Sample records for excitonic molecular complexes

  1. Dynamic coherence in excitonic molecular complexes under various excitation conditions (United States)

    Chenu, Aurélia; Malý, Pavel; Mančal, Tomáš


    We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We derive the time evolution of the density matrix for an open quantum system excited by light or by a neighboring antenna. Unlike in the classical case, the quantum description does not allow for a formal decomposition of the dynamics into sudden jumps in an observable quantity - an expectation value. Rather, there is a natural finite time-scale associated with the excitation process. We propose a simple experiment to test the influence of this time scale on the yield of photosynthesis. We demonstrate, using typical parameters of the Fenna-Matthews-Olson (FMO) complex and a typical energy transfer rate from the chlorosome baseplate, that dynamic coherences are averaged out in the complex even when the FMO model is completely free of all dissipation and dephasing.

  2. Dynamic coherence in excitonic molecular complexes under various excitation conditions

    Energy Technology Data Exchange (ETDEWEB)

    Chenu, Aurélia; Malý, Pavel; Mančal, Tomáš, E-mail:


    Highlights: • Dynamic coherence does not improve energy transfer efficiency in natural conditions. • Photo-induced quantum jumps are discussed in classical context. • Natural time scale of a light excitation event is identified. • Coherence in FMO complex averages out under excitation by neighboring antenna. • This result is valid even in absence of dissipation. - Abstract: We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We derive the time evolution of the density matrix for an open quantum system excited by light or by a neighboring antenna. Unlike in the classical case, the quantum description does not allow for a formal decomposition of the dynamics into sudden jumps in an observable quantity – an expectation value. Rather, there is a natural finite time-scale associated with the excitation process. We propose a simple experiment to test the influence of this time scale on the yield of photosynthesis. We demonstrate, using typical parameters of the Fenna–Matthews–Olson (FMO) complex and a typical energy transfer rate from the chlorosome baseplate, that dynamic coherences are averaged out in the complex even when the FMO model is completely free of all dissipation and dephasing.

  3. Dynamic Coherence in Excitonic Molecular Complexes under Various Excitation Conditions

    CERN Document Server

    Chenu, Aurélia; Mancal, Tomáš


    In this paper, we investigate the relevance of dynamic electronic coherence under conditions natural to light-harvesting systems. We formulate the results of a quantum mechanical treatment of a weak light-matter interaction in terms of experimental observable, such as the incident light spectrum and the absorption spectrum of the material, and we derive the description of the incoherent F\\"orster type energy transfer fully from the wave function formalism. We demonstrate that excitation of a coherent superposition of electronic eigenstates of natural light-harvesting complexes by sunlight or by excitation transfer from a neighboring antenna is unlikely and that dynamical coherence therefore cannot play any significant role in natural photosynthesis, regardless of their life time. Dynamical coherence as a transient phenomenon must be strictly distinguished from the effect of excited state delocalization (also termed quantum coherence in the literature) which is established by interaction between the pigments a...

  4. Bound Exciton Complexes (United States)

    Meyer, B. K.

    In the preceding chapter, we concentrated on the properties of free excitons. These free excitons may move through the sample and hit a trap, a nonradiative or a radiative recombination center. At low temperatures, the latter case gives rise to either deep center luminescence, mentioned in Sect. 7.1 and discussed in detail in Chap. 9, or to the luminescence of bound exciton complexes (BE or BEC). The chapter continues with the most prominent of these BECs, namely A-excitons bound to neutral donors. The next aspects are the more weakly BEs at ionized donors. The Sect. 7.4 treats the binding or localization energies of BEC from a theoretical point of view, while Sect. 7.5 is dedicated to excited states of BECs, which contain either holes from deeper valence bands or an envelope function with higher quantum numbers. The last section is devoted to donor-acceptor pair transitions. There is no section devoted specifically to excitons bound to neutral acceptors, because this topic is still partly controversially discussed. Instead, information on these A0X complexes is scattered over the whole chapter, however, with some special emphasis seen in Sects. 7.1, 7.4, and 7.5.

  5. Excitons in tubular molecular aggregates

    NARCIS (Netherlands)

    Didraga, C; Knoester, J


    We present a brief overview of recent work on the optical properties of molecular aggregates with a tubular (cylindrical) shape. The exciton states responsible for these properties can be distinguished with regard to a transverse wave number, which directly relates to optical selection rules and

  6. Plexcitonic nanoparticles: plasmon-exciton coupling in nanoshell-J-aggregate complexes. (United States)

    Fofang, Nche T; Park, Tae-Ho; Neumann, Oara; Mirin, Nikolay A; Nordlander, Peter; Halas, Naomi J


    Stable Au nanoshell-J-aggregate complexes are formed that exhibit coherent coupling between the localized plasmons of a nanoshell and the excitons of molecular J-aggregates adsorbed on its surface. By tuning the nanoshell plasmon energies across the exciton line of the J-aggregate, plasmon-exciton coupling energies for these complexes are obtained. The strength of this interaction is dependent on the specific plasmon mode of the nanoparticle coupled to the J-aggregate exciton. From a model based on Gans theory, we obtain an expression for the plasmon-exciton hybridized states of the complex.

  7. Exciton dynamics in molecular aggregates

    NARCIS (Netherlands)

    Augulis, R.; Pugžlys, A.; Loosdrecht, P.H.M. van; Pugzlys, A


    The fundamental aspects of exciton dynamics in double-wall cylindrical aggregates of cyanine dyes are studied by means of frequency resolved femtosecond pump-probe spectroscopy. The collective excitations of the aggregates, resulting from intermolecular dipole-dipole interactions have the

  8. Exciton dynamics in perturbed vibronic molecular aggregates

    Directory of Open Access Journals (Sweden)

    C. Brüning


    Full Text Available A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states.

  9. Exciton-vibrational coupling in the dynamics and spectroscopy of Frenkel excitons in molecular aggregates (United States)

    Schröter, M.; Ivanov, S. D.; Schulze, J.; Polyutov, S. P.; Yan, Y.; Pullerits, T.; Kühn, O.


    The influence of exciton-vibrational coupling on the optical and transport properties of molecular aggregates is an old problem that gained renewed interest in recent years. On the experimental side, various nonlinear spectroscopic techniques gave insight into the dynamics of systems as complex as photosynthetic antennae. Striking evidence was gathered that in these protein-pigment complexes quantum coherence is operative even at room temperature conditions. Investigations were triggered to understand the role of vibrational degrees of freedom, beyond that of a heat bath characterized by thermal fluctuations. This development was paralleled by theory, where efficient methods emerged, which could provide the proper frame to perform non-Markovian and non-perturbative simulations of exciton-vibrational dynamics and spectroscopy. This review summarizes the state of affairs of the theory of exciton-vibrational interaction in molecular aggregates and photosynthetic antenna complexes. The focus is put on the discussion of basic effects of exciton-vibrational interaction from the stationary and dynamics points of view. Here, the molecular dimer plays a prominent role as it permits a systematic investigation of absorption and emission spectra by numerical diagonalization of the exciton-vibrational Hamiltonian in a truncated Hilbert space. An extension to larger aggregates, having many coupled nuclear degrees of freedom, becomes possible with the Multi-Layer Multi-Configuration Time-Dependent Hartree (ML-MCTDH) method for wave packet propagation. In fact it will be shown that this method allows one to approach the limit of almost continuous spectral densities, which is usually the realm of density matrix theory. Real system-bath situations are introduced for two models, which differ in the way strongly coupled nuclear coordinates are treated, as a part of the relevant system or the bath. A rather detailed exposition of the Hierarchy Equations Of Motion (HEOM) method will be

  10. Imaging the motion of excitonic complexes in semiconductor quantum wells

    NARCIS (Netherlands)

    Pulizzi, Fabio


    The low temperature optical properties of semiconductor quantum wells are dominated by excitonic complexes, i.e. a few charges bound together by the mutual Coulomb interaction. Excitonic complexes have been widely studied in the past not only for their importance in the physics of semiconductors,

  11. Molecular weight dependence of exciton diffusion in poly(3-hexylthiophene)

    DEFF Research Database (Denmark)

    Masri, Zarifi; Ruseckas, Arvydas; Emelianova, Evguenia V.


    A joint experimental and theoretical study of singlet exciton diffusion in spin-coated poly(3-hexylthiophene) (P3HT) films and its dependence on molecular weight is presented. The results show that exciton diffusion is fast along the co-facial π–π aggregates of polymer chromophores and about 100...... times slower in the lateral direction between aggregates. Exciton hopping between aggregates is found to show a subtle dependence on interchain coupling, aggregate size, and Boltzmann statistics. Additionally, a clear correlation is observed between the effective exciton diffusion coefficient......, the degree of aggregation of chromophores, and exciton delocalization along the polymer chain, which suggests that exciton diffusion length can be enhanced by tailored synthesis and processing conditions....

  12. Exciton Seebeck effect in molecular systems. (United States)

    Yan, Yun-An; Cai, Shaohong


    We investigate the exciton dynamics under temperature difference with the hierarchical equations of motion. Through a nonperturbative simulation of the transient absorption of a heterogeneous trimer model, we show that the temperature difference causes exciton population redistribution and affects the exciton transfer time. It is found that one can reproduce not only the exciton population redistribution but also the change of the exciton transfer time induced by the temperature difference with a proper tuning of the site energies of the aggregate. In this sense, there exists a site energy shift equivalence for any temperature difference in a broad range. This phenomenon is similar to the Seebeck effect as well as spin Seebeck effect and can be named as exciton Seebeck effect.

  13. Increasing applicability of slow light in molecular aggregate nanofilms with two-exciton dynamics. (United States)

    Díaz, E; Martínez-Calzada, G C; Cabrera-Granado, E; Calderón, O G


    We study the slow-light performance in the presence of exciton-exciton interaction in films of linear molecular aggregates at the nanometer scale. In particular, we consider a four-level model to describe the creation/annihilation of two-exciton states that are relevant for high-intensity fields. Numerical simulations show delays comparable to those obtained for longer propagation distances in other media. Two-exciton dynamics could lead to larger fractional delays, even in presence of disorder, in comparison to the two-level approximation. We conclude that slow-light performance is a robust phenomenon in these systems under the increasing complexity of the two-exciton dynamics.

