach, which allows to identify the contributions of the individual excited states. Two separate contributions to NSCD are identified and their physical origins and relative magnitudes...

  15. Spectrally- and Time-Resolved Sum Frequency Generation (STiR-SFG): a new tool for ultrafast hydrogen bond dynamics at interfaces.

    Science.gov (United States)

    Benderskii, Alexander; Bordenyuk, Andrey; Weeraman, Champika

    2006-03-01

    The recently developed spectrally- and time-resolved Sum Frequency Generation (STiR-SFG) is a surface-selective 3-wave mixing (IR+visible) spectroscopic technique capable of measuring ultrafast spectral evolution of vibrational coherences. A detailed description of this measurement will be presented, and a noniterative method or deconvolving the laser pulses will be introduced to obtain the molecular response function. STiR-SFG, combined with the frequency-domain SFG spectroscopy, was applied to study hydrogen bonding dynamics at aqueous interfaces (D2O/CaF2). Spectral dynamics of the OD-stretch on the 50-150 fs time scale provides real-time observation of ultrafast H-bond rearrangement. Tuning the IR wavelength to the blue or red side of the OD-stretch transition, we selectively monitor the dynamics of different sub-ensembles in the distribution of the H-bond structures. The blue-side excitation (weaker H-bonding) shows monotonic red-shift of the OD-frequency. In contrast, the red-side excitation (stronger H-bonding structures) produces a blue-shift and a recursion, which may indicate the presence of an underdamped intermolecular mode of interfacial water. Effect of electrolyte concentration on the H-bond dynamics will be discussed.

  16. Molecular structures of viruses from Raman optical activity

    DEFF Research Database (Denmark)

    Blanch, Ewan W.; Hecht, Lutz; Syme, Christopher D.

    2002-01-01

    A vibrational Raman optical activity (ROA) study of a range of different structural types of virus exemplified by filamentous bacteriophage fd, tobacco mosaic virus, satellite tobacco mosaic virus, bacteriophage MS2 and cowpea mosaic virus has revealed that, on account of its sensitivity to chira......A vibrational Raman optical activity (ROA) study of a range of different structural types of virus exemplified by filamentous bacteriophage fd, tobacco mosaic virus, satellite tobacco mosaic virus, bacteriophage MS2 and cowpea mosaic virus has revealed that, on account of its sensitivity...... (top component) of cowpea mosaic virus from those of the intact middle and bottom-upper components separated by means of a caesium chloride density gradient, the ROA spectrum of the viral RNA was obtained, which revealed that the RNA takes up an A-type single-stranded helical conformation...... and that the RNA conformations in the middle and bottom-upper components are very similar. This information is not available from the X-ray crystal structure of cowpea mosaic virus since no nucleic acid is visible....

  17. Ultrafast transmission electron microscopy using a laser-driven field emitter: Femtosecond resolution with a high coherence electron beam

    Energy Technology Data Exchange (ETDEWEB)

    Feist, Armin; Bach, Nora; Rubiano da Silva, Nara; Danz, Thomas; Möller, Marcel; Priebe, Katharina E.; Domröse, Till; Gatzmann, J. Gregor; Rost, Stefan; Schauss, Jakob; Strauch, Stefanie; Bormann, Reiner; Sivis, Murat; Schäfer, Sascha, E-mail: sascha.schaefer@phys.uni-goettingen.de; Ropers, Claus, E-mail: claus.ropers@uni-goettingen.de

    2017-05-15

    We present the development of the first ultrafast transmission electron microscope (UTEM) driven by localized photoemission from a field emitter cathode. We describe the implementation of the instrument, the photoemitter concept and the quantitative electron beam parameters achieved. Establishing a new source for ultrafast TEM, the Göttingen UTEM employs nano-localized linear photoemission from a Schottky emitter, which enables operation with freely tunable temporal structure, from continuous wave to femtosecond pulsed mode. Using this emission mechanism, we achieve record pulse properties in ultrafast electron microscopy of 9 Å focused beam diameter, 200 fs pulse duration and 0.6 eV energy width. We illustrate the possibility to conduct ultrafast imaging, diffraction, holography and spectroscopy with this instrument and also discuss opportunities to harness quantum coherent interactions between intense laser fields and free-electron beams. - Highlights: • First implementation of an ultrafast TEM employing a nanoscale photocathode. • Localized single photon-photoemission from nanoscopic field emitter yields low emittance ultrashort electron pulses. • Electron pulses focused down to ~9 Å, with a duration of 200 fs and an energy width of 0.6 eV are demonstrated. • Quantitative characterization of ultrafast electron gun emittance and brightness. • A range of applications of high coherence ultrashort electron pulses is shown.

  18. Serotonin neuron development: shaping molecular and structural identities.

    Science.gov (United States)

    Deneris, Evan; Gaspar, Patricia

    2018-01-01

    The continuing fascination with serotonin (5-hydroxytryptamine, 5-HT) as a nervous system chemical messenger began with its discovery in the brains of mammals in 1953. Among the many reasons for this decades-long interest is that the small numbers of neurons that make 5-HT influence the excitability of neural circuits in nearly every region of the brain and spinal cord. A further reason is that 5-HT dysfunction has been linked to a range of psychiatric and neurological disorders many of which have a neurodevelopmental component. This has led to intense interest in understanding 5-HT neuron development with the aim of determining whether early alterations in their generation lead to brain disease susceptibility. Here, we present an overview of the neuroanatomical organization of vertebrate 5-HT neurons, their neurogenesis, and prodigious axonal architectures, which enables the expansive reach of 5-HT neuromodulation in the central nervous system. We review recent findings that have revealed the molecular basis for the tremendous diversity of 5-HT neuron subtypes, the impact of environmental factors on 5-HT neuron development, and how 5-HT axons are topographically organized through disparate signaling pathways. We summarize studies of the gene regulatory networks that control the differentiation, maturation, and maintenance of 5-HT neurons. These studies show that the regulatory factors controlling acquisition of 5-HT-type transmitter identity continue to play critical roles in the functional maturation and the maintenance of 5-HT neurons. New insights are presented into how continuously expressed 5-HT regulatory factors control 5-HT neurons at different stages of life and how the regulatory networks themselves are maintained. WIREs Dev Biol 2018, 7:e301. doi: 10.1002/wdev.301 This article is categorized under: Nervous System Development > Vertebrates: General Principles Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics Gene Expression and

  19. A circumstellar molecular gas structure associated with the massive young star Cepheus A-HW 2

    Science.gov (United States)

    Torrelles, Jose M.; Rodriguez, Luis F.; Canto, Jorge; Ho, Paul T. P.

    1993-01-01

    We report the detection via VLA-D observations of ammonia of a circumstellar high-density molecular gas structure toward the massive young star related to the object Cepheus A-HW 2, a firm candidate for the powering source of the high-velocity molecular outflow in the region. We suggest that the circumstellar molecular gas structure could be related to the circumstellar disk previously suggested from infrared, H2O, and OH maser observations. We consider as a plausible scenario that the double radio continuum source of HW 2 could represent the ionized inner part of the circumstellar disk, in the same way as proposed to explain the double radio source in L1551. The observed motions in the circumstellar molecular gas can be produced by bound motions (e.g., infall or rotation) around a central mass of about 10-20 solar masses (B0.5 V star or earlier).

  20. Electronic structure of surface-supported bis(phthalocyaninato) terbium(III) single molecular magnets.

    Science.gov (United States)

    Vitali, Lucia; Fabris, Stefano; Conte, Adriano Mosca; Brink, Susan; Ruben, Mario; Baroni, Stefano; Kern, Klaus

    2008-10-01

    The electronic structure of isolated bis(phthalocyaninato) terbium(III) molecules, a novel single-molecular-magnet (SMM), supported on the Cu(111) surface has been characterized by density functional theory and scanning tunneling spectroscopy. These studies reveal that the interaction with the metal surface preserves both the molecular structure and the large spin magnetic moment of the metal center. The 4f electron states are not perturbed by the adsorption while a strong molecular/metal interaction can induce the suppression of the minor spin contribution delocalized over the molecular ligands. The calculations show that the inherent spin magnetic moment of the molecule is only weakly affected by the interaction with the surface and suggest that the SMM character might be preserved.

  1. Synthesis, reactivity, and electronic structure of molecular uranium nitrides

    OpenAIRE

    Cleaves, Peter A.

    2016-01-01

    The study of metal-ligand multiple bonding offers insight into the electronic structure and bond of metal systems. Until recently, for uranium, such systems were limited to uranyl, and terminal chalcogenide, imide and carbene complexes. In 2012, this was extended to nitrides with the first preparation of a uranium–nitride (U≡N) species isolable under standard conditions, namely [U(TrenTIPS)(N)][Na(12C4)2] (52), which is prepared by the two-electron reduction of sodium azide with a trivalent u...

  2. Study of the molecular structure of uranium hexafluoride

    International Nuclear Information System (INIS)

    Bougon, R.

    1967-06-01

    The vibrational spectrum of uranium hexafluoride has been studied in both the gaseous and solid states. The study of gaseous UF 6 confirms the regular octahedral structure of the fluorine atoms around the central U atom and makes it possible to evaluate some of the vibrational frequencies. From these, some new force constants have been determined. A tetragonal distortion is observed on solid UF 6 ; this distortion has only observed up till now by means of X-ray diffraction and nuclear magnetic resonance techniques. (author) [fr

  3. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    International Nuclear Information System (INIS)

    Yu, P.

    2007-01-01

    The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  4. Advances in Rosetta structure prediction for difficult molecular-replacement problems

    International Nuclear Information System (INIS)

    DiMaio, Frank

    2013-01-01

    Modeling advances using Rosetta structure prediction to aid in solving difficult molecular-replacement problems are discussed. Recent work has shown the effectiveness of structure-prediction methods in solving difficult molecular-replacement problems. The Rosetta protein structure modeling suite can aid in the solution of difficult molecular-replacement problems using templates from 15 to 25% sequence identity; Rosetta refinement guided by noisy density has consistently led to solved structures where other methods fail. In this paper, an overview of the use of Rosetta for these difficult molecular-replacement problems is provided and new modeling developments that further improve model quality are described. Several variations to the method are introduced that significantly reduce the time needed to generate a model and the sampling required to improve the starting template. The improvements are benchmarked on a set of nine difficult cases and it is shown that this improved method obtains consistently better models in less running time. Finally, strategies for best using Rosetta to solve difficult molecular-replacement problems are presented and future directions for the role of structure-prediction methods in crystallography are discussed

  5. FlaME: Flash Molecular Editor - a 2D structure input tool for the web

    Directory of Open Access Journals (Sweden)

    Dallakian Pavel

    2011-02-01

    Full Text Available Abstract Background So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME. In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. Implementation The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol( and setMol(. In addition, structures can be copied to the system clipboard. Conclusion A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application and the HTML elements on a web page, using JavaScript functions.

  6. Ultrafast Bessel beams: advanced tools for laser materials processing

    Science.gov (United States)

    Stoian, Razvan; Bhuyan, Manoj K.; Zhang, Guodong; Cheng, Guanghua; Meyer, Remy; Courvoisier, Francois

    2018-05-01

    Ultrafast Bessel beams demonstrate a significant capacity of structuring transparent materials with a high degree of accuracy and exceptional aspect ratio. The ability to localize energy on the nanometer scale (bypassing the 100-nm milestone) makes them ideal tools for advanced laser nanoscale processing on surfaces and in the bulk. This allows to generate and combine micron and nano-sized features into hybrid structures that show novel functionalities. Their high aspect ratio and the accurate location can equally drive an efficient material modification and processing strategy on large dimensions. We review, here, the main concepts of generating and using Bessel non-diffractive beams and their remarkable features, discuss general characteristics of their interaction with matter in ablation and material modification regimes, and advocate their use for obtaining hybrid micro and nanoscale structures in two and three dimensions (2D and 3D) performing complex functions. High-throughput applications are indicated. The example list ranges from surface nanostructuring and laser cutting to ultrafast laser welding and the fabrication of 3D photonic systems embedded in the volume.

  7. Structured attachment of bacterial molecular motors for defined microflow induction

    Directory of Open Access Journals (Sweden)

    Woerdemann Mike

    2014-01-01

    Full Text Available Bacterial rotational motor complexes that propel flagellated bacteria possess unique properties like their size of a few nanometres and the ability of selfreproduction that have led to various exciting applications including biohybrid nano-machines. One mandatory prerequisite to utilize bacterial nano motors in fluid applications is the ability to transfer force and torque to the fluid, which usually can be achieved by attachment of the bacterial cell to adequate surfaces. Additionally, for optimal transfer of force or torque, precise control of the position down to the single cell level is of utmost importance. Based on a PIV (particle image velocimetry evaluation of the induced flow of single bacteria,we propose and demonstrate attachment of arbitrary patterns of motile bacterial cells in a fast light-based two-step process for the first time to our knowledge. First, these cells are pre-structured by holographic optical tweezers and then attached to a homogeneous, polystyrene-coated surface. In contrast to the few approaches that have been implemented up to now and which rely on pre-structured surfaces, our scheme allows for precise control on a single bacterium level, is versatile, interactive and has low requirements with respect to the surface preparation.

  8. Crystal and molecular structure of neodymium (3) p-aminobenzoaate

    International Nuclear Information System (INIS)

    Khiyalov, M.S.; Amiraslanov, I.R.; Mamedov, Kh.S.; Movsumov, Eh.M.

    1981-01-01

    X-ray structural study (lambda MoKsub(α), automatic diffractometer, the method of heavy atom, anisotropic specification) of neodymium (3) n-aminobenzoate has been carried out. The crystals are monoclinic: a=9.882 (5), b=22.810 (12), c=9.851 (8)A, β=100.02 (5)deg, v=2186.59 A 3 , Z=4, sp. gr. P2 1 /n, R=0.046. The crystal structure of Nd(OOCC 6 H 4 NH 2 ) 3 xH 2 O consists of dimer-periodic layers alternating along the b axis. Surrounding of Nd atom in the chain is formed with four oxygen atoms of four carboxyl groups of bidentate-bridge and one carboxyl bidentate-cyclic ligands, one water molecule and N atom of ligand aminogroup from the neigbouring chain. The atom simultaneously bonds the neighbouring chains into continuous layer. The mean distances Nd-O, and Nd-N are equal to 2.45 and 2.74 A. An attempt to determine hydrogen atom coordinates has failed [ru

  9. Ultrafast disk lasers and amplifiers

    Science.gov (United States)

    Sutter, Dirk H.; Kleinbauer, Jochen; Bauer, Dominik; Wolf, Martin; Tan, Chuong; Gebs, Raphael; Budnicki, Aleksander; Wagenblast, Philipp; Weiler, Sascha

    2012-03-01

    Disk lasers with multi-kW continuous wave (CW) output power are widely used in manufacturing, primarily for cutting and welding applications, notably in the automotive industry. The ytterbium disk technology combines high power (average and/or peak power), excellent beam quality, high efficiency, and high reliability with low investment and operating costs. Fundamental mode picosecond disk lasers are well established in micro machining at high throughput and perfect precision. Following the world's first market introduction of industrial grade 50 W picosecond lasers (TruMicro 5050) at the Photonics West 2008, the second generation of the TruMicro series 5000 now provides twice the average power (100 W at 1030 nm, or 60 W frequency doubled, green output) at a significantly reduced footprint. Mode-locked disk oscillators achieve by far the highest average power of any unamplified lasers, significantly exceeding the 100 W level in laboratory set-ups. With robust long resonators their multi-microjoule pulse energies begin to compete with typical ultrafast amplifiers. In addition, significant interest in disk technology has recently come from the extreme light laser community, aiming for ultra-high peak powers of petawatts and beyond.

  10. Ultra-Fast Hadronic Calorimetry

    Energy Technology Data Exchange (ETDEWEB)

    Denisov, Dmitri [Fermilab; Lukić, Strahinja [VINCA Inst. Nucl. Sci., Belgrade; Mokhov, Nikolai [Fermilab; Striganov, Sergei [Fermilab; Ujić, Predrag [VINCA Inst. Nucl. Sci., Belgrade

    2017-12-18

    Calorimeters for particle physics experiments with integration time of a few ns will substantially improve the capability of the experiment to resolve event pileup and to reject backgrounds. In this paper time development of hadronic showers induced by 30 and 60 GeV positive pions and 120 GeV protons is studied using Monte Carlo simulation and beam tests with a prototype of a sampling steel-scintillator hadronic calorimeter. In the beam tests, scintillator signals induced by hadronic showers in steel are sampled with a period of 0.2 ns and precisely time-aligned in order to study the average signal waveform at various locations w.r.t. the beam particle impact. Simulations of the same setup are performed using the MARS15 code. Both simulation and test beam results suggest that energy deposition in steel calorimeters develop over a time shorter than 3 ns providing opportunity for ultra-fast calorimetry. Simulation results for an "ideal" calorimeter consisting exclusively of bulk tungsten or copper are presented to establish the lower limit of the signal integration window.

  11. Ultrafast palladium diffusion in germanium

    KAUST Repository

    Tahini, Hassan Ali

    2015-01-01

    The slow transport of dopants through crystal lattices has hindered the development of novel devices. Typically atoms are contained within deep potential energy wells which necessitates multiple attempts to hop between minimum energy positions. This is because the bonds that constrain atoms are strongest at the minimum positions. As they hop between sites the bonds must be broken, only to re-form as the atoms slide into adjacent minima. Here we demonstrate that the Pd atoms introduced into the Ge lattice behave differently. They retain bonds as the atoms shift across so that at the energy maximum between sites Pd still exhibits strong bonding characteristics. This reduces the energy maximum to almost nothing (a migration energy of only 0.03 eV) and means that the transport of Pd through the Ge lattice is ultrafast. We scrutinize the bonding characteristics at the atomic level using quantum mechanical simulation tools and demonstrate why Pd behaves so differently to other metals we investigated (i.e. Li, Cu, Ag, Pt and Au). Consequently, this fundamental understanding can be extended to systems where extremely rapid diffusion is desired, such as radiation sensors, batteries and solid oxide fuel cells.

  12. Pump polarization insensitive and efficient laser-diode pumped Yb:KYW ultrafast oscillator.

    Science.gov (United States)

    Wang, Sha; Wang, Yan-Biao; Feng, Guo-Ying; Zhou, Shou-Huan

    2016-02-01

    We theoretically and experimentally report and evaluate a novel split laser-diode (LD) double-end pumped Yb:KYW ultrafast oscillator aimed at improving the performance of an ultrafast laser. Compared to a conventional unpolarized single-LD end-pumped ultrafast laser system, we improve the laser performance such as absorption efficiency, slope efficiency, cw mode-locking threshold, and output power by this new structure LD-pumped Yb:KYW ultrafast laser. Experiments were carried out with a 1 W output fiber-coupled LD. Experimental results show that the absorption increases from 38.7% to 48.4%, laser slope efficiency increases from 18.3% to 24.2%, cw mode-locking threshold decreases 12.7% from 630 to 550 mW in cw mode-locking threshold, and maximum output-power increases 28.5% from 158.4 to 221.5 mW when we switch the pump scheme from an unpolarized single-end pumping structure to a split LD double-end pumping structure.

  13. Crystal and molecular structure of dysprosium (3) n-aminobenzoate

    International Nuclear Information System (INIS)

    Khiyalov, M.S.; Amiraslanov, I.R.; Mamedov, Kh.S.; Movsumov, Eh.M.

    1981-01-01

    The X ray diffraction investigation of the Dy(NH 2 C 6 H 4 COO) 3 x3H 2 O complex is carried out. Triclinic crystals have lattice parameters α=11.095(15), b=9.099(17), c=12.780 (15)A, α=108.051(12), β=89.072(10); γ=104.954(12) 0 , space group P anti 1, Z=2. The structure consists of dimer molecules. The third water molecule in the formula is an outer spherical one. The average lengths of Dy-O and Dy-OH 2 are 2.39 and 2.40 A respectively, the average value of Dy-O in bridge carboxylates (2.26A) is remarkably shorter. Hydrogen bonds between amine ligand ends, carboxylic groups oxygen and water molecules bind complex molecules into the three-dimensional frame [ru

  14. Human Skin Barrier Structure and Function Analyzed by Cryo-EM and Molecular Dynamics Simulation.

    Science.gov (United States)

    Lundborg, Magnus; Narangifard, Ali; Wennberg, Christian L; Lindahl, Erik; Daneholt, Bertil; Norlén, Lars

    2018-04-24

    In the present study we have analyzed the molecular structure and function of the human skin's permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin. The skin's barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin - the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety. However, knowledge about the lipid structure's detailed molecular organization, and the roles of its different lipid constituents, remains circumstantial. Starting from a molecular dynamics model based on the splayed bilayer model, we have, by stepwise structural and compositional modifications, arrived at a thermodynamically stable molecular dynamics model expressing simulated electron microscopy patterns matching original cryo-electron microscopy patterns from skin extremely closely. Strikingly, the closer the individual molecular dynamics models' lipid composition was to that reported in human stratum corneum, the better was the match between the models' simulated electron microscopy patterns and the original cryo-electron microscopy patterns. Moreover, the closest-matching model's calculated water permeability and thermotropic behaviour were found compatible with that of human skin. The new model may facilitate more advanced physics-based skin permeability predictions of drugs and toxicants. The proposed procedure for molecular dynamics based analysis of cellular cryo-electron microscopy data might be applied to other biomolecular systems. Copyright © 2018. Published by Elsevier Inc.

  15. Coalescence of silver unidimensional structures by molecular dynamics simulation; Coalescencia de estructuras unidimensionales de plata por simulacion dinamica molecular

    Energy Technology Data Exchange (ETDEWEB)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G. [ININ, 52750 La Marquesa, Estado de Mexico (Mexico); Arenas, J. [IFUNAM, 04510 Mexico D.F. (Mexico)

    2007-07-01

    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  16. Multi-scale calculation of the electric properties of organic-based devices from the molecular structure

    KAUST Repository

    Li, Haoyuan; Qiu, Yong; Duan, Lian

    2016-01-01

    A method is proposed to calculate the electric properties of organic-based devices from the molecular structure. The charge transfer rate is obtained using non-adiabatic molecular dynamics. The organic film in the device is modeled using

  17. Ultrafast Raman scattering in gas-filled hollow-core fibers

    OpenAIRE

    Belli, Federico

    2017-01-01

    The experimental and numerical work reported here is rooted in ultrafast molecular phenomena and nonlinear fiber optics, which are brought together in a deceptively simple system: a homo-nuclear molecular gas (e.g. H2,D2) loaded in the hollow-core of a broad-band guiding photonic crystal fiber (PCF) and exposed to ultrashort pulses of moderate energies (∼ μJ). On one hand, the choice of a molecular gas as the nonlinear medium provides a rich playground for light-matter interactions. ...

  18. Ambipolar carrier transport properties and molecular packing structure of octahexyl-substituted copper phthalocyanine

    Science.gov (United States)

    Watanabe, Ken; Watanabe, Koichi; Tohnai, Norimitsu; Itani, Hiromichi; Shimizu, Yo; Fujii, Akihiko; Ozaki, Masanori

    2018-04-01

    The charge carrier mobility of a solution-processable low-molecular-weight organic semiconductor material, i.e., 1,4,8,11,15,18,22,25-octahexylphthalocyanine copper complex (C6PcCu), was investigated by the time-of-flight technique. The anomalous ambipolar carrier mobility was discussed from the viewpoint of the molecular packing structure, which was clarified by single-crystal X-ray structure analysis. In the comparison between the molecular packing structures of C6PcCu and its metal-free-type homologue, it was found that the difference in carrier mobility originates from the rotation of the molecule, which is caused by the steric hindrance due to the introduction of a center metal and the interpenetration of the nonperipheral alkyl chains.

  19. Theoretical study on molecular packing and electronic structure of bi-1,3,4-oxadiazole derivatives

    KAUST Repository

    Wang, Haitao; Bai, Fuquan; Jia, Xiaoshi; Cao, Di; Ravva, Mahesh Kumar; Bredas, Jean-Luc; Qu, Songnan; Bai, Binglian; Zhang, Hongxing; Li, Min

    2014-01-01

    The molecular aggregation structure of 5,5′-bis(naphthalen-2-yl)-2,2′-bi(1,3,4-oxadiazole) (BOXD-NP) was studied by computing the intermolecular interaction potential energy surface (PES) at density functional theory level based on a dimer model. All B3LYP, CAM-B3LYP and M062x functionals can yield a reliable isolated molecular geometry. The conformation of BOXD-NP obtained with all methods is perfectly planar, indicating good conjugation ability between oxadiazole and naphthalene rings. The vibrational frequencies of BOXD-NP were also calculated using the B3LYP/6-311+G∗∗ method, which showed great consistency with the experimental observations and makes the assignments of the IR spectra more solid. It was revealed that the lowest excited state of BOXD-NP should be assigned as a highly allowed π-π∗ state by TD-DFT calculation. Considering the non-covalent interactions in molecular aggregates, the M062x functional was applied in the construction of the PES. Besides the packing structure found in the crystals, PES also predicted several stable structures, indicating that PES has great ability in guiding molecular self-assembly. Symmetry Adapted Perturbation Theory (SAPT) analysis on these energy-minimum molecular stacking structures revealed that London dispersion forces are the strongest attractive component in the binding. This journal is

  20. Exploring astrobiology using in silico molecular structure generation.

    Science.gov (United States)

    Meringer, Markus; Cleaves, H James

    2017-12-28

    The origin of life is typically understood as a transition from inanimate or disorganized matter to self-organized, 'animate' matter. This transition probably took place largely in the context of organic compounds, and most approaches, to date, have focused on using the organic chemical composition of modern organisms as the main guide for understanding this process. However, it has gradually come to be appreciated that biochemistry, as we know it, occupies a minute volume of the possible organic 'chemical space'. As the majority of abiotic syntheses appear to make a large set of compounds not found in biochemistry, as well as an incomplete subset of those that are, it is possible that life began with a significantly different set of components. Chemical graph-based structure generation methods allow for exhaustive in silico enumeration of different compound types and different types of 'chemical spaces' beyond those used by biochemistry, which can be explored to help understand the types of compounds biology uses, as well as to understand the nature of abiotic synthesis, and potentially design novel types of living systems.This article is part of the themed issue 'Reconceptualizing the origins of life'. © 2017 The Authors.

  1. Exploring astrobiology using in silico molecular structure generation

    Science.gov (United States)

    Meringer, Markus; Cleaves, H. James

    2017-11-01

    The origin of life is typically understood as a transition from inanimate or disorganized matter to self-organized, `animate' matter. This transition probably took place largely in the context of organic compounds, and most approaches, to date, have focused on using the organic chemical composition of modern organisms as the main guide for understanding this process. However, it has gradually come to be appreciated that biochemistry, as we know it, occupies a minute volume of the possible organic `chemical space'. As the majority of abiotic syntheses appear to make a large set of compounds not found in biochemistry, as well as an incomplete subset of those that are, it is possible that life began with a significantly different set of components. Chemical graph-based structure generation methods allow for exhaustive in silico enumeration of different compound types and different types of `chemical spaces' beyond those used by biochemistry, which can be explored to help understand the types of compounds biology uses, as well as to understand the nature of abiotic synthesis, and potentially design novel types of living systems. This article is part of the themed issue 'Reconceptualizing the origins of life'.

  2. Cooperative photo-induced effects: from photo-magnetism under continuous irradiation to ultra-fast phenomena - study through optical spectroscopy and X-ray diffraction; Effets photo-induits cooperatifs: du photomagnetisme sous irradiation continue aux phenomenes ultrarapides - etude par spectroscopie optique et diffraction X

    Energy Technology Data Exchange (ETDEWEB)

    Glijer, D

    2006-12-15

    The control with ultra-short laser pulses of the collective and concerted transformation of molecules driving a macroscopic state switching on an ultra-fast time scale in solid state opens new prospects in materials science. The goal is to realize at the material level what happens at the molecular level in femto-chemistry. These processes are highly cooperative and highly non-linear, leading to self-amplification and self-organization within the material, a so-called photo-induced phase transition with a new long range order (structural, magnetic, ferroelectric,...). Two families of molecular compounds have been studied here: first of all, spin transition materials changing from a diamagnetic state over to a paramagnetic state under the effect of temperature or under continuous laser excitation. It concerns photo-active molecular bi-stability prototype materials in solid state, whose switching has been studied during X-ray diffraction, optical reflectivity and magnetism experiments. Then we have studied charge-transfer molecular systems, prototype compounds for ultrafast photo-induced phase transitions: insulator-metal, neutral-ionic....As well as ultrafast optical experiments, time-resolved X ray crystallography is a key technique in order to follow at the atomic level the different steps of the photo-induced transformation and thus to observe the involved mechanisms. We have underlined a process of photo-formation of one-dimensional nano-domains of lattice-relaxed charge-transfer excitations, governing the photo-induced phase transition of the molecular charge-transfer complex TTF-CA by the first time-resolved diffuse scattering measurements. Moreover, a new femtosecond laser-plasma source and a optical pump-probe spectroscopy set-up with a highly sensitive detecting system have been developed in this work. The results presented here will be an illustration of the present scientific challenges existing on the one hand with the development of projects of major

  3. Ultrafast dynamics during the photoinduced phase transition in VO2

    Science.gov (United States)

    Wegkamp, Daniel; Stähler, Julia

    2015-12-01

    The phase transition of VO2 from a monoclinic insulator to a rutile metal, which occurs thermally at TC = 340 K, can also be driven by strong photoexcitation. The ultrafast dynamics during this photoinduced phase transition (PIPT) have attracted great scientific attention for decades, as this approach promises to answer the question of whether the insulator-to-metal (IMT) transition is caused by electronic or crystallographic processes through disentanglement of the different contributions in the time domain. We review our recent results achieved by femtosecond time-resolved photoelectron, optical, and coherent phonon spectroscopy and discuss them within the framework of a selection of latest, complementary studies of the ultrafast PIPT in VO2. We show that the population change of electrons and holes caused by photoexcitation launches a highly non-equilibrium plasma phase characterized by enhanced screening due to quasi-free carriers and followed by two branches of non-equilibrium dynamics: (i) an instantaneous (within the time resolution) collapse of the insulating gap that precedes charge carrier relaxation and significant ionic motion and (ii) an instantaneous lattice potential symmetry change that represents the onset of the crystallographic phase transition through ionic motion on longer timescales. We discuss the interconnection between these two non-thermal pathways with particular focus on the meaning of the critical fluence of the PIPT in different types of experiments. Based on this, we conclude that the PIPT threshold identified in optical experiments is most probably determined by the excitation density required to drive the lattice potential change rather than the IMT. These considerations suggest that the IMT can be driven by weaker excitation, predicting a transiently metallic, monoclinic state of VO2 that is not stabilized by the non-thermal structural transition and, thus, decays on ultrafast timescales.