  14. Ultrafast exciton dynamics at molecular surfaces (United States)

    Monahan, Nicholas R.

    Further improvements to device performance are necessary to make solar energy conversion a compelling alternative to fossil fuels. Singlet exciton fission and charge separation are two processes that can heavily influence the power conversion efficiency of a solar cell. During exciton fission one singlet excitation converts into two triplet excitons, potentially doubling the photocurrent generated by higher energy photons. There is significant discord over the singlet fission mechanism and of particular interest is whether the process involves a multiexciton intermediate state. I used time-resolved two-photon photoemission to investigate singlet fission in hexacene thin films, a model system with strong electronic coupling. My results indicate that a multiexciton state forms within 40 fs of photoexcitation and loses singlet character on a 280 fs timescale, creating two triplet excitons. This is concordant with the transient absorption spectra of hexacene single crystals and definitively proves that exciton fission in hexacene proceeds through a multiexciton state. This state is likely common to all strongly-coupled systems and my results suggest that a reassessment of the generally-accepted singlet fission mechanism is required. Charge separation is the process of splitting neutral excitons into carriers that occurs at donor-acceptor heterojunctions in organic solar cells. Although this process is essential for device functionality, there are few compelling explanations for why it is highly efficient in certain organic photovoltaic systems. To investigate the charge separation process, I used the model system of charge transfer excitons at hexacene surfaces and time-resolved two-photon photoemission. Charge transfer excitons with sufficient energy spontaneously delocalize, growing from about 14 nm to over 50 nm within 200 fs. Entropy drives this delocalization, as the density of states within the Coulomb potential increases significantly with energy. This charge

  15. Exciton band structure in bacterial peripheral light-harvesting complexes. (United States)

    Trinkunas, Gediminas; Zerlauskiene, Oksana; Urbonienė, Vidita; Chmeliov, Jevgenij; Gall, Andrew; Robert, Bruno; Valkunas, Leonas


    The variability of the exciton spectra of bacteriochlorophyll molecules in light-harvesting (LH) complexes of photosynthetic bacteria ensures the excitation energy funneling trend toward the reaction center. The decisive shift of the energies is achieved due to exciton spectra formation caused by the resonance interaction between the pigments. The possibility to resolve the upper Davydov sub-band corresponding to the B850 ring and, thus, to estimate the exciton bandwidth by analyzing the temperature dependence of the steady-state absorption spectra of the LH2 complexes is demonstrated. For this purpose a self-modeling curve resolution approach was applied for analysis of the temperature dependence of the absorption spectra of LH2 complexes from the photosynthetic bacteria Rhodobacter (Rba.) sphaeroides and Rhodoblastus (Rbl.) acidophilus. Estimations of the intradimer resonance interaction values as follows directly from obtained estimations of the exciton bandwidths at room temperature give 385 and 397 cm(-1) for the LH2 complexes from the photosynthetic bacteria Rba. sphaeroides and Rhl. acidophilus, respectively. At 4 K the corresponding couplings are slightly higher (391 and 435 cm(-1), respectively). The retained exciton bandwidth at physiological conditions supports the decisive role of the exciton coherence determining light absorption in bacterial light-harvesting antenna complexes.

  16. The nature of singlet excitons in oligoacene molecular crystals

    KAUST Repository

    Yamagata, H.


    A theory for polarized absorption in crystalline oligoacenes is presented, which includes Frenkel exciton coupling, the coupling between Frenkel and charge-transfer (CT) excitons, and the coupling of all neutral and ionic excited states to the dominant ring-breathing vibrational mode. For tetracene, spectra calculated using all Frenkel couplings among the five lowest energy molecular singlet states predict a Davydov splitting (DS) of the lowest energy (0-0) vibronic band of only -32cm-1, far smaller than the measured value of 631cm-1 and of the wrong sign-a negative sign indicating that the polarizations of the lower and upper Davydov components are reversed from experiment. Inclusion of Frenkel-CT coupling dramatically improves the agreement with experiment, yielding a 0-0 DS of 601cm-1 and a nearly quantitative reproduction of the relative spectral intensities of the 0-n vibronic components. Our analysis also shows that CT mixing increases with the size of the oligoacenes. We discuss the implications of these results on exciton dissociation and transport. © 2011 American Institute of Physics.

  17. Localized diabatization applied to excitons in molecular crystals (United States)

    Jin, Zuxin; Subotnik, Joseph E.


    Traditional ab initio electronic structure calculations of periodic systems yield delocalized eigenstates that should be understood as adiabatic states. For example, excitons are bands of extended states which superimpose localized excitations on every lattice site. However, in general, in order to study the effects of nuclear motion on exciton transport, it is standard to work with a localized description of excitons, especially in a hopping regime; even in a band regime, a localized description can be helpful. To extract localized excitons from a band requires essentially a diabatization procedure. In this paper, three distinct methods are proposed for such localized diabatization: (i) a simple projection method, (ii) a more general Pipek-Mezey localization scheme, and (iii) a variant of Boys diabatization. Approaches (i) and (ii) require localized, single-particle Wannier orbitals, while approach (iii) has no such dependence. These methods should be very useful for studying energy transfer through solids with ab initio calculations.

  18. Energy scaling for multi-exciton complexes in semiconductor quantum dots (United States)

    Ipatov, Andrey; Gerchikov, Leonid; Christiano, Jordan


    The ground state properties of an multi-exciton (ME) complex localized in a nanoscale semiconductor quantum dot (QD) have been studied. The calculations have been performed using the envelope function approximation for electron and hole motion in the QD. The many-body quantum mechanical treatment of the electron-hole dynamics was done within the Density Functional Theory approach. The ground state energy dependencies upon QD radius, number of electron-hole pairs, QD dielectric function and effective masses of electron and holes have been analyzed. It is demonstrated that when multi-exciton complex is strongly localized within the QD, the physical properties of the system are determined by a single parameter, the ratio of QD and free exciton radii, and its binding energy is given by the function of this parameter multiplied by the binding energy of an isolated exciton in bulk semiconductor.

  19. Wannier-Mott Excitons in Nanoscale Molecular Ices (United States)

    Chen, Y.-J.; Muñoz Caro, G. M.; Aparicio, S.; Jiménez-Escobar, A.; Lasne, J.; Rosu-Finsen, A.; McCoustra, M. R. S.; Cassidy, A. M.; Field, D.


    The absorption of light to create Wannier-Mott excitons is a fundamental feature dictating the optical and photovoltaic properties of low band gap, high permittivity semiconductors. Such excitons, with an electron-hole separation an order of magnitude greater than lattice dimensions, are largely limited to these semiconductors but here we find evidence of Wannier-Mott exciton formation in solid carbon monoxide (CO) with a band gap of >8 eV and a low electrical permittivity. This is established through the observation that a change of a few degrees K in deposition temperature can shift the electronic absorption spectra of solid CO by several hundred wave numbers, coupled with the recent discovery that deposition of CO leads to the spontaneous formation of electric fields within the film. These so-called spontelectric fields, here approaching 4 ×107 V m-1 , are strongly temperature dependent. We find that a simple electrostatic model reproduces the observed temperature dependent spectral shifts based on the Stark effect on a hole and electron residing several nm apart, identifying the presence of Wannier-Mott excitons. The spontelectric effect in CO simultaneously explains the long-standing enigma of the sensitivity of vacuum ultraviolet spectra to the deposition temperature.

  20. Strong exciton-photon coupling in organic single crystal microcavity with high molecular orientation

    Energy Technology Data Exchange (ETDEWEB)

    Goto, Kaname [Department of Electronics, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan); Yamashita, Kenichi, E-mail: [Faculty of Electrical Engineering and Electronics, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan); Yanagi, Hisao [Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192 (Japan); Yamao, Takeshi; Hotta, Shu [Faculty of Materials Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan)


    Strong exciton-photon coupling has been observed in a highly oriented organic single crystal microcavity. This microcavity consists of a thiophene/phenylene co-oligomer (TPCO) single crystal laminated on a high-reflection distributed Bragg reflector. In the TPCO crystal, molecular transition dipole was strongly polarized along a certain horizontal directions with respect to the main crystal plane. This dipole polarization causes significantly large anisotropies in the exciton transition and optical constants. Especially the anisotropic exciton transition was found to provide the strong enhancement in the coupling with the cavity mode, which was demonstrated by a Rabi splitting energy as large as ∼100 meV even in the “half-vertical cavity surface emitting lasing” microcavity structure.

  1. Molecular-weight dependence of interchain polaron delocalization and exciton bandwidth in high-mobility conjugated polymers

    DEFF Research Database (Denmark)

    Chang, J.F.; Clark, J.; Zhao, N.


    here a detailed study of interchain interaction effects on both charged polarons as well as neutral excitons in highly crystalline, high-mobility poly-3-hexylthiophene (P3HT) as a function of molecular weight. We find experimental evidence for reduced exciton bandwidth and increased polaron...

  2. Real-time observation of ultrafast Rabi oscillations between excitons and plasmons in metal/molecular aggregate hybrid nanostructures

    Directory of Open Access Journals (Sweden)

    Cerullo G.


    Full Text Available We demonstrate ultrafast coherent manipulation of the normal mode splitting in metal/molecular-aggregate nanostructures by real-time observation of Rabi oscillations between excitons and surface-plasmon-polaritons. Oscillations in exciton density on a 10-fs timescale control the Rabi splitting.

  3. Exciton-phonon dynamics on complex networks: Comparison between a perturbative approach and exact calculations (United States)

    Yalouz, Saad; Pouthier, Vincent; Falvo, Cyril


    A method combining perturbation theory with a simplifying ansatz is used to describe the exciton-phonon dynamics in complex networks. This method, called PT*, is compared to exact calculations based on the numerical diagonalization of the exciton-phonon Hamiltonian for eight small-sized networks. It is shown that the accuracy of PT* depends on the nature of the network, and three different situations were identified. For most graphs, PT* yields a very accurate description of the dynamics. By contrast, for the Wheel graph and the Apollonian network, PT* reproduces the dynamics only when the exciton occupies a specific initial state. Finally, for the complete graph, PT* breaks down. These different behaviors originate in the interplay between the degenerate nature of the excitonic energy spectrum and the strength of the exciton-phonon interaction so that a criterion is established to determine whether or not PT* is relevant. When it succeeds, our study shows the undeniable advantage of PT* in that it allows us to perform very fast simulations when compared to exact calculations that are restricted to small-sized networks.

  4. Multiband theory of multi-exciton complexes in self-assembled quantum dots (United States)

    Sheng, Weidong; Cheng, Shun-Jen; Hawrylak, Pawel


    We report on a multiband microscopic theory of many-exciton complexes in self-assembled quantum dots. The single particle states are obtained by three methods: single-band effective-mass approximation, the multiband k•p method, and the tight-binding method. The electronic structure calculations are coupled with strain calculations via Bir-Pikus Hamiltonian. The many-body wave functions of N electrons and N valence holes are expanded in the basis of Slater determinants. The Coulomb matrix elements are evaluated using statically screened interaction for the three different sets of single particle states and the correlated N -exciton states are obtained by the configuration interaction method. The theory is applied to the excitonic recombination spectrum in InAs/GaAs self-assembled quantum dots. The results of the single-band effective-mass approximation are successfully compared with those obtained by using the of k•p and tight-binding methods.

  5. Ab initio nonadiabatic dynamics of multichromophore complexes: a scalable graphical-processing-unit-accelerated exciton framework. (United States)

    Sisto, Aaron; Glowacki, David R; Martinez, Todd J


    ("fragmenting") a molecular system and then stitching it back together. In this Account, we address both of these problems, the first by using graphical processing units (GPUs) and electronic structure algorithms tuned for these architectures and the second by using an exciton model as a framework in which to stitch together the solutions of the smaller problems. The multitiered parallel framework outlined here is aimed at nonadiabatic dynamics simulations on large supramolecular multichromophoric complexes in full atomistic detail. In this framework, the lowest tier of parallelism involves GPU-accelerated electronic structure theory calculations, for which we summarize recent progress in parallelizing the computation and use of electron repulsion integrals (ERIs), which are the major computational bottleneck in both density functional theory (DFT) and time-dependent density functional theory (TDDFT). The topmost tier of parallelism relies on a distributed memory framework, in which we build an exciton model that couples chromophoric units. Combining these multiple levels of parallelism allows access to ground and excited state dynamics for large multichromophoric assemblies. The parallel excitonic framework is in good agreement with much more computationally demanding TDDFT calculations of the full assembly.

  6. Multiple exciton generation in quantum dots versus singlet fission in molecular chromophores for solar photon conversion. (United States)

    Beard, Matthew C; Johnson, Justin C; Luther, Joseph M; Nozik, Arthur J


    Both multiple exciton generation (MEG) in semiconductor nanocrystals and singlet fission (SF) in molecular chromophores have the potential to greatly increase the power conversion efficiency of solar cells for the production of solar electricity (photovoltaics) and solar fuels (artificial photosynthesis) when used in solar photoconverters. MEG creates two or more excitons per absorbed photon, and SF produces two triplet states from a single singlet state. In both cases, multiple charge carriers from a single absorbed photon can be extracted from the cell and used to create higher power conversion efficiencies for a photovoltaic cell or a cell that produces solar fuels, like hydrogen from water splitting or reduced carbon fuels from carbon dioxide and water (analogous to biological photosynthesis). The similarities and differences in the mechanisms and photoconversion cell architectures between MEG and SF are discussed. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  7. Modelling excitonic-energy transfer in light-harvesting complexes


    Kramer, Tobias; Kreisbeck, Christoph


    The theoretical and experimental study of energy transfer in photosynthesis has revealed an interesting transport regime, which lies at the borderline between classical transport dynamics and quantum-mechanical interference effects. Dissipation is caused by the coupling of electronic degrees of freedom to vibrational modes and leads to a directional energy transfer from the antenna complex to the target reaction-center. The dissipative driving is robust and does not rely on fine-tuning of spe...

  8. Modelling excitonic-energy transfer in light-harvesting complexes

    CERN Document Server

    Kramer, Tobias


    The theoretical and experimental study of energy transfer in photosynthesis has revealed an interesting transport regime, which lies at the borderline between classical transport dynamics and quantum-mechanical interference effects. Dissipation is caused by the coupling of electronic degrees of freedom to vibrational modes and leads to a directional energy transfer from the antenna complex to the target reaction-center. The dissipative driving is robust and does not rely on fine-tuning of specific vibrational modes. For the parameter regime encountered in the biological systems new theoretical tools are required to directly compare theoretical results with experimental spectroscopy data. The calculations require to utilize massively parallel graphics processor units (GPUs) for efficient and exact computations.

  9. Molecular structure and exciton dynamics in organic conjugated polymers (United States)

    Thomas, Alan K.

    , quenchable, isolated singlet excitations. The structure of J aggregates which leads to isolated excitations, and the role which inter-chain contact sites play in triplet formation from these singlet excitations is revealed. New structure-function relationships were uncovered in poly (3-alkyl-thienylenevinylene) (P3ATV) derivatives using resonance Raman and photocurrent spectroscopies. Time-dependent spectroscopic theory was used to interpret experimental Raman and absorption spectra that revealed the presence of structural polymorphs. These polymorphs provide an explanation of the spectroscopic evidence without presumption of a deactivating dark state in this unusually non-fluorescence material. Photovoltaic devices constructed from blends of poly (2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT) and PCBM blends were examined using Raman and photocurrent imaging techniques. These techniques were used to identify different packing states in blended thin films and correlate photocurrent production with local order. Intensity modulated spectroscopic techniques (IMPS) were then used to locate regions of non-geminate charge recombination at interfaces between amorphous and crystalline regions in working devices. Next, P3HT/PCBM OPV devices were exposed to ionizing radiation in a vacuum chamber. These devices were characterized before and after exposure, using standardized solar cell tests, Raman imaging, wide-field IMPS, and IMVS spectroscopies. An analysis of the spectroscopic data determined that the donor polymer is highly resistant to radiation damage, and that the degradation of device performance is due to an effect (cross-linking or degradation) within aggregates of the acceptor. This dissertation concludes with an interpretation of the significance of the findings contained herein to organic electronics, followed by a brief outlook for future work in these fields. Potential theories to describe and predict molecular interactions for organic polymers in

  10. Machine learning exciton dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Häse, Florian [Harvard Univ., Cambridge, MA (United States); Technische Univ. Munchen, Garching (Germany). Dept. Physik; Valleau, Stéphanie [Harvard Univ., Cambridge, MA (United States); Pyzer-Knapp, Edward [Harvard Univ., Cambridge, MA (United States); Aspuru-Guzik, Alán [Harvard Univ., Cambridge, MA (United States)


    Obtaining the exciton dynamics of large photosynthetic complexes by using mixed quantum mechanics/molecular mechanics (QM/MM) is computationally demanding. We propose a machine learning technique, multi-layer perceptrons, as a tool to reduce the time required to compute excited state energies. With this approach we predict time-dependent density functional theory (TDDFT) excited state energies of bacteriochlorophylls in the Fenna–Matthews–Olson (FMO) complex. Additionally we compute spectral densities and exciton populations from the predictions. Different methods to determine multi-layer perceptron training sets are introduced, leading to several initial data selections. In addition, we compute spectral densities and exciton populations. Once multi-layer perceptrons are trained, predicting excited state energies was found to be significantly faster than the corresponding QM/MM calculations. We showed that multi-layer perceptrons can successfully reproduce the energies of QM/MM calculations to a high degree of accuracy with prediction errors contained within 0.01 eV (0.5%). Spectral densities and exciton dynamics are also in agreement with the TDDFT results. The acceleration and accurate prediction of dynamics strongly encourage the combination of machine learning techniques with ab initio methods.

  11. Molecular dynamics simulations of a silver atom in water: evidence for a dipolar excitonic state. (United States)

    Spezia, Riccardo; Nicolas, Cédric; Boutin, Anne; Vuilleumier, Rodolphe


    The properties of a silver atom in bulk water were studied for the first time by molecular dynamics simulations using two complementary mixed quantum-classical approaches. The first one consists of treating by quantum mechanics one electron only, which interacts with a classical silver cation and solvent through one-electron pseudopotentials. The second one is Car-Parrinello molecular dynamics that treats all the valence electrons quantum-mechanically. Very good agreement is obtained between these two methods, and the calculated absorption spectrum of the solvated silver atom agrees very well with experimental data. Both simulations reveal that the silver atom is in the critical region for the appearance of a dipolar excitonic state and exhibits a dipole moment of approximately 2 D with large fluctuations of +/-1 D. The structure of the solvation shell is also analyzed.

  12. Quantum simulator of an open quantum system using superconducting qubits: exciton transport in photosynthetic complexes (United States)

    Mostame, Sarah; Rebentrost, Patrick; Eisfeld, Alexander; Kerman, Andrew J.; Tsomokos, Dimitris I.; Aspuru-Guzik, Alán


    Open quantum system approaches are widely used in the description of physical, chemical and biological systems. A famous example is electronic excitation transfer in the initial stage of photosynthesis, where harvested energy is transferred with remarkably high efficiency to a reaction center. This transport is affected by the motion of a structured vibrational environment, which makes simulations on a classical computer very demanding. Here we propose an analog quantum simulator of complex open system dynamics with a precisely engineered quantum environment. Our setup is based on superconducting circuits, a well established technology. As an example, we demonstrate that it is feasible to simulate exciton transport in the Fenna-Matthews-Olson photosynthetic complex. Our approach allows for a controllable single-molecule simulation and the investigation of energy transfer pathways as well as non-Markovian noise-correlation effects.