  4. A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.

    Science.gov (United States)

    Davenport, Jodi; Pique, Michael; Getzoff, Elizabeth; Huntoon, Jon; Gardner, Adam; Olson, Arthur

    2017-04-04

    Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Ultrafast Nonlinear Signal Processing in Silicon Waveguides

    DEFF Research Database (Denmark)

    Oxenløwe, Leif Katsuo; Mulvad, Hans Christian Hansen; Hu, Hao

    2012-01-01

    We describe recent demonstrations of exploiting highly nonlinear silicon waveguides for ultrafast optical signal processing. We describe wavelength conversion and serial-to-parallel conversion of 640 Gbit/s data signals and 1.28 Tbit/s demultiplexing and all-optical sampling.......We describe recent demonstrations of exploiting highly nonlinear silicon waveguides for ultrafast optical signal processing. We describe wavelength conversion and serial-to-parallel conversion of 640 Gbit/s data signals and 1.28 Tbit/s demultiplexing and all-optical sampling....

  6. The molecular structure of the insoluble organic matter isolated from Murchison carbonaceous chondrite.

    Science.gov (United States)

    Robert, F.; Derenne, S.

    2009-04-01

    During these last 10 years, our group has characterized the various molecular moieties of the insoluble organic matter (IOM) isolated from carbonaceous meteorites with the aim of reconstructing its overall molecular structure. Indeed, a precise knowledge of the structure of an organic macromolecule contains irreplaceable information that traces its mechanisms of synthesis and its conditions of formation. Such a modelled structure will be presented. Carbonaceous chondrites contain up to 3 wt % of carbon that is under the form of soluble and insoluble fractions. The IOM, which constitutes more than 75 wt% of the bulk organic matter, was isolated from the bulk rock through successive acid dissolutions. The chemical structure of the isolated IOM has been studied by both (1) destructive and (2) non destructive methods. Methods include thermal and chemical degradations followed by GC/MS, spectroscopic techniques (nuclear magnetic resonance, Fourier transform infra red spectroscopy; X-ray absorption near-edge spectroscopy, electron paramagnetic resonance) along with high resolution transmission electron microscopy. Although each technique alone cannot provide definite information on the chemical structure of such a complex material, the combination of the results can be used to reconstruct the molecular structure of the IOM. The proposed structure accounts for all these measured parameters. The details of this structure reveal information of the conditions of its formation in space and allow to discuss the mechanisms of organo-synthesis in the cosmochemical context of the formation of the solar system.

  7. Structure-Activity Relationships on the Molecular Descriptors Family Project at the End

    Directory of Open Access Journals (Sweden)

    Lorentz JÄNTSCHI

    2007-12-01

    Full Text Available Molecular Descriptors Family (MDF on the Structure-Activity Relationships (SAR, a promising approach in investigation and quantification of the link between 2D and 3D structural information and the activity, and its potential in the analysis of the biological active compounds is summarized. The approach, attempts to correlate molecular descriptors family generated and calculated on a set of biological active compounds with their observed activity. The estimation as well as prediction abilities of the approach are presented. The obtained MDF SAR models can be used to predict the biological activity of unknown substrates in a series of compounds.

  8. Two-dimensional dynamics of a free molecular chain with a secondary structure

    DEFF Research Database (Denmark)

    Zolotaryuk, Alexander; Christiansen, Peter Leth; Savin, A.V.

    1996-01-01

    A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model of an anharmo......A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model...

  9. Effect of molecular weight on the vibronic structure of a diketopyrrolopyrrole polymer

    KAUST Repository

    Hayes, Sophia C.

    2016-09-27

    Resonance Raman Spectroscopy (RRS) is employed in this study to examine the influence of molecular weight on the optical response of a diketopyrrolopyrrole polymer (DPP-TT-T) in solution. The vibronic structure observed for the ground state absorption of this polymer is found to vary with molecular weight and solvent. Resonance Raman Intensity Analysis (RRIA) revealed that the absorption spectra can be described by at least two dipole-allowed transitions and the vibronic structure variation is due to differing contributions from linear and curved segments of the polymer.

  10. Effect of molecular weight on the vibronic structure of a diketopyrrolopyrrole polymer

    KAUST Repository

    Hayes, Sophia C.; Pieridou, Galatia; Vezie, Michelle; Few, Sheridan; Bronstein, Hugo; Meager, Iain; McCulloch, Iain; Nelson, Jenny

    2016-01-01

    Resonance Raman Spectroscopy (RRS) is employed in this study to examine the influence of molecular weight on the optical response of a diketopyrrolopyrrole polymer (DPP-TT-T) in solution. The vibronic structure observed for the ground state absorption of this polymer is found to vary with molecular weight and solvent. Resonance Raman Intensity Analysis (RRIA) revealed that the absorption spectra can be described by at least two dipole-allowed transitions and the vibronic structure variation is due to differing contributions from linear and curved segments of the polymer.

  11. Study of the molecular structure and dynamics of bakelite with neutron cross section measurements

    International Nuclear Information System (INIS)

    Voi, D.L.

    1990-06-01

    The molecular structure and dynamics of calcined bakelite were studied with neutron transmission and scattering cross section measurements. The total cross sections determined were correlated with data obtained with infra-red spectroscopy, elemental analysis and other techniques to get the probable molecular formulae of bakelite. The total cross section determined showed a deviation smaller than 5% from the literature values. The frequency distribution as well as overall experimental results allowed to suggest a structural model like polycyclic hydrocarbons for bakelite calcined at 800 0 C. (F.E.). 65 refs, 31 figs, 5 tabs

  12. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

    Science.gov (United States)

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-12-10

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

  13. PREFACE: Ultrafast and nonlinear optics in carbon nanomaterials

    Science.gov (United States)

    Kono, Junichiro

    2013-02-01

    Carbon-based nanomaterials—single-wall carbon nanotubes (SWCNTs) and graphene, in particular—have emerged in the last decade as novel low-dimensional systems with extraordinary properties. Because they are direct-bandgap systems, SWCNTs are one of the leading candidates to unify electronic and optical functions in nanoscale circuitry; their diameter-dependent bandgaps can be utilized for multi-wavelength devices. Graphene's ultrahigh carrier mobilities are promising for high-frequency electronic devices, while, at the same time, it is predicted to have ideal properties for terahertz generation and detection due to its unique zero-gap, zero-mass band structure. There have been a large number of basic optical studies on these materials, but most of them were performed in the weak-excitation, quasi-equilibrium regime. In order to probe and assess their performance characteristics as optoelectronic materials under device-operating conditions, it is crucial to strongly drive them and examine their optical properties in highly non-equilibrium situations and with ultrashot time resolution. In this section, the reader will find the latest results in this rapidly growing field of research. We have assembled contributions from some of the leading experts in ultrafast and nonlinear optical spectroscopy of carbon-based nanomaterials. Specific topics featured include: thermalization, cooling, and recombination dynamics of photo-generated carriers; stimulated emission, gain, and amplification; ultrafast photoluminescence; coherent phonon dynamics; exciton-phonon and exciton-plasmon interactions; exciton-exciton annihilation and Auger processes; spontaneous and stimulated emission of terahertz radiation; four-wave mixing and harmonic generation; ultrafast photocurrents; the AC Stark and Franz-Keldysh effects; and non-perturbative light-mater coupling. We would like to express our sincere thanks to those who contributed their latest results to this special section, and the

  14. Profiling of the Molecular Weight and Structural Isomer Abundance of Macroalgae-Derived Phlorotannins

    Directory of Open Access Journals (Sweden)

    Natalie Heffernan

    2015-01-01

    Full Text Available Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis. Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW phlorotannins were found to have a molecular weight range equivalent to 4–12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs. These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

  15. Ultrafast laser-semiconductor interactions

    International Nuclear Information System (INIS)

    Schile, L.A.

    1996-01-01

    Studies of the ultrafast (< 100 fs) interactions of infrared, sub-100 fs laser pulses with IR, photosensitive semiconductor materials InGaAs, InSb, and HgCdTe are reported. Both the carrier dynamics and the associated Terahertz radiation from these materials are discussed. The most recent developments of femtosecond (< 100 fs) Optical Parametric Oscillators (OPO) has extended the wavelength range from the visible to 5.2 μm. The photogenerated semiconductor free carrier dynamics are determined in the 77 to 300 degrees K temperature range using the Transmission Correlation Peak (TCP) method. The electron-phonon scattering times are typically 200 - 600 fs. Depending upon the material composition and substrate on which the IR crystalline materials are deposited, the nonlinear TCP absorption gives recombination rates as fast as 10's of picoseconds. For the HgCdTe, there exists a 400 fs electron-phonon scattering process along with a much longer 3600 fs loss process. Studies of the interactions of these ultrashort laser pulses with semiconductors produce Terahertz (Thz) radiative pulses. With undoped InSb, there is a substantial change in the spectral content of this THz radiation between 80 - 260 degrees K while the spectrum of Te-doped InSb remains nearly unchanged, an effect attributed to its mobility being dominated by impurity scattering. At 80 degrees K, the terahertz radiation from undoped InSb is dependent on wavelength, with both a higher frequency spectrum and much larger amplitudes generated at longer wavelengths. No such effect is observed at 260 degrees K. Finally, new results on the dependence of the emitted THz radiation on the InSb crystal's orientation is presented

  16. Measuring protein dynamics with ultrafast two-dimensional infrared spectroscopy

    International Nuclear Information System (INIS)

    Adamczyk, Katrin; Candelaresi, Marco; Hunt, Neil T; Robb, Kirsty; Hoskisson, Paul A; Tucker, Nicholas P; Gumiero, Andrea; Walsh, Martin A; Parker, Anthony W

    2012-01-01

    Recent advances in the methodology and application of ultrafast two-dimensional infrared (2D-IR) spectroscopy to biomolecular systems are reviewed. A description of the 2D-IR technique and the molecular contributions to the observed spectra are presented followed by a discussion of recent literature relating to the use of 2D-IR and associated approaches for measuring protein dynamics. In particular, these include the use of diatomic ligand groups for measuring haem protein dynamics, isotopic labelling strategies and the use of vibrational probe groups. The final section reports on the current state of the art regarding the use of 2D-IR methods to provide insights into biological reaction mechanisms. (topical review)

  17. Photoionization-regulated star formation and the structure of molecular clouds

    Science.gov (United States)

    Mckee, Christopher F.

    1989-01-01

    A model for the rate of low-mass star formation in Galactic molecular clouds and for the influence of this star formation on the structure and evolution of the clouds is presented. The rate of energy injection by newly formed stars is estimated, and the effect of this energy injection on the size of the cloud is determined. It is shown that the observed rate of star formation appears adequate to support the observed clouds against gravitational collapse. The rate of photoionization-regulated star formation is estimated and it is shown to be in agreement with estimates of the observed rate of star formation if the observed molecular cloud parameters are used. The mean cloud extinction and the Galactic star formation rate per unit mass of molecular gas are predicted theoretically from the condition that photionization-regulated star formation be in equilibrium. A simple model for the evolution of isolated molecular clouds is developed.

  18. Determination of molecular-ion structures through the use of accelerated beams

    International Nuclear Information System (INIS)

    Gemmell, D.S.

    1987-01-01

    In this talk we report on recent research on molecular-ion structures using fast molecular-ion beams provided by Argonne's 5-MV Dynamitron accelerator. The method has become known as the ''Coulomb-explosion'' technique. When molecular-ion projectiles travelling at velocities of a few percent of the velocity of light strike a foil, the electrons that bind the molecular projectiles are almost always totally stripped off within the first few Angstroms of penetration into the solid target. This leaves a cluster of bare (or nearly bare) nuclei which separate rapidly as a result of their mutual Coulomb repulsion. This violent dissociation process in which the initial electrostatic potential energy is converted into kinetic energy of relative motion in the center-of-mass, has been termed a ''Coulomb explosion.'' 4 refs., 2 figs

  19. Molecular structure of self-assembled chiral nanoribbons and nanotubules revealed in the hydrated state.

    Science.gov (United States)

    Oda, Reiko; Artzner, Franck; Laguerre, Michel; Huc, Ivan

    2008-11-05

    A detailed molecular organization of racemic 16-2-16 tartrate self-assembled multi-bilayer ribbons in the hydrated state is proposed where 16-2-16 amphiphiles, tartrate ions, and water molecules are all accurately positioned by comparing experimental X-ray powder diffraction and diffraction patterns derived from modeling studies. X-ray diffuse scattering studies show that molecular organization is not fundamentally altered when comparing the flat ribbons of the racemate to chirally twisted or helical ribbons of the pure tartrate enantiomer. Essential features of the three-dimensional molecular organizations of these structures include interdigitation of alkyl chains within each bilayer and well-defined networks of ionic and hydrogen bonds between cations, anions, and water molecules between bilayers. The detailed study of diffraction patterns also indicated that the gemini headgroups are oriented parallel to the long edge of the ribbons. The structure thus possesses a high cohesion and good crystallinity, and for the first time, we could relate the packing of the chiral molecules to the expression of the chirality at a mesoscopic scale. The organization of the ribbons at the molecular level sheds light on a number of their macroscopic features. Among these are the reason why enantiomerically pure 16-2-16 tartrate forms ribbons that consist of exactly two bilayers, and a plausible mechanism by which a chirally twisted or helical shape may emerge from the packing of chiral tartrate ions. Importantly, the distinction between commonly observed helical and twisted morphologies could be related to a subtle symmetry breaking. These results demonstrate that accurately solving the molecular structure of self-assembled soft materials--a process rarely achieved--is within reach, that it is a valid approach to correlate molecular parameters to macroscopic properties, and thus that it offers opportunities to modulate properties through molecular design.

  20. Atomic-scale structure of dislocations revealed by scanning tunneling microscopy and molecular dynamics

    DEFF Research Database (Denmark)

    Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob

    2002-01-01

    The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations, the simulati......The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations......, the simulations can be used to determine dislocation structure and orientation in the near-surface region. In a similar way, the subsurface structure of other extended defects can be studied. The simulations show dislocations to reorient the partials in the surface region leading to an increased splitting width...