  13. Impacts of Coulomb Interactions on the Magnetic Responses of Excitonic Complexes in Single Semiconductor Nanostructures

    Directory of Open Access Journals (Sweden)

    Fu Ying-Jhe


    Full Text Available Abstract We report on the diamagnetic responses of different exciton complexes in single InAs/GaAs self-assembled quantum dots (QDs and quantum rings (QRs. For QDs, the imbalanced magnetic responses of inter-particle Coulomb interactions play a crucial role in the diamagnetic shifts of excitons (X, biexcitons (XX, and positive trions (X−. For negative trions (X− in QDs, anomalous magnetic responses are observed, which cannot be described by the conventional quadratic energy shift with the magnetic field. The anomalous behavior is attributed to the apparent change in the electron wave function extent after photon emission due to the strong Coulomb attraction by the hole in its initial state. In QRs, the diamagnetic responses of X and XX also show different behaviors. Unlike QDs, the diamagnetic shift of XX in QRs is considerably larger than that of X. The inherent structural asymmetry combined with the inter-particle Coulomb interactions makes the wave function distribution of XX very different from that of X in QRs. Our results suggest that the phase coherence of XX in QRs may survive from the wave function localization due to the structural asymmetry or imperfections.

  14. A New Efficient Method for Calculation of Frenkel Exciton Parameters in Molecular Aggregates

    CERN Document Server

    Plötz, Per-Arno; Kühn, Oliver


    The Frenkel exciton Hamiltonian is at the heart of many simulations of excitation energy transfer in molecular aggregates. It separates the aggregate into Coulomb-coupled monomers. Here it is shown that the respective parameters, i.e. monomeric excitation energies and Coulomb couplings between transition densities, can be efficiently calculated using time-dependent tight-binding-based density functional theory (TD-DFTB). Specifically, Coulomb couplings are expressed in terms of self-consistently determined Mulliken transition charges. The determination of the sign of the coupling requires an additional super-molecule calculation. The approach is applied to two dimer systems. First, formaldehyde oxime for which a detailed comparison with standard DFT using the B3LYP and the PBE functionals is provided. Second, the Coulomb coupling is explored in dependence on the intermolecular coordinates for a perylene bisimide dimer. This provides structural evidence for the previously observed biphasic aggregation behavior...

  15. Room-Temperature Micron-Scale Exciton Migration in a Stabilized Emissive Molecular Aggregate. (United States)

    Caram, Justin R; Doria, Sandra; Eisele, Dörthe M; Freyria, Francesca S; Sinclair, Timothy S; Rebentrost, Patrick; Lloyd, Seth; Bawendi, Moungi G


    We report 1.6 ± 1 μm exciton transport in self-assembled supramolecular light-harvesting nanotubes (LHNs) assembled from amphiphillic cyanine dyes. We stabilize LHNs in a sucrose glass matrix, greatly reducing light and oxidative damage and allowing the observation of exciton-exciton annihilation signatures under weak excitation flux. Fitting to a one-dimensional diffusion model, we find an average exciton diffusion constant of 55 ± 20 cm2/s, among the highest measured for an organic system. We develop a simple model that uses cryogenic measurements of static and dynamic energetic disorder to estimate a diffusion constant of 32 cm2/s, in agreement with experiment. We ascribe large exciton diffusion lengths to low static and dynamic energetic disorder in LHNs. We argue that matrix-stabilized LHNS represent an excellent model system to study coherent excitonic transport.

  16. Exciton modeling of energy-transfer dynamics in the LHCII complex of higher plants: A redfield theory approach

    NARCIS (Netherlands)

    Novoderezhkin, V.; Salverda, J.M.; van Amerongen, H.; van Grondelle, R.


    We propose an exciton model for the peripheral plant light-harvesting complex LHCII that allows us to explain the absorption (OD) and linear dichroism (LD) spectra, the superradiance (SR), the pump-probe transient absorption (TA), the three-pulse photon echo peak shift (3PEPS), and transient grating

  17. Exciton modeling of energy-transfer dynamics in the LHCII complex of higher plants: a Redfield theory approach

    NARCIS (Netherlands)

    Novoderezhkin, V.; Salverda, J.M.; Amerongen, van H.; Grondelle, van R.


    We propose an exciton model for the peripheral plant light-harvesting complex LHCII that allows us to explain the absorption (OD) and linear dichroism (LD) spectra, the superradiance (SR), the pump-probe transient absorption (TA), the three-pulse photon echo peak shift (3PEPS), and transient grating

  18. Quantum simulator of an open quantum system using superconducting qubits: exciton transport in photosynthetic complexes (United States)

    Mostame, Sarah; Rebentrost, Patrick; Eisfeld, Alexander; Kerman, Andrew J.; Tsomokos, Dimitris I.; Aspuru-Guzik, Alan


    In the initial stage of photosynthesis, light-harvested energy is transferred with remarkably high efficiency to a reaction center, with the vibrational environment assisting the transport mechanism. It is of great interest to mimic this process with present-day technologies. Here we propose an analog quantum simulator of open system dynamics, where noise engineering of the environment has a central role. In particular, we propose the use of superconducting qubits for the simulation of exciton transport in the Fenna-Matthew-Olson protein, a prototypical photosynthetic complex. Our method allows for a single-molecule implementation and the investigation of energy transfer pathways as well as non-Markovian and spatiotemporal noise-correlation effects.

  19. Manifestations of Vibronic Coupling Effects in Molecular Spectroscopy: from the Quenching of Excitonic Energy Splittings to the Clements Bands of SO2 (United States)

    Koppel, Horst


    We investigate the excitation of vibrational modes and its impact on the excitonic energy splittings in doubly hydrogen-bonded molecular dimers. The experimental analysis, performed in collaboration by S. Leutwyler and coworkers (Univ. Bern), is based on high-resolution resonant two-photon ionization spectroscopy. The potential energy surfaces underlying the theoretical investigation are obtained at the RICC2/aug-cc-pVTZ level and are used for the dynamical analysis in the framework of a well-established vibronic coupling approach. The vertical electronic Davydov splitting of the S_1 and S_2 excited states exceeds the observed excitonic splitting by a factor of 10--40. This discrepancy can be understood by considering the quenching of the excitonic splitting by the excitation of vibrational modes in the electronic transition. Two different approaches have been employed and found to reconcile theory and experiment. The analysis of the vibronic structure of the S_2 ← S_0 excitation spectrum focusses on the ortho-cyanophenol dimer as a representative example. Most of the observed spectral features can be reproduced by the calculations, although some deviations remain. In the second part, new results on the UV absorption spectrum of SO_2 will be presented. This is complementary to the excitonic systems in that higher vibrational energies are involved and a conical intersection is accessible to the nuclear motion. Using the concept of regularized diabatic states in combination with high-accuracy MRCI potential energy surfaces, semi-quantitative agreement with the complex experimental (low-resolution) spectrum has been achieved for the first time. P. Ottiger, S. Leutwyler and H. Köppel, J. Chem. Phys. 136, 174308 (2012). S. Kopec, P. Ottiger, S. Leutwyler and H. Köppel, J. Chem. Phys. 137, 184312 (2012). H. Köppel and B. Schubert, Mol. Phys. 104, 1069 (2006). C. Leveque, A. Komainda, R. Taieb and H. Köppel, J. Chem. Phys. 138, 044320 (2013).

  20. Optical spectroscopy and system–bath interactions in molecular aggregates with full configuration interaction Frenkel exciton model

    Energy Technology Data Exchange (ETDEWEB)

    Seibt, Joachim; Sláma, Vladislav; Mančal, Tomáš, E-mail:


    Highlights: • Standard Frenkel exciton model is extended to include inter-band coupling. • It is formally linked with configuration interaction method of quantum chemistry. • Spectral shifts due to inter-band coupling are found in molecular aggregates. • Effects of peak amplitude redistribution in two-dimensional spectra are found. - Abstract: Standard application of the Frenkel exciton model neglects resonance coupling between collective molecular aggregate states with different number of excitations. These inter-band coupling terms are, however, of the same magnitude as the intra-band coupling between singly excited states. We systematically derive the Frenkel exciton model from quantum chemical considerations, and identify it as a variant of the configuration interaction method. We discuss all non-negligible couplings between collective aggregate states, and provide compact formulae for their calculation. We calculate absorption spectra of molecular aggregate of carotenoids and identify significant band shifts as a result of inter-band coupling. The presence of inter-band coupling terms requires renormalization of the system–bath coupling with respect to standard formulation, but renormalization effects are found to be weak. We present detailed discussion of molecular dimer and calculate its time-resolved two-dimensional Fourier transformed spectra to find weak but noticeable effects of peak amplitude redistribution due to inter-band coupling.

  1. Theoretical study of excitonic complexes in semiconductors quantum wells; Estudo teorico de complexos excitonicos em pocos quanticos de semicondutores

    Energy Technology Data Exchange (ETDEWEB)

    Dacal, Luis Carlos Ogando


    A physical system where indistinguishable particles interact with each other creates the possibility of studying correlation and exchange effect. The simplest system is that one with only two indistinguishable particles. In condensed matter physics, these complexes are represented by charged excitons, donors and acceptors. In quantum wells, the valence band is not parabolic, therefore, the negatively charged excitons and donors are theoretically described in a simpler way. Despite the fact that the stability of charged excitons (trions) is known since the late 50s, the first experimental observation occurred only at the early 90s in quantum well samples, where their binding energies are one order of magnitude larger due to the one dimensional carriers confinement. After this, these complexes became the subject of an intense research because the intrinsic screening of electrical interactions in semiconductor materials allows that magnetic fields that are usual in laboratories have strong effects on the trion binding energy. Another rich possibility is the study of trions as an intermediate state between the neutral exciton and the Fermi edge singularity when the excess of doping carriers is increased. In this thesis, we present a theoretical study of charged excitons and negatively charged donors in GaAs/Al{sub 0.3}Ga{sub 0.7}As quantum wells considering the effects of external electric and magnetic fields. We use a simple, accurate and physically clear method to describe these systems in contrast with the few and complex treatments s available in the literature. Our results show that the QW interface defects have an important role in the trion dynamics. This is in agreement with some experimental works, but it disagrees with other ones. (author)

  2. Exciton transport in the PE545 complex: insight from atomistic QM/MM-based quantum master equations and elastic network models (United States)

    Pouyandeh, Sima; Iubini, Stefano; Jurinovich, Sandro; Omar, Yasser; Mennucci, Benedetta; Piazza, Francesco


    In this paper, we work out a parameterization of environmental noise within the Haken–Strobl–Reinenker (HSR) model for the PE545 light-harvesting complex, based on atomic-level quantum mechanics/molecular mechanics (QM/MM) simulations. We use this approach to investigate the role of various auto- and cross-correlations in the HSR noise tensor, confirming that site-energy autocorrelations (pure dephasing) terms dominate the noise-induced exciton mobility enhancement, followed by site energy-coupling cross-correlations for specific triplets of pigments. Interestingly, several cross-correlations of the latter kind, together with coupling–coupling cross-correlations, display clear low-frequency signatures in their spectral densities in the 30–70 cm-1 region. These slow components lie at the limits of validity of the HSR approach, which requires that environmental fluctuations be faster than typical exciton transfer time scales. We show that a simple coarse-grained elastic-network-model (ENM) analysis of the PE545 protein naturally spotlights collective normal modes in this frequency range that represent specific concerted motions of the subnetwork of cysteines covalenty linked to the pigments. This analysis strongly suggests that protein scaffolds in light-harvesting complexes are able to express specific collective, low-frequency normal modes providing a fold-rooted blueprint of exciton transport pathways. We speculate that ENM-based mixed quantum classical methods, such as Ehrenfest dynamics, might be promising tools to disentangle the fundamental designing principles of these dynamical processes in natural and artificial light-harvesting structures.

  3. Excitonic complexes in natural InAs/GaAs quantum dots (United States)

    Zieliński, M.; Gołasa, K.; Molas, M. R.; Goryca, M.; Kazimierczuk, T.; Smoleński, T.; Golnik, A.; Kossacki, P.; Nicolet, A. A. L.; Potemski, M.; Wasilewski, Z. R.; Babiński, A.


    The quantum confinement in a typical quantum dot (QD) is determined primarily by the nanosystem's dimensions and average composition. We demonstrate, however, that excitonic properties of natural QDs formed in the InAs/GaAs wetting layer are governed predominantly by effects of random fluctuations of the lattice composition. It is shown that the biexciton binding energy is a very sensitive function of the lattice randomness with a nearly flat dependence on the exciton energy. The large variation in different random realizations of a QD structure is shown to lead in some cases to the reversal of the order of excitonic lines. Results of theoretical calculations correspond to statistical properties of neutral excitons and biexcitons as well as trions confined to single natural QDs studied in our microspectroscopic measurements. We observe substantial variation of the biexciton and trion binding energies as well as a correlation of the trion and the biexciton energies. The transition from the negative to the positive binding energy of the trion is also observed, which strongly supports the attribution of the observed trion to the positively charged exciton.

  4. Accelerating FRET between Near-Infrared Emitting Quantum Dots Using a Molecular J-Aggregate as an Exciton Bridge. (United States)

    Wang, Chen; Weiss, Emily A


    Fast energy transfer (EnT) among quantum dots (QDs) with near-infrared (NIR) emission is essential for fully exploiting their light harvesting and photon downconversion (multiexciton generation) abilities. This paper demonstrates a relayed EnT mechanism that accelerates the migration of NIR excitons between PbS QDs by a factor of 20 from that of one-step EnT through a polyelectrolyte and even a factor of ∼2 from that of one-step EnT between QDs in direct contact, by employing a J-aggregate (J-agg) of a cyanine dye as an exciton bridge. The donor QDs, acceptor QDs, and J-agg are electrostatically assembled into a sandwich structure with layer-by-layer deposition. Estimates of EnT rate and yield from transient and steady-state absorption and photoluminescence spectroscopies show that the rate-limiting step in the relay is EnT from the donor QD to the J-agg, while EnT from the J-agg to the acceptor QD occurs in J-agg with more intermolecular order. This work demonstrates the viability of relayed EnT through a molecular bridge as a strategy for accelerating long-distance exciton migration in assemblies of QDs, in particular in the near-infrared.

  5. Microsolvation in molecular complexes

    Energy Technology Data Exchange (ETDEWEB)

    Pasquini, M; Schiccheri, N; Piani, G; Pietraperzia, G; Becucci, M; Castellucci, E [European Laboratory for Non-Linear Spectroscopy (LENS), Polo Scientifico e Tecnologico Universita di Firenze, Via Nello Carrara 1, 50019 Sesto Fiorentino (Italy)], E-mail:


    In this paper, we report the results of our study of the microsolvation process involving the anisole molecule. We are able to study bimolecular complexes of different compositions. Changing the second partner molecule bound to anisole, we observed complexes of different geometries, because of the large variety of interactions possible for the anisole. High-resolution electronic spectroscopy is the best tool to reveal the correct vibrationally (zero-point) averaged geometry of the complex. That is done by analysing the rovibronic structure of the electronic spectra, which are related to the equilibrium geometry of the complex as well as dynamical processes, both in the ground and in the excited state. The interpretation of the experimental results is supported by high-level quantum calculations.

  6. Scaling Relations and Optimization of Excitonic Energy Transfer Rates between One-Dimensional Molecular Aggregates

    NARCIS (Netherlands)

    Chuang, Chern; Knoester, Jasper; Cao, Jianshu


    We theoretically study the distance, chain length, and temperature dependence of the electronic couplings as well as the excitonic energy transfer rates between one-dimensional (1D) chromophore aggregates. In addition to the well-known geometry dependent factor that leads to the deviation from

  7. Communication: Broad manifold of excitonic states in light-harvesting complex 1 promotes efficient unidirectional energy transfer in vivo (United States)

    Sohail, Sara H.; Dahlberg, Peter D.; Allodi, Marco A.; Massey, Sara C.; Ting, Po-Chieh; Martin, Elizabeth C.; Hunter, C. Neil; Engel, Gregory S.


    In photosynthetic organisms, the pigment-protein complexes that comprise the light-harvesting antenna exhibit complex electronic structures and ultrafast dynamics due to the coupling among the chromophores. Here, we present absorptive two-dimensional (2D) electronic spectra from living cultures of the purple bacterium, Rhodobacter sphaeroides, acquired using gradient assisted photon echo spectroscopy. Diagonal slices through the 2D lineshape of the LH1 stimulated emission/ground state bleach feature reveal a resolvable higher energy population within the B875 manifold. The waiting time evolution of diagonal, horizontal, and vertical slices through the 2D lineshape shows a sub-100 fs intra-complex relaxation as this higher energy population red shifts. The absorption (855 nm) of this higher lying sub-population of B875 before it has red shifted optimizes spectral overlap between the LH1 B875 band and the B850 band of LH2. Access to an energetically broad distribution of excitonic states within B875 offers a mechanism for efficient energy transfer from LH2 to LH1 during photosynthesis while limiting back transfer. Two-dimensional lineshapes reveal a rapid decay in the ground-state bleach/stimulated emission of B875. This signal, identified as a decrease in the dipole strength of a strong transition in LH1 on the red side of the B875 band, is assigned to the rapid localization of an initially delocalized exciton state, a dephasing process that frustrates back transfer from LH1 to LH2.

  8. Coherent wavepackets in the Fenna-Matthews-Olson complex are robust to excitonic-structure perturbations caused by mutagenesis (United States)

    Maiuri, Margherita; Ostroumov, Evgeny E.; Saer, Rafael G.; Blankenship, Robert E.; Scholes, Gregory D.


    Femtosecond pulsed excitation of light-harvesting complexes creates oscillatory features in their response. This phenomenon has inspired a large body of work aimed at uncovering the origin of the coherent beatings and possible implications for function. Here we exploit site-directed mutagenesis to change the excitonic level structure in Fenna-Matthews-Olson (FMO) complexes and compare the coherences using broadband pump-probe spectroscopy. Our experiments detect two oscillation frequencies with dephasing on a picosecond timescale—both at 77 K and at room temperature. By studying these coherences with selective excitation pump-probe experiments, where pump excitation is in resonance only with the lowest excitonic state, we show that the key contributions to these oscillations stem from ground-state vibrational wavepackets. These experiments explicitly show that the coherences—although in the ground electronic state—can be probed at the absorption resonances of other bacteriochlorophyll molecules because of delocalization of the electronic excitation over several chromophores.

  9. Coherent wavepackets in the Fenna-Matthews-Olson complex are robust to excitonic-structure perturbations caused by mutagenesis. (United States)

    Maiuri, Margherita; Ostroumov, Evgeny E; Saer, Rafael G; Blankenship, Robert E; Scholes, Gregory D


    Femtosecond pulsed excitation of light-harvesting complexes creates oscillatory features in their response. This phenomenon has inspired a large body of work aimed at uncovering the origin of the coherent beatings and possible implications for function. Here we exploit site-directed mutagenesis to change the excitonic level structure in Fenna-Matthews-Olson (FMO) complexes and compare the coherences using broadband pump-probe spectroscopy. Our experiments detect two oscillation frequencies with dephasing on a picosecond timescale-both at 77 K and at room temperature. By studying these coherences with selective excitation pump-probe experiments, where pump excitation is in resonance only with the lowest excitonic state, we show that the key contributions to these oscillations stem from ground-state vibrational wavepackets. These experiments explicitly show that the coherences-although in the ground electronic state-can be probed at the absorption resonances of other bacteriochlorophyll molecules because of delocalization of the electronic excitation over several chromophores.