  1. Probing the Structure and Dynamics of Proteins by Combining Molecular Dynamics Simulations and Experimental NMR Data.

    Science.gov (United States)

    Allison, Jane R; Hertig, Samuel; Missimer, John H; Smith, Lorna J; Steinmetz, Michel O; Dolenc, Jožica

    2012-10-09

    NMR experiments provide detailed structural information about biological macromolecules in solution. However, the amount of information obtained is usually much less than the number of degrees of freedom of the macromolecule. Moreover, the relationships between experimental observables and structural information, such as interatomic distances or dihedral angle values, may be multiple-valued and may rely on empirical parameters and approximations. The extraction of structural information from experimental data is further complicated by the time- and ensemble-averaged nature of NMR observables. Combining NMR data with molecular dynamics simulations can elucidate and alleviate some of these problems, as well as allow inconsistencies in the NMR data to be identified. Here, we use a number of examples from our work to highlight the power of molecular dynamics simulations in providing a structural interpretation of solution NMR data.

  2. De Novo generation of molecular structures using optimization to select graphs on a given lattice

    DEFF Research Database (Denmark)

    Bywater, R.P.; Poulsen, Thomas Agersten; Røgen, Peter

    2004-01-01

    A recurrent problem in organic chemistry is the generation of new molecular structures that conform to some predetermined set of structural constraints that are imposed in an endeavor to build certain required properties into the newly generated structure. An example of this is the pharmacophore...... model, used in medicinal chemistry to guide de novo design or selection of suitable structures from compound databases. We propose here a method that efficiently links up a selected number of required atom positions while at the same time directing the emergent molecular skeleton to avoid forbidden...... positions. The linkage process takes place on a lattice whose unit step length and overall geometry is designed to match typical architectures of organic molecules. We use an optimization method to select from the many different graphs possible. The approach is demonstrated in an example where crystal...

  3. Resolving ultrafast exciton migration in organic solids at the nanoscale

    Science.gov (United States)

    Ginsberg, Naomi

    The migration of Frenkel excitons, tightly-bound electron-hole pairs, in photosynthesis and in organic semiconducting films is critical to the efficiency of natural and artificial light harvesting. While these materials exhibit a high degree of structural heterogeneity on the nanoscale, traditional measurements of exciton migration lengths are performed on bulk samples. Since both the characteristic length scales of structural heterogeneity and the reported bulk diffusion lengths are smaller than the optical diffraction limit, we adapt far-field super-resolution fluorescence imaging to uncover the correlations between the structural and energetic landscapes that the excitons explore. By combining the ultrafast super-resolved measurements with exciton hopping simulations we furthermore specify the nature (in addition to the extent) of exciton migration as a function of the intrinsic and ensemble chromophore energy scales that determine a spatio-energetic landscape for migration. In collaboration with: Samuel Penwell, Lucas Ginsberg, University of California, Berkeley and Rodrigo Noriega University of Utah.

  4. CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures

    Directory of Open Access Journals (Sweden)

    Drefahl Axel

    2011-01-01

    Full Text Available Abstract CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and nanodevices. Annotations are enclosed in curly braces and anchored to an atomic node or at the end of the molecular graph depending on the annotation type. CurlySMILES includes predefined annotations for stereogenicity, electron delocalization charges, extra-molecular interactions and connectivity, surface attachment, solutions, and crystal structures and allows extensions for domain-specific annotations. CurlySMILES provides a shorthand format to encode molecules with repetitive substructural parts or motifs such as monomer units in macromolecules and amino acids in peptide chains. CurlySMILES further accommodates special formats for non-molecular materials that are commonly denoted by composition of atoms or substructures rather than complete atom connectivity.

  5. 16O + 16O molecular structures of superdeformed states in S isotopes

    Science.gov (United States)

    Taniguchi, Y.

    2017-06-01

    Structures of excited states in S isotopes are investigated by using the antisymmetrized molecular dynamics and generator coordinate method (GCM). The GCM basis wave functions are calculated via energy variation with a constraint on the quadrupole deformation parameter β. By applying the GCM after parity and angular momentum projections, the coexistence of positive- and negative-parity superdeformed (SD) bands are predicted in 33-36S except for negative-parity states in 36S. The SD bands have structures of 16O + 16O + valence neutron(s) in molecular orbitals around the two 16O cores in a cluster picture. The configurations of the valence neutron(s) in the SD states are δ and/or π molecular orbitals.

  6. NATO Advanced Research Workshop on Vectorization of Advanced Methods for Molecular Electronic Structure

    CERN Document Server

    1984-01-01

    That there have been remarkable advances in the field of molecular electronic structure during the last decade is clear not only to those working in the field but also to anyone else who has used quantum chemical results to guide their own investiga­ tions. The progress in calculating the electronic structures of molecules has occurred through the truly ingenious theoretical and methodological developments that have made computationally tractable the underlying physics of electron distributions around a collection of nuclei. At the same time there has been consider­ able benefit from the great advances in computer technology. The growing sophistication, declining costs and increasing accessibi­ lity of computers have let theorists apply their methods to prob­ lems in virtually all areas of molecular science. Consequently, each year witnesses calculations on larger molecules than in the year before and calculations with greater accuracy and more com­ plete information on molecular properties. We can surel...

  7. The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.

    Science.gov (United States)

    Ghanbari, Z; Housaindokht, M R; Bozorgmehr, M R; Izadyar, M

    2016-09-07

    Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Quantum Computation with Ultrafast Laser Pulse Shaping

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 6. Quantum Computation with Ultrafast Laser Pulse Shaping. Debabrata Goswami. General Article Volume 10 Issue 6 June 2005 pp 8-14. Fulltext. Click here to view fulltext PDF. Permanent link:

  9. Photonic-assisted ultrafast THz wireless access

    DEFF Research Database (Denmark)

    Yu, Xianbin; Chen, Ying; Galili, Michael

    THz technology has been considered feasible for ultrafast wireless data communi- cation, to meet the increasing demand on next-generation fast wireless access, e.g., huge data file transferring and fast mobile data stream access. This talk reviews recent progress in high-speed THz wireless...

  10. Structural investigation of bistrifluron using x-ray crystallography, NMR spectroscopy, and molecular modeling

    CERN Document Server

    Moon, J K; Rhee, S K; Kim, G B; Yun, H S; Chung, B J; Lee, S S; Lim, Y H

    2002-01-01

    A new insecticide, bistrifluron acts as an inhibitor of insect development and interferes with the cuticle formation of insects. Since it shows low acute oral and dermal toxicities, it can be one of potent insecticides. Based on X-ray crystallography, NMR spectroscopy and molecular modeling, the structural studies of bistrifluron have been carried out.

  11. Refinement of homology-based protein structures by molecular dynamics simulation techniques

    NARCIS (Netherlands)

    Fan, H; Mark, AE

    The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to

  12. Origami: A Versatile Modeling System for Visualising Chemical Structure and Exploring Molecular Function

    Science.gov (United States)

    Davis, James; Leslie, Ray; Billington, Susan; Slater, Peter R.

    2010-01-01

    The use of "Origami" is presented as an accessible and transferable modeling system through which to convey the intricacies of molecular shape and highlight structure-function relationships. The implementation of origami has been found to be a versatile alternative to conventional ball-and-stick models, possessing the key advantages of being both…

  13. Molecular systematics of Barbatosphaeria (Sordariomycetes): multigene phylogeny and secondary ITS structure

    Czech Academy of Sciences Publication Activity Database

    Réblová, Martina; Réblová, K.; Štěpánek, Václav

    2015-01-01

    Roč. 35, December 2015 (2015), s. 21-38 ISSN 0031-5850 R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 ; RVO:61388971 Keywords : Barbatosphaeria * molecular systematic * ITS secondary structures Subject RIV: EF - Botanics; EE - Microbiology, Virology (MBU-M) Impact factor: 5.725, year: 2015

  14. (TMTSF)2X materials and structural implications for low-dimensional polymeric and disordered molecular semiconductors

    DEFF Research Database (Denmark)

    Bechgaard, Klaus; Nielsen, Martin Meedom; Krebs, Frederik C

    2000-01-01

    The structural characteristics and the relation to the electronic properties of three types of molecular materials are discussed. In TMTSF2X salts a triclinic unit cell it suggested to be important in avoiding a 2k(F) Peierls distortion. In polythiophenes appropriate ordering of microcrystallites...

  15. Well-ordered monolayers of alkali-doped coronene and picene: Molecular arrangements and electronic structures

    Energy Technology Data Exchange (ETDEWEB)

    Yano, M.; Endo, M.; Hasegawa, Y.; Okada, R.; Yamada, Y., E-mail: yamada@bk.tsukuba.ac.jp; Sasaki, M. [Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573 (Japan)

    2014-07-21

    Adsorptions of alkali metals (such as K and Li) on monolayers of coronene and picene realize the formation of ordered phases, which serve as well-defined model systems for metal-intercalated aromatic superconductors. Upon alkali-doping of the monolayers of coronene and picene, scanning tunneling microscopy and X-ray absorption spectroscopy revealed the rearrangement of the entire molecular layer. The K-induced reconstruction of both monolayers resulted in the formation of a structure with a herringbone-like arrangement of molecules, suggesting the intercalation of alkali metals between molecular planes. Upon reconstruction, a shift in both the vacuum level and core levels of coronene was observed as a result of a charge transfer from alkali metals to coronene. In addition, a new density of states near the Fermi level was formed in both the doped coronene and the doped picene monolayers. This characteristic electronic feature of the ordered monolayer has been also reported in the multilayer picene films, ensuring that the present monolayer can model the properties of the metal-intercalated aromatic hydrocarbons. It is suggested that the electronic structure near the Fermi level is sensitive to the molecular arrangement, and that both the strict control and determinations of the molecular structure in the doped phase should be important for the determination of the electronic structure of these materials.

  16. The History of Molecular Structure Determination Viewed through the Nobel Prizes.

    Science.gov (United States)

    Jensen, William P.; Palenik, Gus J.; Suh, Il-Hwan

    2003-01-01

    Discusses the importance of complex molecular structures. Emphasizes their individual significance through examination of the Nobel Prizes of the 20th century. Highlights prizes awarded to Conrad Rontgen, Francis H.C. Crick, James D. Watson, Maurice H.F. Wilkins, and others. (SOE)

  17. The structure of quasi-molecular KX-ray spectra from heavy ion collisions

    International Nuclear Information System (INIS)

    Kaun, K.-N.; Frank, W.; Manfrass, P.

    1976-01-01

    In the experiments with Ge, Nb, Kr and La ions continuum X-ray spectra having a two-component structure have been observed. Both components atr interpreted as quasi-molecular X-radiation caused by transitions to the 2psigma and 1ssigma states in the quasimolecule

  18. Structure and properties of simple molecular systems at very high density

    International Nuclear Information System (INIS)

    LeSar, R.

    1989-01-01

    The use of computer simulations in the study of molecular systems at very high density is reviewed. Applications to the thermodynamics of dense fluid nitrogen and phase transitions in solid oxygen are presented. The effects of changes in the atomic electronic structure on the equation of state of very dense helium are discussed. 19 refs., 2 figs

  19. Ultrafast laser pump/x-ray probe experiments

    International Nuclear Information System (INIS)

    Larsson, J.; Judd, E.; Schuck, P.J.

    1997-01-01

    In an ongoing project aimed at probing solids using x-rays obtained at the ALS synchrotron with a sub-picosecond time resolution following interactions with a 100 fs laser pulse, the authors have successfully performed pump-probe experiments limited by the temporal duration of ALS-pulse. They observe a drop in the diffraction efficiency following laser heating. They can attribute this to a disordering of the crystal. Studies with higher temporal resolution are required to determine the mechanism. The authors have also incorporated a low-jitter streakcamera as a diagnostic for observing time-dependant x-ray diffraction. The streakcamera triggered by a photoconductive switch was operated at kHz repetition rates. Using UV-pulses, the authors obtain a temporal response of 2 ps when averaging 5000 laser pulses. They demonstrate the ability to detect monochromatized x-ray radiation from a bend-magnet with the streak camera by measuring the pulse duration of a x-ray pulse to 70 ps. In conclusion, the authors show a rapid disordering of an InSb crystal. The resolution was determined by the duration of the ALS pulse. They also demonstrate that they can detect x-ray radiation from a synchrotron source with a temporal resolution of 2ps, by using an ultrafast x-ray streak camera. Their set-up will allow them to pursue laser pump/x-ray probe experiments to monitor structural changes in materials with ultrafast time resolution

  20. Ultrafast X-Ray Spectroscopy of Conical Intersections

    Science.gov (United States)

    Neville, Simon P.; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

    2018-06-01

    Ongoing developments in ultrafast x-ray sources offer powerful new means of probing the complex nonadiabatically coupled structural and electronic dynamics of photoexcited molecules. These non-Born-Oppenheimer effects are governed by general electronic degeneracies termed conical intersections, which play a key role, analogous to that of a transition state, in the electronic-nuclear dynamics of excited molecules. Using high-level ab initio quantum dynamics simulations, we studied time-resolved x-ray absorption (TRXAS) and photoelectron spectroscopy (TRXPS) of the prototypical unsaturated organic chromophore, ethylene, following excitation to its S2(π π*) state. The TRXAS, in particular, is highly sensitive to all aspects of the ensuing dynamics. These x-ray spectroscopies provide a clear signature of the wave packet dynamics near conical intersections, related to charge localization effects driven by the nuclear dynamics. Given the ubiquity of charge localization in excited state dynamics, we believe that ultrafast x-ray spectroscopies offer a unique and powerful route to the direct observation of dynamics around conical intersections.

  1. Band Structure Engineering of the Carrier-Induced Refractive Index in High-Power Midwave-Infrared Laser Diodes

    National Research Council Canada - National Science Library

    Boggess, Thomas

    2000-01-01

    .... The program incorporated elements of theory, semiconductor growth by molecular beam epitaxy, ultrafast and continuous-wave optical characterization, and device processing, fabrication, and testing...

  2. Perspective: Ultrafast magnetism and THz spintronics

    Energy Technology Data Exchange (ETDEWEB)

    Walowski, Jakob; Münzenberg, Markus [Institut für Physik, Ernst-Moritz-Arndt-Universität Greifswald, 17489 Greifswald (Germany)

    2016-10-14

    This year the discovery of femtosecond demagnetization by laser pulses is 20 years old. For the first time, this milestone work by Bigot and coworkers gave insight directly into the time scales of microscopic interactions that connect the spin and electron system. While intense discussions in the field were fueled by the complexity of the processes in the past, it now became evident that it is a puzzle of many different parts. Rather than providing an overview that has been presented in previous reviews on ultrafast processes in ferromagnets, this perspective will show that with our current depth of knowledge the first applications are developed: THz spintronics and all-optical spin manipulation are becoming more and more feasible. The aim of this perspective is to point out where we can connect the different puzzle pieces of understanding gathered over 20 years to develop novel applications. Based on many observations in a large number of experiments. Differences in the theoretical models arise from the localized and delocalized nature of ferromagnetism. Transport effects are intrinsically non-local in spintronic devices and at interfaces. We review the need for multiscale modeling to address the processes starting from electronic excitation of the spin system on the picometer length scale and sub-femtosecond time scale, to spin wave generation, and towards the modeling of ultrafast phase transitions that altogether determine the response time of the ferromagnetic system. Today, our current understanding gives rise to the first usage of ultrafast spin physics for ultrafast magnetism control: THz spintronic devices. This makes the field of ultrafast spin-dynamics an emerging topic open for many researchers right now.