  10. Visualization of Excitonic Structure in the Fenna-Matthews-OlsonPhotosynthetic Complex by Polarization-Dependent Two-DimensionalElectronic Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Department of Chemistry, The University of Chicago; Department of Biology, Department of Chemistry, Washington University; Fleming, Graham; Read, Elizabeth L.; Schlau-Cohen, Gabriela S.; Engel, Gregory S.; Wen, Jianzhong; Blankenship, Robert E.; Fleming, Graham R.


    Photosynthetic light-harvesting proceeds by the collection and highly efficient transfer of energy through a network of pigment-protein complexes. Inter-chromophore electronic couplings and interactions between pigments and the surrounding protein determine energy levels of excitonic states and dictate the mechanism of energy flow. The excitonic structure (orientation of excitonic transition dipoles) of pigment-protein complexes is generally deduced indirectly from x-ray crystallography in combination with predictions of transition energies and couplings in the chromophore site basis. Here, we demonstrate that coarse-grained excitonic structural information in the form of projection angles between transition dipole moments can be obtained from polarization-dependent two-dimensional electronic spectroscopy of an isotropic sample, particularly when the nonrephasing or free polarization decay signal rather than the photon echo signal is considered. The method provides an experimental link between atomic and electronic structure and accesses dynamical information with femtosecond time resolution. In an investigation of the Fenna-Matthews-Olson complex from green sulfur bacteria, energy transfer connecting two particular exciton states in the protein is isolated as being the primary contributor to a cross peak in the nonrephasing 2D spectrum at 400 fs under a specific sequence of polarized excitation pulses. The results suggest the possibility of designing experiments using combinations of tailored polarization sequencesto separate and monitor individual relaxation pathways.

  11. Scalable high-performance algorithm for the simulation of exciton-dynamics. Application to the light harvesting complex II in the presence of resonant vibrational modes

    DEFF Research Database (Denmark)

    Kreisbeck, Christoph; Kramer, Tobias; Aspuru-Guzik, Alán


    the exciton dynamics within a density-matrix formalism are known, but are restricted to small systems with less than ten sites due to their computational complexity. To study the excitonic energy transfer in larger systems, we adapt and extend the exact hierarchical equation of motion (HEOM) method to various...... high-performance many-core platforms using the Open Compute Language (OpenCL). For the light-harvesting complex II (LHC II) found in spinach, the HEOM results deviate from predictions of approximate theories and clarify the time-scale of the transfer-process. We investigate the impact of resonantly...

  12. Dynamic Tuning of Plasmon-Exciton Coupling in Arrays of Nanodisk-J-aggregate Complexes

    KAUST Repository

    Zheng, Yue Bing


    Figure Presented Dynamic tuning of plasmon-exclton resonant coupling in arrays of nanodisk-J-aggregate complexes is demonstrated. The angle-resolved spectra of an array of bare gold nanodisks exhibit continuous shifting of localized surface plasmon resonance. This characteristic enables the production of real-time, controllable spectral overlap between molecular resonance and plasmóme resonance. The resonant interaction strength as a function of spectral overlap is explored and the coupling strength changes with the incident angle of a probe light, in accord with simulations based on coupled dipóle approximation method. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Molecular Rheology of Complex Fluids

    DEFF Research Database (Denmark)

    Huang, Qian; Rasmussen, Henrik Koblitz

    fluids as a function of molecular chemistry has attracted a long history of collaboration between industry and academia. In industrial polymer processes, there is usually a combination of both shear and extensional flows. In some processing operations such as blow molding and fiber spinning, extensional......–state viscosity between melts and solutions is still an open question. Branched polymer melts have more complex molecular structures. A stress maximum during the start–up of uniaxial extensional flow was reported in 1979 for a low–density polyethylene (LDPE) melt. Subsequently observations of a steady stress...

  14. Effects of inter-molecular charge-transfer excitons on the external quantum efficiency of zinc-porphyrin/C{sub 60} heterojunction photovoltaic cells

    Energy Technology Data Exchange (ETDEWEB)

    Ryuzaki, Sou; Kai, Toshihiro; Onoe, Jun [Department of Nuclear Engineering, Tokyo Institute of Technology, Tokyo 152-8550 (Japan); Toda, Yasunori; Adachi, Satoru, E-mail: [Department of Applied Physics, Hokkaido University, Sapporo, Hokkaido 060-8628 (Japan)


    We have examined the structural effects of zinc-octaethylporphyrin [Zn(OEP)] films used as a donor on the external quantum efficiency (EQE) of organic heterojunction photovoltaic (OPV) cells [ITO/Zn(OEP)/C{sub 60}/Al], and investigated what exactly causes the improvement of EQE. When the structure of the Zn(OEP) films changed from amorphous to crystalline, the maximum EQE increased from 36% to 42%, which is greater than that of around 35% for previously reported OPV cells using buffer materials (Peumans and Forrest 2001 Appl. Phys. Lett. 79 126). The crystallization of Zn(OEP) films is found to increase the number of inter-molecular charge-transfer (IMCT) excitons and to enlarge the mobility of carriers and IMCT excitons, thus significantly improving the EQE of the photoabsorption band under illumination due to the IMCT excitons.

  15. The relationship between the electric field induced dissociation of charge transfer (CT) excitons and the photocurrent in novel hybrid small molecular/polymeric solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Inal, Sahika; Neher, Dieter [Universitaet Potsdam (Germany). Institut fuer Physik und Astronomie; Sellinger, Alan [Institute of Materials Research and Engineering, Singapore (China)


    Complete dissociation of coulombically bound interfacial states is an ultimate step accounting for photovoltaic performance. Recent work has proposed that the emission of CT-exciton, i.e. an exciplex, is a competing process to the generation of free charges. Here, we investigated the photophysical processes in a bulk heterojunction system using a soluble poly(p-phenylenevinylene) donor and a novel small molecular electron acceptor based on Vinazene (2-vinyl-4,5-dicyanoimidazole). Recent work has shown that this blend exhibits a featureless emission, prominent at long wavelengths of the spectrum, which was attributed to a CT-exciton. We monitored the field induced dissociation of these CT-excitons by means of steady state and time resolved PL spectroscopy. Shortened decay times and reduced PL emission in blend film evidence the dissociation of the emissive intermolecular pair by the external electric field. Analyzing the dependence of the photocurrent and external quantum efficiency on the external field, the fate of the separated exciplex pairs is tackled. It is suggested that the formation of free carriers involves channels other than CT-excitons in such blends.

  16. Two-photon excited fluorescence from higher electronic states of chlorophylls in photosynthetic antenna complexes a new approach to detect strong excitonic chlorophyll a/b coupling

    CERN Document Server

    Leupold, D; Ehlert, J; Irrgang, K D; Renger, G; Lokstein, H


    Stepwise two-photon excitation of chlorophyll a and b in the higher plant main light-harvesting complex (LHC II) and the minor complex CP29 (as well as in organic solution) with 100-fs pulses in the Q/sub y/ region results in a weak blue fluorescence. The dependence of the spectral shape of the blue fluorescence on excitation wavelength offers a new approach to elucidate the long-standing problem of the origin of spectral "chlorophyll forms" in pigment-protein complexes, in particular the characterization of chlorophyll a/b-heterodimers. As a first result we present evidence for the existence of strong chlorophyll a/b-interactions (excitonically coupled transitions at 650 and 680 nm) in LHC II at ambient temperature. In comparison with LHC II, the experiments with CP29 provide further evidence that the lowest energy chlorophyll a transition (at ~680 nm) is not excitonically coupled to chlorophyll b. (22 refs).

  17. Molecular modeling of polynucleotide complexes. (United States)

    Meneksedag-Erol, Deniz; Tang, Tian; Uludağ, Hasan


    Delivery of polynucleotides into patient cells is a promising strategy for treatment of genetic disorders. Gene therapy aims to either synthesize desired proteins (DNA delivery) or suppress expression of endogenous genes (siRNA delivery). Carriers constitute an important part of gene therapeutics due to limitations arising from the pharmacokinetics of polynucleotides. Non-viral carriers such as polymers and lipids protect polynucleotides from intra and extracellular threats and facilitate formation of cell-permeable nanoparticles through shielding and/or bridging multiple polynucleotide molecules. Formation of nanoparticulate systems with optimal features, their cellular uptake and intracellular trafficking are crucial steps for an effective gene therapy. Despite the great amount of experimental work pursued, critical features of the nanoparticles as well as their processing mechanisms are still under debate due to the lack of instrumentation at atomic resolution. Molecular modeling based computational approaches can shed light onto the atomic level details of gene delivery systems, thus provide valuable input that cannot be readily obtained with experimental techniques. Here, we review the molecular modeling research pursued on critical gene therapy steps, highlight the knowledge gaps in the field and providing future perspectives. Existing modeling studies revealed several important aspects of gene delivery, such as nanoparticle formation dynamics with various carriers, effect of carrier properties on complexation, carrier conformations in endosomal stages, and release of polynucleotides from carriers. Rate-limiting steps related to cellular events (i.e. internalization, endosomal escape, and nuclear uptake) are now beginning to be addressed by computational approaches. Limitations arising from current computational power and accuracy of modeling have been hindering the development of more realistic models. With the help of rapidly-growing computational power

  18. A comparative theoretical study of exciton-dissociation and charge-recombination processes in oligothiophene/fullerene and oligothiophene/perylenediimide complexes for organic solar cells

    KAUST Repository

    Yi, Yuanping


    The exciton-dissociation and charge-recombination processes in donor-acceptor complexes found in α-sexithienyl/C60 and α-sexithienyl/perylenetetracarboxydiimide (PDI) solar cells are investigated by means of quantum-chemical methods. The electronic couplings and exciton-dissociation and charge-recombination rates have been evaluated for various configurations of the complexes. The results suggest that the decay of the lowest charge-transfer state to the ground state in the PDI-based devices: (i) is faster than that in the fullerene-based devices and (ii) in most cases, can compete with the dissociation of the charge-transfer state into mobile charge carriers. This faster charge-recombination process is consistent with the lower performance observed experimentally for the devices using PDI derivatives as the acceptor. © 2011 The Royal Society of Chemistry.