  3. Perspective: Ultrafast magnetism and THz spintronics

    International Nuclear Information System (INIS)

    Walowski, Jakob; Münzenberg, Markus

    2016-01-01

    This year the discovery of femtosecond demagnetization by laser pulses is 20 years old. For the first time, this milestone work by Bigot and coworkers gave insight directly into the time scales of microscopic interactions that connect the spin and electron system. While intense discussions in the field were fueled by the complexity of the processes in the past, it now became evident that it is a puzzle of many different parts. Rather than providing an overview that has been presented in previous reviews on ultrafast processes in ferromagnets, this perspective will show that with our current depth of knowledge the first applications are developed: THz spintronics and all-optical spin manipulation are becoming more and more feasible. The aim of this perspective is to point out where we can connect the different puzzle pieces of understanding gathered over 20 years to develop novel applications. Based on many observations in a large number of experiments. Differences in the theoretical models arise from the localized and delocalized nature of ferromagnetism. Transport effects are intrinsically non-local in spintronic devices and at interfaces. We review the need for multiscale modeling to address the processes starting from electronic excitation of the spin system on the picometer length scale and sub-femtosecond time scale, to spin wave generation, and towards the modeling of ultrafast phase transitions that altogether determine the response time of the ferromagnetic system. Today, our current understanding gives rise to the first usage of ultrafast spin physics for ultrafast magnetism control: THz spintronic devices. This makes the field of ultrafast spin-dynamics an emerging topic open for many researchers right now.

  4. Ultrafast excited-state deactivation of 9-methylhypoxanthine in aqueous solution: A QM/MM MD study.

    Science.gov (United States)

    Guo, Xugeng; Yuan, Huijuan; An, Beibei; Zhu, Qiuling; Zhang, Jinglai

    2016-04-21

    Photoinduced ultrafast non-adiabatic decay of 9-methylhypoxanthine (9MHPX) in aqueous solution was investigated by ab initio surface-hopping dynamics calculations using a combined quantum mechanical/molecular mechanical approach. The absorption spectra of 9MHPX in aqueous solution were also explored by the hybrid cluster-continuum model at the level of time-dependent density functional theory along with the polarizable continuum model (PCM). The static electronic-structure calculations indicate that the absorption spectra of 9MHPX simulated by TD-B3LYP/PCM and TD-X3LYP/PCM can reproduce very well the experimental findings, with the accuracy of about 0.20 eV. According to dynamics simulations, irradiation of 9MHPX populates the bright excited singlet S1 state, which may undergo an ultrafast non-radiative deactivation to the S0 state. The lifetime of the S1 state of 9MHPX in aqueous solution is predicted to be 115.6 fs, slightly longer than that in the gas phase (88.8 fs), suggesting that the solventwater has no significant influence on the excited-state lifetime of 9MHPX. Such a behavior in 9MHPX is distinctly different from its parent hypoxanthine keto-N9H tautomer in which the excited-state lifetime of the latter in watersolution was remarkably enhanced as compared to the gas phase. The significant difference of the photodynamical behaviors between 9MHPX and keto-N9H can be ascribed to their different hydrogen bond environment in aqueous solution.

  5. Ultrafast measurements of chlorine dioxide photochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Ludowise, P.D.

    1997-08-01

    Time-resolved mass spectrometry and time-resolved photoelectron spectroscopy are used to study the ultrafast photodissociation dynamics of chlorine dioxide, an important constituent in stratospheric ozone depletion. Chapter 1 introduces these pump/probe techniques, in which a femtosecond pump pulse excites a molecule to a dissociative state. At a later time, a second femtosecond probe pulse ionizes the molecule. The resulting mass and photoelectron spectra are acquired as a function of the delay between the pump and probe pulses, which follows the evolution of the molecule on the excited state. A comparison to other techniques used to study reaction dynamics is discussed. Chapter 2 includes a detailed description of the design and construction of the experimental apparatus, which consists of a femtosecond laser system, a molecular beam time-of-flight spectrometer, and a data acquisition system. The time-of-flight spectrometer is specifically designed to have a short flight distance to maximize the photoelectron collection efficiency without degrading the resolution, which is limited by the bandwidth of the femtosecond laser system. Typical performance of the apparatus is demonstrated in a study of the time-resolved photoelectron spectroscopy of nitric oxide. The results of the time-resolved mass spectrometry experiments of chlorine dioxide are presented in Chapter 3. Upon excitation to the A {sup 2}A{sub 2} state near 3.2 eV, the molecule dissociates through an indirect two-step mechanism. The direct dissociation channel has been predicted to be open, but is not observed. A quantum beat is observed in the OClO{sup +} species, which is described as a vibrational coherence of the optically prepared A {sup 2}A{sub 2} state. Chapter 4 presents the results of the time-resolved photoelectron experiments of chlorine dioxide. At short delay time, the quantum beat of the OClO{sup +} species is observed in the X {sup 1}A{sub 1} state of the ion. At infinite delay, the signal

  6. Graph theoretical ordering of structures as a basis for systematic searches for regularities in molecular data

    International Nuclear Information System (INIS)

    Randic, M.; Wilkins, C.L.

    1979-01-01

    Selected molecular data on alkanes have been reexamined in a search for general regularities in isomeric variations. In contrast to the prevailing approaches concerned with fitting data by searching for optimal parameterization, the present work is primarily aimed at established trends, i.e., searching for relative magnitudes and their regularities among the isomers. Such an approach is complementary to curve fitting or correlation seeking procedures. It is particularly useful when there are incomplete data which allow trends to be recognized but no quantitative correlation to be established. One proceeds by first ordering structures. One way is to consider molecular graphs and enumerate paths of different length as the basic graph invariant. It can be shown that, for several thermodynamic molecular properties, the number of paths of length two (p 2 ) and length three (p 3 ) are critical. Hence, an ordering based on p 2 and p 3 indicates possible trends and behavior for many molecular properties, some of which relate to others, some which do not. By considering a grid graph derived by attributing to each isomer coordinates (p 2 ,p 3 ) and connecting points along the coordinate axis, one obtains a simple presentation useful for isomer structural interrelations. This skeletal frame is one upon which possible trends for different molecular properties may be conveniently represented. The significance of the results and their conceptual value is discussed. 16 figures, 3 tables

  7. Molecular dynamics simulations of H2 adsorption in tetramethyl ammonium lithium phthalocyanine crystalline structures.

    Science.gov (United States)

    Lamonte, Kevin; Gómez Gualdrón, Diego A; Cabrales-Navarro, Fredy A; Scanlon, Lawrence G; Sandi, Giselle; Feld, William; Balbuena, Perla B

    2008-12-11

    Tetramethyl ammonium lithium phthalocyanine is explored as a potential material for storage of molecular hydrogen. Density functional theory calculations are used to investigate the molecular structure and the dimer conformation. Additional scans performed to determine the interactions of a H2 molecule located at various distances from the molecular sites are used to generate a simple force field including dipole-induced-dipole interactions. This force field is employed in molecular dynamics simulations to calculate adsorption isotherms at various pressures. The regions of strongest adsorption are quantified as functions of temperature, pressure, and separation between molecules in the adsorbent phase, and compared to the regions of strongest binding energy as given by the proposed force field. It is found that the total adsorption could not be predicted only from the spatial distribution of the strongest binding energies; the available volume is the other contributing factor even if the volume includes regions of much lower binding energy. The results suggest that the complex anion is primarily involved in the adsorption process with molecular hydrogen, whereas the cation serves to provide access for hydrogen adsorption in both sides of the anion molecular plane, and spacing between the planes.

  8. Skin hydration: interplay between molecular dynamics, structure and water uptake in the stratum corneum.

    Science.gov (United States)

    Mojumdar, Enamul Haque; Pham, Quoc Dat; Topgaard, Daniel; Sparr, Emma

    2017-11-16

    Hydration is a key aspect of the skin that influences its physical and mechanical properties. Here, we investigate the interplay between molecular and macroscopic properties of the outer skin layer - the stratum corneum (SC) and how this varies with hydration. It is shown that hydration leads to changes in the molecular arrangement of the peptides in the keratin filaments as well as dynamics of C-H bond reorientation of amino acids in the protruding terminals of keratin protein within the SC. The changes in molecular structure and dynamics occur at a threshold hydration corresponding to ca. 85% relative humidity (RH). The abrupt changes in SC molecular properties coincide with changes in SC macroscopic swelling properties as well as mechanical properties in the SC. The flexible terminals at the solid keratin filaments can be compared to flexible polymer brushes in colloidal systems, creating long-range repulsion and extensive swelling in water. We further show that the addition of urea to the SC at reduced RH leads to similar molecular and macroscopic responses as the increase in RH for SC without urea. The findings provide new molecular insights to deepen the understanding of how intermediate filament organization responds to changes in the surrounding environment.

  9. Lifetime broadening of atomic lines produced upon ultrafast dissociation of HCl and HBr

    Energy Technology Data Exchange (ETDEWEB)

    Lablanquie, P., E-mail: pascal.lablanquie@upmc.fr [Sorbonne Universités, UPMC Univ Paris 06, LCPMR, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); CNRS, LCPMR (UMR 7614), 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Iwayama, H. [UVSOR Facility, Institute for Molecular Science, Okazaki 444-8585 (Japan); Penent, F. [Sorbonne Universités, UPMC Univ Paris 06, LCPMR, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); CNRS, LCPMR (UMR 7614), 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Soejima, K. [Department of Environmental Science, Niigata University, Niigata 950-2181 (Japan); Shigemasa, E. [UVSOR Facility, Institute for Molecular Science, Okazaki 444-8585 (Japan)

    2014-08-15

    Highlights: • Ultrafast dissociation of HCl is triggered by 2p{sub 3/2} → σ* excitation. • Ultrafast dissociation of HBr is triggered by 3d{sub 5/2} → σ* excitation. • Photoelectron spectroscopy reveals sharp vibrational molecular lines and broad atomic lines. • The profiles of the atomic lines are analyzed in detail. • We extract the lifetime of the inner shell hole in the neutral atomic fragment. - Abstract: Ultrafast dissociation of the HCl and HBr molecules excited respectively to the 2p{sub 3/2} → σ* and 3d{sub 5/2} → σ* resonances are studied with high resolution photoelectron spectroscopy. Sharp vibrational molecular lines and broad atomic lines are observed. The analysis of the profile of the atomic lines gives access to the lifetimes of the inner shell 2p{sub 3/2} hole in the Cl* (2p{sub 3/2}){sup −1} 3s{sup 2}3p{sup 6} configuration, and the inner shell 3d{sub 5/2} hole in the Br* (3d{sub 5/2}){sup −1} 4s{sup 2}4p{sup 6} configuration.

  10. More Than Filaments and Cores: Statistical Study of Structure Formation and Dynamics in Nearby Molecular Clouds

    Science.gov (United States)

    Chen, How-Huan; Goodman, Alyssa

    2018-01-01

    In the past decade, multiple attempts at understanding the connection between filaments and star forming cores have been made using observations across the entire epectrum. However, the filaments and the cores are usually treated as predefined--and well-defined--entities, instead of structures that often come at different sizes, shapes, with substantially different dynamics, and inter-connected at different scales. In my dissertation, I present an array of studies using different statistical methods, including the dendrogram and the probability distribution function (PDF), of structures at different size scales within nearby molecular clouds. These structures are identified using observations of different density tracers, and where possible, in the multi-dimensional parameter space of key dynamic properties--the LSR velocity, the velocity dispersion, and the column density. The goal is to give an overview of structure formation in nearby star-forming clouds, as well as of the dynamics in these structures. I find that the overall statistical properties of a larger structure is often the summation/superposition of sub-structures within, and that there could be significant variations due to local physical processes. I also find that the star formation process within molecular clouds could in fact take place in a non-monolithic manner, connecting potentially merging and/or transient structures, at different scales.

  11. SGC method for predicting the standard enthalpy of formation of pure compounds from their molecular structures

    International Nuclear Information System (INIS)

    Albahri, Tareq A.; Aljasmi, Abdulla F.

    2013-01-01

    Highlights: • ΔH° f is predicted from the molecular structure of the compounds alone. • ANN-SGC model predicts ΔH° f with a correlation coefficient of 0.99. • ANN-MNLR model predicts ΔH° f with a correlation coefficient of 0.90. • Better definition of the atom-type molecular groups is presented. • The method is better than others in terms of combined simplicity, accuracy and generality. - Abstract: A theoretical method for predicting the standard enthalpy of formation of pure compounds from various chemical families is presented. Back propagation artificial neural networks were used to investigate several structural group contribution (SGC) methods available in literature. The networks were used to probe the structural groups that have significant contribution to the overall enthalpy of formation property of pure compounds and arrive at the set of groups that can best represent the enthalpy of formation for about 584 substances. The 51 atom-type structural groups listed provide better definitions of group contributions than others in the literature. The proposed method can predict the standard enthalpy of formation of pure compounds with an AAD of 11.38 kJ/mol and a correlation coefficient of 0.9934 from only their molecular structure. The results are further compared with those of the traditional SGC method based on MNLR as well as other methods in the literature

  12. Molecular dynamics simulations of structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces.

    Science.gov (United States)

    He, Guangzhi; Zhang, Meiyi; Zhou, Qin; Pan, Gang

    2015-09-01

    Concentration and salinity conditions are the dominant environmental factors affecting the behavior of perfluorinated compounds (PFCs) on the surfaces of a variety of solid matrices (suspended particles, sediments, and natural minerals). However, the mechanism has not yet been examined at molecular scales. Here, the structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces induced by changes of the concentration level of PFOS and salt condition was investigated using molecular dynamics (MD) simulations. At low and intermediate concentrations all PFOS molecules directly interacted with the rutile (110) surface mainly by the sulfonate headgroups through electrostatic attraction, yielding a typical monolayer structure. As the concentration of PFOS increased, the molecules aggregated in a complex multi-layered structure, where an irregular assembling configuration was adsorbed on the monolayer structure by the van der Waals interactions between the perfluoroalkyl chains. When adding CaCl2 to the system, the multi-layered structure changed to a monolayer again, indicating that the addition of CaCl2 enhanced the critical concentration value to yield PFOS multilayer assemblies. The divalent Ca(2+) substituted for monovalent K(+) as the bridging counterion in PFOS adsorption. MD simulation may trigger wide applications in study of perfluorinated compounds (PFCs) from atomic/molecular scale. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. The diverse and expanding role of mass spectrometry in structural and molecular biology.

    Science.gov (United States)

    Lössl, Philip; van de Waterbeemd, Michiel; Heck, Albert Jr

    2016-12-15

    The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

  14. Cationic lipids: molecular structure/ transfection activity relationships and interactions with biomembranes.

    Science.gov (United States)

    Koynova, Rumiana; Tenchov, Boris

    2010-01-01

    Abstract Synthetic cationic lipids, which form complexes (lipoplexes) with polyanionic DNA, are presently the most widely used constituents of nonviral gene carriers. A large number of cationic amphiphiles have been synthesized and tested in transfection studies. However, due to the complexity of the transfection pathway, no general schemes have emerged for correlating the cationic lipid chemistry with their transfection efficacy and the approaches for optimizing their molecular structures are still largely empirical. Here we summarize data on the relationships between transfection activity and cationic lipid molecular structure and demonstrate that the transfection activity depends in a systematic way on the lipid hydrocarbon chain structure. A number of examples, including a large series of cationic phosphatidylcholine derivatives, show that optimum transfection is displayed by lipids with chain length of approximately 14 carbon atoms and that the transfection efficiency strongly increases with increase of chain unsaturation, specifically upon replacement of saturated with monounsaturated chains.

  15. [Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

    Science.gov (United States)

    Abaturov, L V; Nosova, N G

    2013-01-01

    The mechanisms of the three-dimensional crambin structure alterations in the crystalline environments and in the trajectories of the molecular dynamics simulations in the vacuum and crystal surroundings have been analyzed. In the crystalline state and in the solution the partial regrouping of remote intramolecular packing contacts, involved in the formation and stabilization of the tertiary structure of the crambin molecule, occurs in NMR structures. In the crystalline state it is initiated by the formation of the intermolecular contacts, the conformational influence of its appearance is distributed over the structure. The changes of the conformations and positions of the residues of the loop segments, where the intermolecular contacts of the crystal surroundings are preferably concentrated, are most observable. Under the influence of these contacts the principal change of the regular secondary structure of crambin is taking place: extension of the two-strand beta structure to the three-strand structure with the participation of the single last residue N46 of the C-terminal loop. In comparison with the C-terminal loop the more profound changes are observed in the conformation and the atomic positions of the backbone atoms and in the solvent accessibility of the residues of the interhelical loop. In the solution of the ensemble of the 8 NMR structures relative accessibility to the solvent differs more noticeably also in the region of the loop segments and rather markedly in the interhelical loop. In the crambin cryogenic crystal structures the positions of the atoms of the backbone and/or side chain of 14-18 of 46 residues are discretely disordered. The disorganizations of at least 8 of 14 residues occur directly in the regions of the intermolecular contacts and another 5 residues are disordered indirectly through the intramolecular contacts with the residues of the intermolecular contacts. Upon the molecular dynamics simulation in the vacuum surrounding as in the

  16. Model of molecular structure of the insoluble organic matter isolated from Murchison meteorite

    Science.gov (United States)

    Derenne, Sylvie; Robert, François

    2010-09-01

    The molecular structure of the insoluble organic matter (IOM) from Murchison meteorite has been investigated by our group for several years using a large set of analytical methods including various spectroscopies (Fourier transform infrared spectroscopy, nuclear magnetic resonance, electron paramagnetic resonance, X-ray absorption near-edge spectroscopy), high resolution electron microscopy, and thermal (pyrolyses in the presence or not of tetramethylammonium hydroxide) and chemical (RuO4 oxidation) degradations. Taken together, these techniques provided a wealth of qualitative and quantitative information, from which we derived 11 elemental and molecular parameters on the same IOM residue. In addition to the basic elemental composition, these parameters describe the distribution of the different types of carbon, nitrogen, and sulfur atoms as well as the size of the polyaromatic units. For this molecular structure, we therefore propose a model which fits with these 11 molecular quantitative parameters. Several cosmochemical implications are derived from this structure. Based on the fact that aromatic moieties are highly substituted and aliphatic chains highly branched, it can be anticipated that the synthesis of this IOM occurred through successive additions of single carbon units in the gas-phase ending by a spontaneous cyclization for chain length ≥7 C. As a whole, these observations favor an organosynthesis in the solar T-Tauri disk.

  17. Establishing whether the structural feature controlling the mechanical properties of starch films is molecular or crystalline.

    Science.gov (United States)

    Li, Ming; Xie, Fengwei; Hasjim, Jovin; Witt, Torsten; Halley, Peter J; Gilbert, Robert G

    2015-03-06

    The effects of molecular and crystalline structures on the tensile mechanical properties of thermoplastic starch (TPS) films from waxy, normal, and high-amylose maize were investigated. Starch structural variations were obtained through extrusion and hydrothermal treatment (HTT). The molecular and crystalline structures were characterized using size-exclusion chromatography and X-ray diffractometry, respectively. TPS from high-amylose maize showed higher elongation at break and tensile strength than those from normal maize and waxy maize starches when processed with 40% plasticizer. Within the same amylose content, the mechanical properties were not affected by amylopectin molecular size or the crystallinity of TPS prior to HTT. This lack of correlation between the molecular size, crystallinity and mechanical properties may be due to the dominant effect of the plasticizer on the mechanical properties. Further crystallization of normal maize TPS by HTT increased the tensile strength and Young's modulus, while decreasing the elongation at break. The results suggest that the crystallinity from the remaining ungelatinized starch granules has less significant effect on the mechanical properties than that resulting from starch recrystallization, possibly due to a stronger network from leached-out amylose surrounding the remaining starch granules. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Atomic spectral-product representations of molecular electronic structure: metric matrices and atomic-product composition of molecular eigenfunctions.

    Science.gov (United States)

    Ben-Nun, M; Mills, J D; Hinde, R J; Winstead, C L; Boatz, J A; Gallup, G A; Langhoff, P W

    2009-07-02

    Recent progress is reported in development of ab initio computational methods for the electronic structures of molecules employing the many-electron eigenstates of constituent atoms in spectral-product forms. The approach provides a universal atomic-product description of the electronic structure of matter as an alternative to more commonly employed valence-bond- or molecular-orbital-based representations. The Hamiltonian matrix in this representation is seen to comprise a sum over atomic energies and a pairwise sum over Coulombic interaction terms that depend only on the separations of the individual atomic pairs. Overall electron antisymmetry can be enforced by unitary transformation when appropriate, rather than as a possibly encumbering or unnecessary global constraint. The matrix representative of the antisymmetrizer in the spectral-product basis, which is equivalent to the metric matrix of the corresponding explicitly antisymmetric basis, provides the required transformation to antisymmetric or linearly independent states after Hamiltonian evaluation. Particular attention is focused in the present report on properties of the metric matrix and on the atomic-product compositions of molecular eigenstates as described in the spectral-product representations. Illustrative calculations are reported for simple but prototypically important diatomic (H(2), CH) and triatomic (H(3), CH(2)) molecules employing algorithms and computer codes devised recently for this purpose. This particular implementation of the approach combines Slater-orbital-based one- and two-electron integral evaluations, valence-bond constructions of standard tableau functions and matrices, and transformations to atomic eigenstate-product representations. The calculated metric matrices and corresponding potential energy surfaces obtained in this way elucidate a number of aspects of the spectral-product development, including the nature of closure in the representation, the general redundancy or

  19. The general atomic and molecular electronic structure system HONDO: Version 7.0

    International Nuclear Information System (INIS)

    Dupuis, M.; Watts, J.D.; Villar, H.O.; Hurst, G.J.B.

    1989-01-01

    We describe a computer program for ab initio quantum mechanical calculations of atomic and molecular wavefunctions and energies. Capabilities for the calculation of energy gradients and second derivatives with respect to nuclear coordinates are provided for several types of wavefunctions. Calculations of many molecular properties based on the electron density are possible. The program contains automated algorithms for the determination of equilibrium structures, saddle points, reaction pathways, vibrational spectra including infrared and Raman intensities. We illustrate the capabilities of the program by highlighting research problems recently investigated with the present program. (orig.)

  20. Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow

    DEFF Research Database (Denmark)

    Lemarchand, Claire; Bailey, Nicholas; Daivis, Peter

    2015-01-01

    The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear...... rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates...

  1. Theoretical Study of Copper Complexes: Molecular Structure, Properties, and Its Application to Solar Cells

    Directory of Open Access Journals (Sweden)

    Jesus Baldenebro-Lopez

    2013-01-01

    Full Text Available We present a theoretical investigation of copper complexes with potential applications as sensitizers for solar cells. The density functional theory (DFT and time-dependent DFT were utilized, using the M06 hybrid meta-GGA functional with the LANL2DZ (D95V on first row and DZVP basis sets. This level of calculation was used to find the optimized molecular structure, the absorption spectra, the molecular orbitals energies, and the chemical reactivity parameters that arise from conceptual DFT. Solvent effects have been taken into account by an implicit approach, namely, the polarizable continuum model (PCM, using the nonequilibrium version of the IEF-PCM model.

  2. Nanocylindrical confinement imparts highest structural order in molecular self-assembly of organophosphonates on aluminum oxide.

    Science.gov (United States)

    Pathak, Anshuma; Bora, Achyut; Braunschweig, Björn; Meltzer, Christian; Yan, Hongdan; Lemmens, Peter; Daum, Winfried; Schwartz, Jeffrey; Tornow, Marc

    2017-05-18

    We report the impact of geometrical constraint on intramolecular interactions in self-assembled monolayers (SAMs) of alkylphosphonates grown on anodically oxidized aluminum (AAO). Molecular order in these films was determined by sum frequency generation (SFG) spectroscopy, a more sensitive measure of order than infrared absorption spectroscopy. Using SFG we show that films grown on AAO are, within detection limits, nearly perfectly ordered in an all-trans alkyl chain configuration. In marked contrast, films formed on planar, plasma-oxidized aluminum oxide or α-Al 2 O 3 (0001) are replete with gauche defects. We attribute these differences to the nanocylindrical structure of AAO, which enforces molecular confinement.

  3. Demonstration of molecular beam epitaxy and a semiconducting band structure for I-Mn-V compounds

    International Nuclear Information System (INIS)

    Jungwirth, T.; Novak, V.; Cukr, M.; Zemek, J.; Marti, X.; Horodyska, P.; Nemec, P.; Holy, V.; Maca, F.; Shick, A. B.; Masek, J.; Kuzel, P.; Nemec, I.; Gallagher, B. L.; Campion, R. P.; Foxon, C. T.; Wunderlich, J.

    2011-01-01

    Our ab initio theory calculations predict a semiconducting band structure of I-Mn-V compounds. We demonstrate on LiMnAs that high-quality materials with group-I alkali metals in the crystal structure can be grown by molecular beam epitaxy. Optical measurements on the LiMnAs epilayers are consistent with the theoretical electronic structure. Our calculations also reproduce earlier reports of high antiferromagnetic ordering temperature and predict large, spin-orbit-coupling-induced magnetic anisotropy effects. We propose a strategy for employing antiferromagnetic semiconductors in high-temperature semiconductor spintronics.

  4. Structural, dynamical, and electronic properties of amorphous silicon: An ab initio molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Car, R.; Parrinello, M.

    1988-01-18

    An amorphous silicon structure is obtained with a computer simulation based on a new molecular-dynamics technique in which the interatomic potential is derived from a parameter-free quantum mechanical method. Our results for the atomic structure, the phonon spectrum, and the electronic properties are in excellent agreement with experiment. In addition we study details of the microscopic dynamics which are not directly accessible to experiment. We find in particular that structural defects are associated with weak bonds. These may give rise to low-frequency vibrational modes.

  5. Molecules and Models The molecular structures of main group element compounds

    CERN Document Server

    Haaland, Arne

    2008-01-01

    This book provides a systematic description of the molecular structures and bonding in simple compounds of the main group elements with particular emphasis on bond distances, bond energies and coordination geometries. The description includes the structures of hydrogen, halogen and methyl derivatives of the elements in each group, some of these molecules are ionic, some polar covalent. The survey of molecules whose structures conform to well-established trends is followed byrepresentative examples of molecules that do not conform. We also describe electron donor-acceptor and hydrogen bonded co

  6. Molecular design chemical structure generation from the properties of pure organic compounds

    CERN Document Server

    Horvath, AL

    1992-01-01

    This book is a systematic presentation of the methods that have been developed for the interpretation of molecular modeling to the design of new chemicals. The main feature of the compilation is the co-ordination of the various scientific disciplines required for the generation of new compounds. The five chapters deal with such areas as structure and properties of organic compounds, relationships between structure and properties, and models for structure generation. The subject is covered in sufficient depth to provide readers with the necessary background to understand the modeling

  7. The impact of chemical structure and molecular packing on the electronic polarisation of fullerene arrays.

    Science.gov (United States)

    Few, Sheridan; Chia, Cleaven; Teo, Daniel; Kirkpatrick, James; Nelson, Jenny

    2017-07-19

    Electronic polarisation contributes to the electronic landscape as seen by separating charges in organic materials. The nature of electronic polarisation depends on the polarisability, density, and arrangement of polarisable molecules. In this paper, we introduce a microscopic, coarse-grained model in which we treat each molecule as a polarisable site, and use an array of such polarisable dipoles to calculate the electric field and associated energy of any arrangement of charges in the medium. The model incorporates chemical structure via the molecular polarisability and molecular packing patterns via the structure of the array. We use this model to calculate energies of charge pairs undergoing separation in finite fullerene lattices of different chemical and crystal structures. The effective dielectric constants that we estimate from this approach are in good quantitative agreement with those measured experimentally in C 60 and phenyl-C 61 -butyric acid methyl ester (PCBM) films, but we find significant differences in dielectric constant depending on packing and on direction of separation, which we rationalise in terms of density of polarisable fullerene cages in regions of high field. In general, we find lattices containing molecules of more isotropic polarisability tensors exhibit higher dielectric constants. By exploring several model systems we conclude that differences in molecular polarisability (and therefore, chemical structure) appear to be less important than differences in molecular packing and separation direction in determining the energetic landscape for charge separation. We note that the results are relevant for finite lattices, but not necessarily for infinite systems. We propose that the model could be used to design molecular systems for effective electronic screening.

  8. Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.

    Science.gov (United States)

    Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi

    2017-10-12

    Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.

  9. Ultrafast time-resolved spectroscopy of xanthophylls at low temperature.

    Science.gov (United States)

    Cong, Hong; Niedzwiedzki, Dariusz M; Gibson, George N; Frank, Harry A

    2008-03-20

    Many of the spectroscopic features and photophysical properties of xanthophylls and their role in energy transfer to chlorophyll can be accounted for on the basis of a three-state model. The characteristically strong visible absorption of xanthophylls is associated with a transition from the ground state S0 (1(1)Ag-) to the S2 (1(1)Bu+) excited state. The lowest lying singlet state denoted S1 (2(1)Ag-), is a state into which absorption from the ground state is symmetry forbidden. Ultrafast optical spectroscopic studies and quantum computations have suggested the presence of additional excited singlet states in the vicinity of S1 (2(1)Ag-) and S2 (1(1)Bu+). One of these is denoted S* and has been suggested in previous work to be associated with a twisted molecular conformation of the molecule in the S1 (2(1)Ag-) state. In this work, we present the results of a spectroscopic investigation of three major xanthophylls from higher plants: violaxanthin, lutein, and zeaxanthin. These molecules have systematically increasing extents of pi-electron conjugation from nine to eleven conjugated carbon-carbon double bonds. All-trans isomers of the molecules were purified by high-performance liquid chromatography (HPLC) and studied by steady-state and ultrafast time-resolved optical spectroscopy at 77 K. Analysis of the data using global fitting techniques has revealed the inherent spectral properties and ultrafast dynamics of the excited singlet states of each of the molecules. Five different global fitting models were tested, and it was found that the data are best explained using a kinetic model whereby photoexcitation results in the promotion of the molecule into the S2 (1(1)Bu+) state that subsequently undergoes decay to a vibrationally hot S1 (1(1)Ag-) state and with the exception of violaxanthin also to the S* state. The vibrationally hot S1 (1(1)Ag-) state then cools to a vibrationally relaxed S1 (2(1)Ag-) state in less than a picosecond. It was also found that a portion

  10. Structural and Conformational Chemistry from Electrochemical Molecular Machines. Replicating Biological Functions. A Review.