  19. Analysis of the Complex Gross-Pitaevskii Equation for the Bose-Einstein Condensation of Exciton-Polaritons

    KAUST Repository

    Núñez, Jesus


    Considered as a fundamental step for the development of the atomic laser and quantum computing, as well as the theoretical explanation of super fluidity, the Bose- Einstein condensate (BEC) has emerged as one of the most important topics in modern physics. This project is devoted to the analysis of a condensate based on exciton-polaritons. This BEC is characterized by a high critical temperature of condensation (about 20 K) and non-equilibrium dynamics. A mathematical model called complex Gross- Pitaevskii equation (cGPE) is used to describe its behavior. The steady state solutions of the cGPE are studied and a numerical method based on a collocation method is proposed in order to find these solutions. Once the steady state solutions are found, a linear stability analysis is performed, demonstrating that the steady state solutions become unstable as the pumping spot radius increases. Finally, the manifestations of these instabilities are analyzed by direct simulation of the cGPE, using a second order time-splitting spectral method. As a result, it is possible to see the formation of quantum vortices, which increase in number as the pumping spot radius increases.

  20. Excitonic emission of colloidal nano-crystals embedded in Molecular Beam Epitaxy grown ZnSe

    Energy Technology Data Exchange (ETDEWEB)

    Rashad, M; Pawlis, A; Schikora, D; Lischka, K [Department Physik, Universitaet Paderborn, Paderborn (Germany); Schoeps, O; Artemyev, M V; Woggon, U, E-mail: mahmed@mail.uni-paderborn.d [Technische Universitaet Berlin, Berlin (Germany)


    We combine ZnSe layers grown by molecular beam epitaxy with colloidal CdSe core, CdSe/ZnSe and CdSe/ZnS core/shell nano-crystals (NCs) to achieve monolithic NC-semiconductor heterostructures. The NCs are prepared in solution and deposited by spray-coating on ZnSe buffer layers and subsequently overgrown by ZnSe. We find a blue shift of the photoluminescence of core/shell dots when they are overgrown by ZnSe. Rapid thermal annealing is used to improve the interface region between the NCs and the ZnSe matrix. The effect of different annealing temperatures on the optical properties of CdSe core, CdSe/ZnSe and CdSe/ZnS core/shell NCs overgrown with a cap layer of ZnSe is investigated. After annealing at 673 K the photoluminescence of these samples is red-shifted as compared to unprocessed samples. All photoluminescence results are explained by a model calculation with the following assumption about the 3D confining potential of the NCs: (i) the shell of core/shell NCs dissolves during ZnSe overgrowth, (ii) after overgrowth NCs are separated from the ZnSe matrix by an interface barrier, (iii) the height of this barrier is significantly reduced by annealing. For all three types of NCs we find an excellent quantitative agreement between the experimental and calculated NC transition energies. The absence of the barrier after annealing is further demonstrated by low temperature photoluminescence data of annealed samples which show enhanced diffusion of electron-hole pairs from ZnSe into the NCs.

  1. Binary Molecular Complexes and the Nature of Molecular Association

    African Journals Online (AJOL)

    Asurvey is presented of the results of some ab initio calculations of the properties of a variety of binary molecular complexes. The properties include the molecular structures, the interaction energies and the vibrational spectra. The interaction energies have been correlated with some physical properties of the interacting ...

  2. Excitonic nonlinearities in single-wall carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, D.T.; Voisin, C.; Roussignol, P. [Laboratoire Pierre Aigrain, Ecole Normale Superieure, UPMC, Universite Paris Diderot, CNRS UMR8551, Paris (France); Roquelet, C.; Lauret, J.S. [Laboratoire de Photonique Quantique et Moleculaire de l' Ecole Normale Superieure de Cachan (France); Cassabois, G. [Laboratoire Pierre Aigrain, Ecole Normale Superieure, UPMC, Universite Paris Diderot, CNRS UMR8551, Paris (France); Laboratoire Charles Coulomb, UMR5221, Universite Montpellier 2, Montpellier (France); CNRS, Laboratoire Charles Coulomb, UMR5221, Montpellier (France)


    Excitons are composite bosons that allow a fair description of the optical properties in solid state systems. The quantum confinement in nanostructures enhances the excitonic effects and impacts the exciton-exciton interactions, which tailor the performances of classical and quantum optoelectronic devices, such as lasers or single-photon emitters. The excitonic nonlinearities exhibit significant differences between organic and inorganic compounds. Tightly bound Frenkel excitons in molecular crystals are for instance affected by an efficient exciton-exciton annihilation (EEA). This Auger process also governs the population relaxation dynamics in carbon nanotubes that share many physical properties with organic materials. Here, we show that this similarity breaks down for the excitonic decoherence in carbon nanotubes. Original nonlinear spectral-hole burning experiments bring evidence of pure dephasing induced by exciton-exciton scattering (EES) in the k-space. This mechanism controls the exciton collision-induced broadening, as for Wannier excitons in inorganic semiconductors. We demonstrate that this singular behavior originates from the intrinsic one-dimensionality of excitons in carbon nanotubes, which display unique hybrid features of organic and inorganic systems. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  3. Control of excitons in a bent bunch of molecular aggregates by dipole-dipole interaction with quantum dots (United States)

    Zabolotskii, A. A.


    The nonlocal dipole-dipole interaction is studied between excitations in chromophores forming a bunch or a tube of J-aggregates and closely spaced quantum dots (QDs). Equations describing the evolution of exciton pulses in a quasi-one-dimensional medium are derived taking into account the interaction with the transition resonant to nanoparticles. It is shown that the efficient controllable resonance energy transfer can occur in the system between QDs and an exciton pulse. The efficiency of this process significantly increases if the bunch of aggregates is deformed to bend nanoparticles round. It is shown that the interaction of permanent dipole moments of QDs and chromophores leads to the formation of a potential barrier or a well. It is found that the combined influence of these factors can be used to efficiently control the dynamics of pulses in aggregates.

  4. The Symmetrical Quasi-Classical Model for Electronically Non-Adiabatic Processes Applied to Energy Transfer Dynamics in Site-Exciton Models of Light-Harvesting Complexes. (United States)

    Cotton, Stephen J; Miller, William H


    In a recent series of papers, it has been illustrated that a symmetrical quasi-classical (SQC) windowing model applied to the Meyer-Miller (MM) classical vibronic Hamiltonian provides an excellent description of a variety of electronically non-adiabatic benchmark model systems for which exact quantum results are available for comparison. In this paper, the SQC/MM approach is used to treat energy transfer dynamics in site-exciton models of light-harvesting complexes, and in particular, the well-known 7-state Fenna-Mathews-Olson (FMO) complex. Again, numerically "exact" results are available for comparison, here via the hierarchical equation of motion (HEOM) approach of Ishizaki and Fleming, and it is seen that the simple SQC/MM approach provides very reasonable agreement with the previous HEOM results. It is noted, however, that unlike most (if not all) simple approaches for treating these systems, because the SQC/MM approach presents a fully atomistic simulation based on classical trajectory simulation, it places no restrictions on the characteristics of the thermal baths coupled to each two-level site, e.g., bath spectral densities (SD) of any analytic functional form may be employed as well as discrete SD determined experimentally or from MD simulation (nor is there any restriction that the baths be harmonic), opening up the possibility of simulating more realistic variations on the basic site-exciton framework for describing the non-adiabatic dynamics of photosynthetic pigment complexes.

  5. Molecular identification of the Sporothrix schenckii complex. (United States)

    Oliveira, Manoel Marques Evangelista; Almeida-Paes, Rodrigo; Gutierrez-Galhardo, Maria Clara; Zancope-Oliveira, Rosely M


    Sporothrix schenckii, an ascomycetous dimorphic organism that for over a century was recognized as the sole agent of sporotrichosis, a subcutaneous mycosis with a worldwide distribution. However, it has been proposed, based on physiologic and molecular aspects, that S. schenckii is a complex of distinct species: Sporothrix brasiliensis, Sporothrix mexicana, Sporothrix globosa, S. schenckii sensu strictu, Sporothrix luriei, and Sporothrix albicans (formerly Sporothrix pallida). Human disease has a broad range of clinical manifestations and can be classified into fixed cutaneous, lymphocutaneous, disseminated cutaneous, and extracutaneous sporotrichosis. The gold standard for the diagnosis of sporotrichosis is the culture; however, serologic, histopathologic and molecular approaches have been recently adopted for the diagnosis of this mycosis. Few molecular methods have been applied to the diagnosis of sporotrichosis to detect S. schenckii DNA from clinical specimens, and to identify Sporothrix spp. in culture. Until now, Sporothrix is the unique clinically relevant dimorphic fungus without an elucidated genome sequence, thus limiting molecular knowledge about the cryptic species of this complex, and the sexual form of all S. schenckii complex species. In this review we shall focus on the current diagnosis of the sporotrichosis, and discuss the current molecular tools applied to the diagnosis and identification of the Sporothrix complex species. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  6. Molecular simulation and modeling of complex I. (United States)

    Hummer, Gerhard; Wikström, Mårten


    Molecular modeling and molecular dynamics simulations play an important role in the functional characterization of complex I. With its large size and complicated function, linking quinone reduction to proton pumping across a membrane, complex I poses unique modeling challenges. Nonetheless, simulations have already helped in the identification of possible proton transfer pathways. Simulations have also shed light on the coupling between electron and proton transfer, thus pointing the way in the search for the mechanistic principles underlying the proton pump. In addition to reviewing what has already been achieved in complex I modeling, we aim here to identify pressing issues and to provide guidance for future research to harness the power of modeling in the functional characterization of complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Plasmon-Exciton-Polariton Lasing

    CERN Document Server

    Ramezani, Mohammad; Fernández-Domínguez, Antonio I; Feist, Johannes; Rodriguez, Said Rahimzadeh-Kalaleh; Garcia-Vidal, Francisco J; Gómez-Rivas, Jaime


    Strong coupling of Frenkel excitons with surface plasmons leads to the formation of bosonic quasi-particles known as plasmon-exciton-polaritons (PEPs).Localized surface plasmons in nanoparticles are lossy due to radiative and nonradiative decays, which has hampered the realization of polariton lasing in a plasmonic system, i.e., PEP lasing. These losses can be reduced in collective plasmonic resonances supported by arrays of nanoparticles. Here we demonstrate PEP lasing in arrays of silver nanoparticles by showing the emergence of a threshold in the photoluminescence accompanied by both a superlinear increase of the emission and spectral narrowing. We also observe a reduction of the threshold by increasing the coupling between the molecular excitons and the resonances supported by the array despite the reduction of the quantum efficiency of the emitters. The coexistence of bright and dark collective modes in this plasmonic system allows for a 90?-change of polarization in the emission beyond the threshold.