    Science.gov (United States)

    Otero, Toribio F

    2017-12-14

    Each constitutive chain of a conducting polymer electrode acts as a reversible multi-step electrochemical molecular motor: reversible reactions drive reversible conformational movements of the chain. The reaction-driven cooperative actuation of those molecular machines generates, or destroys, inside the film the free volume required to lodge/expel balancing counterions and solvent: reactions drive reversible film volume variations, which basic structural components are here identified and quantified from electrochemical responses. The content of the reactive dense gel (chemical molecular machines, ions and water) mimics that of the intracellular matrix in living functional cells. Reaction-driven properties (composition-dependent properties) and devices replicate biological functions and organs. An emerging technological world of soft, wet, reaction-driven, multifunctional and biomimetic devices and the concomitant zoomorphic or anthropomorphic robots is presented. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Hsp90 molecular chaperone: structure, functions and participation in cardio-vascular pathologies

    Directory of Open Access Journals (Sweden)

    Kroupskaya I. V.

    2009-10-01

    Full Text Available The review is devoted to the analysis of structural and functional properties of molecular chaperon Hsp90. Hsp90 is a representative of highly widespread family of heat shock proteins. The protein is found in eubacteria and all branches of eukarya, but it is apparently absent in archaea. It is one of key regulators of numerous signalling pathways, cell growth and development, apoptosis, induction of autoimmunity, and progression of heart failure. The full functional activity of Hsp90 shows up in a complex with other molecular chaperones and co-chaperones. Molecular interactions between chaperones, different signalling proteins and protein-partners are highly crucial for the normal functioning of signalling pathways and their destruction causes an alteration in the cell physiology up to its death.

  12. Using an electrostatic accelerator to determine the stereochemical structures of molecular ions

    International Nuclear Information System (INIS)

    Gemmell, D.S.

    1980-01-01

    Recent high-resolution measurements on the energy and angle distributions of the fragments produced when fast (MeV) molecular-ion beams from an electrostatic accelerator dissociate (Coulomb explode) in thin foils and in gases, offer promising possibilities for deducing the stereochemical structures of the molecular ions constituting the incident beams. Bond lengths have been determined in this way for several diatomic projectiles (H 2 + , HeH + , CH + , NH + , OH + , N 2 + , O 2 + , etc.) with an accuracy of approx. 0.01 A. H 3 + has been demonstrated (for the first time) to be equilateral triangular and the interproton distance measured. Measurements on single fragments from CO 2 + , N 2 O + , C 3 H 3 + , and CH/sub n/ + have revealed the gross structures of the projectiles. An apparatus has recently been constructed at Argonne to permit precise measurements on fragments in coincidence. The apparatus has been tested on a known structure (OH 2 + ). The O-H bond length was found to be 1.0 +- 0.04 A and the H-O-H bond angle was measured as 110 +- 2 0 . These values are in excellent agreement with those found in optical experiments (0.999 A and 110.5 0 ). This Coulomb explosion technique can be expected to be refined in accuracy and to be extended to a wide range of molecular ions whose structures are inaccessible by other means

  13. Shear response of grain boundaries with metastable structures by molecular dynamics simulations

    Science.gov (United States)

    Zhang, Liang; Lu, Cheng; Shibuta, Yasushi

    2018-04-01

    Grain boundaries (GBs) can play a role as the favored locations to annihilate point defects, such as interstitial atoms and vacancies. It is thus highly probable that different boundary structures can be simultaneously present in equilibrium with each other in the same GB, and thus the GB achieves a metastable state. However, the structural transition and deformation mechanism of such GBs are currently not well understood. In this work, molecular dynamics simulations were carried out to study the multiple structures of a Σ5(310)/[001] GB in bicrystal Al and to investigate the effect of structural multiplicity on the mechanical and kinetic properties of such a GB. Different GB structures were obtained by changing the starting atomic configuration of the bicrystal model, and the GB structures had significantly different atomic density. For the Σ5(310) GB with metastable structures, GB sliding was the dominant mechanism at a low temperature (T = 10 K) under shear stress. The sliding mechanism resulted from the uncoordinated transformation of the inhomogeneous structural units. The nucleation of voids was observed during GB sliding at the low temperature, and the voids subsequently evolved to a nanocrack at the boundary plane. Increasing the temperature can induce the structural transition of local GB structures and can change their overall kinetic properties. GB migration with occasional GB sliding dominated the deformation mechanism at elevated temperatures (T = 300 and 600 K), and the migration process of the metastable GB structures is closely related to the thermally assisted diffusion mechanism.

  14. Coulomb-explosion technique for determining geometrical structures of molecular ions

    International Nuclear Information System (INIS)

    Gemmell, D.S.

    1981-01-01

    Traditional experimental techniques (e.g. studies on photon absorption or emission) for determining the sterochemical structures of neutral molecules are extremeley difficult to apply to molecular ions because of problems in obtaining a sufficient spatial density of the ions to be studied. Recent high-resolution measurements on the energy and angle distributions of the fragments produced when fast (MeV) molecular-ion beams from an electrostatic accelerator dissociate (Coulomb explode) in thin foils and in gases, offer promising possibilities for deducing the sterochemical structures of the molecular ions constituting the incident beams. Bond lengths have been determined in this way for several diatomic projectiles (H 2+ , HeH + , CH + , NH + , OH + , N 2+ , O 2+ , etc.) with an accuracy of approx. 0.01 A. H 3+ has been demonstrated (for the first time) to be equilateral triangular and the interproton distance measured. Measurements on single fragments from CO 2+ , N 2 O + , C 3 H 3+ , and CH/sub n/ + have revealed the gross structures of the projectiles. An apparatus has recently been constructed at Argonne to permit precise measurements on fragments in coincidence. The apparatus has been tested on a known structure (OH 2+ ). The O-H bond length was found to be 1.0 +- 0.04 A and the H-O-H bond angle was measured as 110 --- 2 0 . These values are in excellent agreement with those found in optical experiments (0.999 A and 110.5 0 ). This Coulomb explosion technique can be expected to be refined in accuracy and to be extended to a wide range of molecular ions whose structures are inaccessible by other means

  15. Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

    International Nuclear Information System (INIS)

    Sidhu, Navdeep S.; Schreiber, Kathrin; Pröpper, Kevin; Becker, Stefan; Usón, Isabel; Sheldrick, George M.; Gärtner, Jutta; Krätzner, Ralph; Steinfeld, Robert

    2014-01-01

    Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder

  16. Electron Scattering Studies of Gas Phase Molecular Structure at High Temperature

    Science.gov (United States)

    Mawhorter, Richard J., Jr.

    A high precision counting electron diffraction study of the structure of gaseous sulfur dioxide as a function of temperature from 300(DEGREES) to 1000(DEGREES)K is presented. The results agree well with current theory, and yield insight into the effects of anharmonicity on molecular structure. Another aspect of molecular structure is the molecular charge density distribution. The difference (DELTA)(sigma) is between the electron scattering cross sections for the actual molecule and independent atom model (IAM) are a sensitive measure of the change in this distribution due to bond formation. These difference cross sections have been calculated using ab initio methods, and the results for a wide range of simple polyatomic molecules are presented. Such calculations are routinely done for a single, fixed molecular geometry, an approach which neglects the effects of the vibrational motion of real molecules. The effect of vibrational averaging is studied in detail for the three normal vibrational modes of H(,2)O in the ground state. The effects are small, lending credence to the practice of comparing cross sections calculated at a fixed geometry with inherently averaged experimental data. The efficacy of the standard formula used to account for vibrational averaging in the IAM is also examined. Finally, the nature of the ionic bond is probed with an experimental study of the structure of alkali chlorides, NaCl, KCl, RbCl, and CsCl, in the gas phase. Temperatures from 840-960(DEGREES)K were required to achieve the necessary vapor pressures of approximately 0.01 torr. A planar rhombic structure for the dimer molecule is confirmed, with a fairly uniform decrease of the chlorine-alkali-chlorine angle as the alkalis increase in size. The experiment also yields information on the amount of dimer present in the vapor, and these results are compared with thermodynamic values.

  17. Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

    Energy Technology Data Exchange (ETDEWEB)

    Sidhu, Navdeep S. [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany); University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Schreiber, Kathrin [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany); Pröpper, Kevin [University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Becker, Stefan [Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany); Usón, Isabel [Instituto de Biologia Molecular de Barcelona (IBMB–CSIC), Barcelona Science Park, Baldiri Reixach 15, 08028 Barcelona (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), (Spain); Sheldrick, George M. [University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Gärtner, Jutta; Krätzner, Ralph, E-mail: rkraetz@gwdg.de; Steinfeld, Robert, E-mail: rkraetz@gwdg.de [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany)

    2014-05-01

    Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.

  18. Multiplane wave imaging increases signal-to-noise ratio in ultrafast ultrasound imaging

    International Nuclear Information System (INIS)

    Tiran, Elodie; Deffieux, Thomas; Correia, Mafalda; Maresca, David; Osmanski, Bruno-Felix; Pernot, Mathieu; Tanter, Mickael; Sieu, Lim-Anna; Bergel, Antoine; Cohen, Ivan

    2015-01-01

    Ultrafast imaging using plane or diverging waves has recently enabled new ultrasound imaging modes with improved sensitivity and very high frame rates. Some of these new imaging modalities include shear wave elastography, ultrafast Doppler, ultrafast contrast-enhanced imaging and functional ultrasound imaging. Even though ultrafast imaging already encounters clinical success, increasing even more its penetration depth and signal-to-noise ratio for dedicated applications would be valuable.Ultrafast imaging relies on the coherent compounding of backscattered echoes resulting from successive tilted plane waves emissions; this produces high-resolution ultrasound images with a trade-off between final frame rate, contrast and resolution. In this work, we introduce multiplane wave imaging, a new method that strongly improves ultrafast images signal-to-noise ratio by virtually increasing the emission signal amplitude without compromising the frame rate. This method relies on the successive transmissions of multiple plane waves with differently coded amplitudes and emission angles in a single transmit event. Data from each single plane wave of increased amplitude can then be obtained, by recombining the received data of successive events with the proper coefficients.The benefits of multiplane wave for B-mode, shear wave elastography and ultrafast Doppler imaging are experimentally demonstrated. Multiplane wave with 4 plane waves emissions yields a 5.8  ±  0.5 dB increase in signal-to-noise ratio and approximately 10 mm in penetration in a calibrated ultrasound phantom (0.7 d MHz −1 cm −1 ). In shear wave elastography, the same multiplane wave configuration yields a 2.07  ±  0.05 fold reduction of the particle velocity standard deviation and a two-fold reduction of the shear wave velocity maps standard deviation. In functional ultrasound imaging, the mapping of cerebral blood volume results in a 3 to 6 dB increase of the contrast-to-noise ratio in

  19. New trends in atomic and molecular physics advanced technological applications

    CERN Document Server

    2013-01-01

    The field of Atomic and Molecular Physics (AMP) has reached significant advances in high–precision experimental measurement techniques. The area covers a wide spectrum ranging from conventional to new emerging multi-disciplinary areas like physics of highly charged ions (HCI), molecular physics, optical science, ultrafast laser technology etc. This book includes the important topics of atomic structure, physics of atomic collision, photoexcitation, photoionization processes, Laser cooling and trapping, Bose Einstein condensation and advanced technology applications of AMP in the fields of astronomy , astrophysics , fusion, biology and nanotechnology. This book is useful for researchers, professors, graduate, post graduate and PhD students dealing with atomic and molecular physics. The book has a wide scope with applications in neighbouring fields like plasma physics, astrophysics, cold collisions, nanotechnology and future fusion energy sources like ITER (international Thermonuclear Experimental Reactor) To...

  20. Anti-symmetrized molecular dynamics: a new insight into the structure of nuclei

    International Nuclear Information System (INIS)

    Yoshiko, Kanada-En'yo; Masaaki, Kimura; Hisashi, Horiuchi

    2003-01-01

    The AMD (anti-symmetrized molecular dynamics) theory for nuclear structure is explained by showing its actual applications. First the formulation of AMD including various refined versions is briefly presented and its characteristics are discussed, putting a stress on its nature as an 'ab initio' theory. Then we demonstrate fruitful applications to various structure problems in stable nuclei, in order to explicitly verify the 'ab initio' nature of AMD, especially the ability to describe both mean-field-type structure and cluster structure. Finally, we show the results of applications of AMD to unstable nuclei, from which we see that AMD is powerful in elucidating and understanding various types of nuclear structure of unstable nuclei. (authors)

  1. Methodology for studying molecular and supramolecular structures of coals and carbonaceous materials

    Energy Technology Data Exchange (ETDEWEB)

    G.B. Skripchenko [Russian Academy of Sciences, Moscow (Russian Federation). Russia Institute for Fossil Fuels - Science and Technology Center for Complex Processing of Solid Fossil Fuels

    2009-07-01

    Those studying coals have to account for petrographic nonuniformity (the optical structural level), different types of chemical bonding between structural fragments, the existence of aromatic clusters in the organic matter, the appearance of a supramolecular order between aromatic clusters, and further orientation ordering of crystallites under the action of the geological pressure. Combinations of conventional chemical strategies with advanced physicochemical methods, such as IR, NMR, EPR, and X-ray spectroscopy; X-ray diffraction; electronic and scanning microscopy; and some others, are pertinent for structure determination. The appearance of supramolecular structures is a manifestation of molecular-level structural rearrangements, which are characteristic of coals, cokes, pitches, and various pyrolytic carbons. This necessitates the use of optical, electronic, and scanning microscopy along with other chemical methods. The occurrence of mineral components in coals can appreciably limit the resolution of IR spectroscopy and X-ray crystallography.

  2. Raman spectroscopy as an advanced structural nanoprobe for conjugated molecular semiconductors

    International Nuclear Information System (INIS)

    Wood, Sebastian; Hollis, Joseph Razzell; Kim, Ji-Seon

    2017-01-01

    Raman spectroscopy has emerged as a powerful and important characterisation tool for probing molecular semiconducting materials. The useful optoelectronic properties of these materials arise from the delocalised π -electron density in the conjugated core of the molecule, which also results in large Raman scattering cross-sections and a strong coupling between its electronic states and vibrational modes. For this reason, Raman spectroscopy offers a unique insight into the properties of molecular semiconductors, including: chemical structure, molecular conformation, molecular orientation, and fundamental photo- and electro-chemical processes—all of which are critically important to the performance of a wide range of optical and electronic organic semiconductor devices. Experimentally, Raman spectroscopy is non-intrusive, non-destructive, and requires no special sample preparation, and so is suitable for a wide range of in situ measurements, which are particularly relevant to issues of thermal and photochemical stability. Here we review the development of the family of Raman spectroscopic techniques, which have been applied to the study of conjugated molecular semiconductors. We consider the suitability of each technique for particular circumstances, and the unique insights it can offer, with a particular focus on the significance of these measurements for the continuing development of stable, high performance organic electronic devices. (topical review)

  3. Modelling multi-pulse population dynamics from ultrafast spectroscopy.

    Directory of Open Access Journals (Sweden)

    Luuk J G W van Wilderen

    2011-03-01

    Full Text Available Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio- physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox that describes the finite bleach (orientation effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective excitation (photoselection and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical

  4. Modelling multi-pulse population dynamics from ultrafast spectroscopy.

    Science.gov (United States)

    van Wilderen, Luuk J G W; Lincoln, Craig N; van Thor, Jasper J

    2011-03-21

    Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio-) physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function) for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox) that describes the finite bleach (orientation) effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective) excitation (photoselection) and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical modelling is

  5. Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair.

    Science.gov (United States)

    Zhang, Yuchen; Alsop, Richard J; Soomro, Asfia; Yang, Fei-Chi; Rheinstädter, Maikel C

    2015-01-01

    The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3-90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers.

  6. Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair

    Directory of Open Access Journals (Sweden)

    Yuchen Zhang

    2015-10-01

    Full Text Available The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3–90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers.

  7. Impact of local order and stoichiometry on the ultrafast magnetization dynamics of Heusler compounds

    International Nuclear Information System (INIS)

    Steil, Daniel; Schmitt, Oliver; Fetzer, Roman; Aeschlimann, Martin; Cinchetti, Mirko; Kubota, Takahide; Naganuma, Hiroshi; Oogane, Mikihiko; Ando, Yasuo; Rodan, Steven; Blum, Christian G F; Wurmehl, Sabine; Balke, Benjamin

    2015-01-01

    Nowadays, a wealth of information on ultrafast magnetization dynamics of thin ferromagnetic films exists in the literature. Information is, however, scarce on bulk single crystals, which may be especially important for the case of multi-sublattice systems. In Heusler compounds, representing prominent examples for such multi-sublattice systems, off-stoichiometry and degree of order can significantly change the magnetic properties of thin films, while bulk single crystals may be generally produced with a much more well-defined stoichiometry and a higher degree of ordering. A careful characterization of the local structure of thin films versus bulk single crystals combined with ultrafast demagnetization studies can, thus, help to understand the impact of stoichiometry and order on ultrafast spin dynamics.Here, we present a comparative study of the structural ordering and magnetization dynamics for thin films and bulk single crystals of the family of Heusler alloys with composition Co 2 Fe 1 − x Mn x Si. The local ordering is studied by 59 Co nuclear magnetic resonance (NMR) spectroscopy, while the time-resolved magneto-optical Kerr effect gives access to the ultrafast magnetization dynamics. In the NMR studies we find significant differences between bulk single crystals and thin films, both regarding local ordering and stoichiometry. The ultrafast magnetization dynamics, on the other hand, turns out to be mostly unaffected by the observed structural differences, especially on the time scale of some hundreds of femtoseconds. These results confirm hole-mediated spin-flip processes as the main mechanism for ultrafast demagnetization and the robustness of this demagnetization channel against defect states in the minority band gap as well as against the energetic position of the band gap with respect to the Fermi energy. The very small differences observed in the magnetization dynamics on the picosecond time-scale, on the other hand, can be explained by considering the

  8. Molecular Dynamics Simulation of the Structure and Properties of Lithium Phosphate Glasses

    Energy Technology Data Exchange (ETDEWEB)

    Liang, J-J; Cygan, R.T.; Alam, T.M.

    1999-07-09

    A new forcefield model was developed for the computer simulation of phosphate materials that have many important applications in the electronics and biomedical industries. The model provides a fundamental basis for the evaluation of phosphate glass structure and thermodynamics. Molecular dynamics simulations of a series of lithium phosphate glass compositions were performed using the forcefield model. A high concentration of three-membered rings (P{sub 3}O{sub 3}) occurs in the glass of intermediate composition (0.2 Li{sub 2}O {center_dot} 0.8P{sub 2}O{sub 5}) that corresponds to the minimum in the glass transition temperature curve for the compositional series. Molecular orbital calculations of various phosphate ring clusters indicate an increasing stabilization of the phosphate ring structure going from two- to four-membered rings.

  9. Molecular dynamical and structural studies for the bakelite by neutron cross section measurements

    International Nuclear Information System (INIS)

    Voi, D.L.

    1992-05-01

    Neutron reaction cross sections were determined by transmission and scattering measurements, to study the dynamics and molecular structure of calcined bakelites. Total cross sections were determined, with a deviation smaller than 5%, from the literature values, by neutron transmission method and a specially devised approximation. These cross sections were then correlated with data obtained with infra-red spectroscopy, elemental analysis and other techniques to get the probable molecular formulae of bakelite. Double differential scattering cross sections, scattering law values and frequency distributions were determined with 15% error using the neutron inelastic scattering method. The frequency distributions as well as the overall results from all experimental techniques used in this work allowed to suggest a structural model like polycyclic hydrocarbons, for calcined bakelite at 800 0 C. (author)

  10. Splitting of α-Helical Structure as Molecular Basis for Abolishing an Amyloid Formation by Multiple Glycosylation: A Molecular Dynamics Simulation Study

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Youngjin [Hoseo University, Asan (Korea, Republic of); Cho, Eunae; Jung, Seunho [Konkuk University, Seoul (Korea, Republic of)

    2016-07-15

    Molecular details played by glycosylation are complicated by the subtle nature of variations in the glycan structure, and this complexity is one of the research barriers to establish structure-function relationship on the protein modification. This is particularly true for understanding the exact structural consequence of the glycosylation of the biological proteins. The present MD simulation revealed molecular-level mechanism of the glycosylation effect on the peptide to understand the experimentally observed phenomenon for inhibiting amyloid formation in the model peptide. The galactose residue on the Ser17 undermined the helical integrity of main protein region by enhancing sugar–amino acid interaction and perturbing natural interactions between amino acid residues.

  11. Study of inter species diversity and population structure by molecular genetic method in Iranian Artemia

    OpenAIRE

    Hajirostamloo, Mahbobeh

    2005-01-01

    Artemia is a small crustacean that adapted to live in brine water and has been seen in different brine water sources in Iran. Considering the importance of genetic studies manifest inter population differences in species, to estimate genetic structure, detect difference at molecular level and separate different Artemia populations of Iran, also study of phylogenic relationships among them, samples of Artemia were collected from nine region: Urmia lake in West Azerbaijan, Sh...

  12. Machine learning for the structure-energy-property landscapes of molecular crystals.

    Science.gov (United States)

    Musil, Félix; De, Sandip; Yang, Jack; Campbell, Joshua E; Day, Graeme M; Ceriotti, Michele

    2018-02-07

    Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol -1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure-property relations in molecular crystal engineering.

  13. Ultrafast surface-enhanced Raman spectroscopy.

    Science.gov (United States)

    Keller, Emily L; Brandt, Nathaniel C; Cassabaum, Alyssa A; Frontiera, Renee R

    2015-08-07

    Ultrafast surface-enhanced Raman spectroscopy (SERS) with pico- and femtosecond time resolution has the ability to elucidate the mechanisms by which plasmons mediate chemical reactions. Here we review three important technological advances in these new methodologies, and discuss their prospects for applications in areas including plasmon-induced chemistry and sensing at very low limits of detection. Surface enhancement, arising from plasmonic materials, has been successfully incorporated with stimulated Raman techniques such as femtosecond stimulated Raman spectroscopy (FSRS) and coherent anti-Stokes Raman spectroscopy (CARS). These techniques are capable of time-resolved measurement on the femtosecond and picosecond time scale and can be used to follow the dynamics of molecules reacting near plasmonic surfaces. We discuss the potential application of ultrafast SERS techniques to probe plasmon-mediated processes, such as H2 dissociation and solar steam production. Additionally, we discuss the possibilities for high sensitivity SERS sensing using these stimulated Raman spectroscopies.

  14. Ultrafast magnetodynamics with free-electron lasers

    Science.gov (United States)

    Malvestuto, Marco; Ciprian, Roberta; Caretta, Antonio; Casarin, Barbara; Parmigiani, Fulvio

    2018-02-01

    The study of ultrafast magnetodynamics has entered a new era thanks to the groundbreaking technological advances in free-electron laser (FEL) light sources. The advent of these light sources has made possible unprecedented experimental schemes for time-resolved x-ray magneto-optic spectroscopies, which are now paving the road for exploring the ultimate limits of out-of-equilibrium magnetic phenomena. In particular, these studies will provide insights into elementary mechanisms governing spin and orbital dynamics, therefore contributing to the development of ultrafast devices for relevant magnetic technologies. This topical review focuses on recent advancement in the study of non-equilibrium magnetic phenomena from the perspective of time-resolved extreme ultra violet (EUV) and soft x-ray spectroscopies at FELs with highlights of some important experimental results.

  15. Ultra-fast framing camera tube

    Science.gov (United States)

    Kalibjian, Ralph

    1981-01-01

    An electronic framing camera tube features focal plane image dissection and synchronized restoration of the dissected electron line images to form two-dimensional framed images. Ultra-fast framing is performed by first streaking a two-dimensional electron image across a narrow slit, thereby dissecting the two-dimensional electron image into sequential electron line images. The dissected electron line images are then restored into a framed image by a restorer deflector operated synchronously with the dissector deflector. The number of framed images on the tube's viewing screen is equal to the number of dissecting slits in the tube. The distinguishing features of this ultra-fast framing camera tube are the focal plane dissecting slits, and the synchronously-operated restorer deflector which restores the dissected electron line images into a two-dimensional framed image. The framing camera tube can produce image frames having high spatial resolution of optical events in the sub-100 picosecond range.

  16. Ultrafast Terahertz Conductivity of Photoexcited Nanocrystalline Silicon

    DEFF Research Database (Denmark)

    Cooke, David; MacDonald, A. Nicole; Hryciw, Aaron

    2007-01-01

    The ultrafast transient ac conductivity of nanocrystalline silicon films is investigated using time-resolved terahertz spectroscopy. While epitaxial silicon on sapphire exhibits a free carrier Drude response, silicon nanocrystals embedded in glass show a response that is best described by a class...... in the silicon nanocrystal films is dominated by trapping at the Si/SiO2 interface states, occurring on a 1–100 ps time scale depending on particle size and hydrogen passivation......The ultrafast transient ac conductivity of nanocrystalline silicon films is investigated using time-resolved terahertz spectroscopy. While epitaxial silicon on sapphire exhibits a free carrier Drude response, silicon nanocrystals embedded in glass show a response that is best described...

  17. Development of Scanning Ultrafast Electron Microscope Capability.

    Energy Technology Data Exchange (ETDEWEB)

    Collins, Kimberlee Chiyoko [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Talin, Albert Alec [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Chandler, David W. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Michael, Joseph R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2016-11-01

    Modern semiconductor devices rely on the transport of minority charge carriers. Direct examination of minority carrier lifetimes in real devices with nanometer-scale features requires a measurement method with simultaneously high spatial and temporal resolutions. Achieving nanometer spatial resolutions at sub-nanosecond temporal resolution is possible with pump-probe methods that utilize electrons as probes. Recently, a stroboscopic scanning electron microscope was developed at Caltech, and used to study carrier transport across a Si p-n junction [ 1 , 2 , 3 ] . In this report, we detail our development of a prototype scanning ultrafast electron microscope system at Sandia National Laboratories based on the original Caltech design. This effort represents Sandia's first exploration into ultrafast electron microscopy.

  18. Coherent combination of ultrafast fiber amplifiers

    International Nuclear Information System (INIS)

    Hanna, Marc; Guichard, Florent; Druon, Frédéric; Georges, Patrick; Zaouter, Yoann; Papadopoulos, Dimitris N

    2016-01-01

    We review recent progress in coherent combining of femtosecond pulses amplified in optical fibers as a way to scale the peak and average power of ultrafast sources. Different methods of achieving coherent pulse addition in space (beam combining) and time (divided pulse amplification) domains are described. These architectures can be widely classified into active methods, where the relative phases between pulses are subject to a servomechanism, and passive methods, where phase matching is inherent to the geometry. Other experiments that combine pulses with different spectral contents, pulses that have been nonlinearly broadened or successive pulses from a mode-locked laser oscillator, are then presented. All these techniques allow access to unprecedented parameter range for fiber ultrafast sources. (topical review)

  19. Silicon based ultrafast optical waveform sampling

    DEFF Research Database (Denmark)

    Ji, Hua; Galili, Michael; Pu, Minhao

    2010-01-01

    A 300 nmx450 nmx5 mm silicon nanowire is designed and fabricated for a four wave mixing based non-linear optical gate. Based on this silicon nanowire, an ultra-fast optical sampling system is successfully demonstrated using a free-running fiber laser with a carbon nanotube-based mode-locker as th......A 300 nmx450 nmx5 mm silicon nanowire is designed and fabricated for a four wave mixing based non-linear optical gate. Based on this silicon nanowire, an ultra-fast optical sampling system is successfully demonstrated using a free-running fiber laser with a carbon nanotube-based mode......-locker as the sampling source. A clear eye-diagram of a 320 Gbit/s data signal is obtained. The temporal resolution of the sampling system is estimated to 360 fs....

  20. Cladding-like waveguide fabricated by cooperation of ultrafast laser writing and ion irradiation: characterization and laser generation.

    Science.gov (United States)

    Lv, Jinman; Shang, Zhen; Tan, Yang; Vázquez de Aldana, Javier Rodríguez; Chen, Feng

    2017-08-07

    We report the surface cladding-like waveguide fabricated by the cooperation of the ultrafast laser writing and the ion irradiation. The ultrafast laser writes tracks near the surface of the Nd:YAG crystal, constructing a semi-circle columnar structure with a decreased refractive index of - 0.00208. Then, the Nd:YAG crystal is irradiated by the Carbon ion beam, forming an enhanced-well in the semi-circle columnar with an increased refractive index of + 0.0024. Tracks and the enhanced-well consisted a surface cladding-like waveguide. Utilizing this cladding-like waveguide as the gain medium for the waveguide lasing, optimized characterizations were observed compared with the monolayer waveguide. This work demonstrates the refractive index of the Nd:YAG crystal can be well tailored by the cooperation of the ultrafast laser writing and the ion irradiation, which provides an convenient way to fabricate the complex and multilayered photonics devices.