  8. Exciton-phonon bound complex in single-walled carbon nanotubes revealed by high-field magneto-optical spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Weihang; Nakamura, Daisuke; Takeyama, Shojiro, E-mail: [Institute for Solid State Physics, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8581 (Japan); Sasaki, Tatsuya; Saito, Hiroaki [Institute for Solid State Physics, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8581 (Japan); Department of Applied Physics, University of Tokyo, Hongo 113-8656 (Japan); Liu, Huaping [Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Kataura, Hiromichi [Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8562 (Japan)


    High-field magneto-optical spectroscopy was performed on highly enriched (6,5) single-walled carbon nanotubes. Spectra of phonon sidebands in both 1st and 2nd sub-bands were unchanged by an external magnetic field up to 52 T. The dark K-momentum singlet (D-K-S) exciton, which plays an important role for the external quantum efficiency of the system for both sub-bands in the near-infrared and the visible light region, respectively, was clarified to be the origin of the phonon sidebands.

  9. Properties of Excitons Bound to Ionized Donors

    DEFF Research Database (Denmark)

    Skettrup, Torben; Suffczynski, M.; Gorzkowski, W.


    Binding energies, interparticle distances, oscillator strengths, and exchange corrections are calculated for the three-particle complex corresponding to an exciton bound to an ionized donor. The results are given as functions of the mass ratio of the electron and hole. Binding of the complex...... is obtained for mass ratios up to 0.426. The interparticle distances are up to 50 times larger than the corresponding exciton radius. The oscillator strengths are about 104 times greater than those of free excitons, while the exchange corrections for the complex are comparable to those of free excitions...

  10. Nonlocal excitonic-mechanical interaction in a nanosystem (United States)

    Zabolotskii, A. A.


    The dynamics of a nanoparticle during its dipole interaction with an excitonic excitation in an extended quasi-one-dimensional polarizable medium is investigated. Bundles of J-aggregates of dye molecules are considered as an example of the latter. The nonlocal excitonic-mechanical interaction between the field of an amplifying or absorbing nanoparticle and excitons in a bundle has been simulated numerically. It has been found that the interaction between the field of the induced nanoparticle dipole and the fields of the molecular dipoles in an aggregate can lead to a change in the particle trajectory and excitonic pulse shape. The possibility of controlling the nanoparticle by excitonic pulses and the reverse effect of the nanoparticle field on the dynamics of excitons due to the nonlocal excitonic-mechanical interaction has been demonstrated.

  11. Optically detected magnetic resonance of intact membranes from Chloroflexus aurantiacus. Evidence for exciton interaction between the RC and the B808-866 complex. (United States)

    Bordignon, Enrica; Scarzello, Marco; Agostini, Giancarlo; Giacometti, Giovanni; Vianelli, Alberto; Vannini, Candida; Carbonera, Donatella


    Optically detected magnetic resonance of chlorosome-containing membranes from the green filamentous bacterium Chloroflexus aurantiacus has been performed both by fluorescence and absorption detection. Triplet states localized in the chlorosomes and in the B808-866 complex have been characterized. After chemical reduction with ascorbate followed by illumination at 200 K, recombination triplet state localized in the primary donor becomes largely populated under illumination at low temperature while all the antenna triplet states, which are localized in carotenoids and BChl a molecules, are strongly quenched. We were able to obtain the T-S spectrum of the primary donor P870 surrounded by all the antenna complexes connected to the RC via energy transfer and then in its intact environment. We found clear spectroscopic evidence for exciton interaction between the RC and the B808-866 antenna complex. This evidence was provided by the comparison of the T-S spectrum of P870 in the membranes with that of isolated RC. The analogy of some features of the difference spectra with those previously found in the same kind of experiments for Rb. sphaeroides, allows to predict a similar coupling among the primary donor and the nearby antenna BChl a molecules, assembled as circular aggregate.

  12. Dark excitons in transition metal dichalcogenides (United States)

    Malic, Ermin; Selig, Malte; Feierabend, Maja; Brem, Samuel; Christiansen, Dominik; Wendler, Florian; Knorr, Andreas; Berghäuser, Gunnar


    Monolayer transition metal dichalcogenides (TMDs) exhibit a remarkably strong Coulomb interaction that manifests in tightly bound excitons. Due to the complex electronic band structure exhibiting several spin-split valleys in the conduction and valence band, dark excitonic states can be formed. They are inaccessibly by light due to the required spin-flip and/or momentum transfer. The relative position of these dark states with respect to the optically accessible bright excitons has a crucial impact on the emission efficiency of these materials and thus on their technological potential. Based on the solution of the Wannier equation, we present the excitonic landscape of the most studied TMD materials including the spectral position of momentum- and spin-forbidden excitonic states. We show that the knowledge of the electronic dispersion does not allow to conclude about the nature of the material's band gap since excitonic effects can give rise to significant changes. Furthermore, we reveal that an exponentially reduced photoluminescence yield does not necessarily reflect a transition from a direct to a nondirect gap material, but can be ascribed in most cases to a change of the relative spectral distance between bright and dark excitonic states.

  13. Direct Imaging of Frenkel Exciton Transport by Ultrafast Microscopy. (United States)

    Zhu, Tong; Wan, Yan; Huang, Libai


    Long-range transport of Frenkel excitons is crucial for achieving efficient molecular-based solar energy harvesting. Understanding of exciton transport mechanisms is important for designing materials for solar energy applications. One major bottleneck in unraveling of exciton transport mechanisms is the lack of direct measurements to provide information in both spatial and temporal domains, imposed by the combination of fast energy transfer (typically ≤1 ps) and short exciton diffusion lengths (typically ≤100 nm). This challenge requires developing experimental tools to directly characterize excitation energy transport, and thus facilitate the elucidation of mechanisms. To address this challenge, we have employed ultrafast transient absorption microscopy (TAM) as a means to directly image exciton transport with ∼200 fs time resolution and ∼50 nm spatial precision. By mapping population in spatial and temporal domains, such approach has unraveled otherwise obscured information and provided important parameters for testing exciton transport models. In this Account, we discuss the recent progress in imaging Frenkel exciton migration in molecular crystals and aggregates by ultrafast microscopy. First, we establish the validity of the TAM methods by imaging singlet and triplet exciton transport in a series of polyacene single crystals that undergo singlet fission. A new singlet-mediated triplet transport pathway has been revealed by TAM, resulting from the equilibrium between triplet and singlet exciton populations. Such enhancement of triplet exciton transport enables triplet excitons to migrate as singlet excitons and leads to orders of magnitude faster apparent triplet exciton diffusion rate in the picosecond and nanosecond time scales, favorable for solar cell applications. Next we discuss how information obtained by ultrafast microscopy can evaluate coherent effects in exciton transport. We use tubular molecular aggregates that could support large exciton

  14. Exciton scattering approach for optical spectra calculations in branched conjugated macromolecules

    Energy Technology Data Exchange (ETDEWEB)

    Li, Hao [Department of Chemistry, University of Houston, Houston, TX 77204 (United States); Wu, Chao [Electronic Structure Lab, Center of Microscopic Theory and Simulation, Frontier Institute of Science and Technology, Xian Jiaotong University, Xian 710054 (China); Malinin, Sergey V. [Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202 (United States); Tretiak, Sergei, E-mail: [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Chernyak, Vladimir Y., E-mail: [Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202 (United States)


    The exciton scattering (ES) technique is a multiscale approach based on the concept of a particle in a box and developed for efficient calculations of excited-state electronic structure and optical spectra in low-dimensional conjugated macromolecules. Within the ES method, electronic excitations in molecular structure are attributed to standing waves representing quantum quasi-particles (excitons), which reside on the graph whose edges and nodes stand for the molecular linear segments and vertices, respectively. Exciton propagation on the linear segments is characterized by the exciton dispersion, whereas exciton scattering at the branching centers is determined by the energy-dependent scattering matrices. Using these ES energetic parameters, the excitation energies are then found by solving a set of generalized “particle in a box” problems on the graph that represents the molecule. Similarly, unique energy-dependent ES dipolar parameters permit calculations of the corresponding oscillator strengths, thus, completing optical spectra modeling. Both the energetic and dipolar parameters can be extracted from quantum-chemical computations in small molecular fragments and tabulated in the ES library for further applications. Subsequently, spectroscopic modeling for any macrostructure within a considered molecular family could be performed with negligible numerical effort. We demonstrate the ES method application to molecular families of branched conjugated phenylacetylenes and ladder poly-para-phenylenes, as well as structures with electron donor and acceptor chemical substituents. Time-dependent density functional theory (TD-DFT) is used as a reference model for electronic structure. The ES calculations accurately reproduce the optical spectra compared to the reference quantum chemistry results, and make possible to predict spectra of complex macromolecules, where conventional electronic structure calculations are unfeasible.

  15. Exciton Resonances in Novel Silicon Carbide Polymers (United States)

    Burggraf, Larry; Duan, Xiaofeng


    A revolutionary technology transformation from electronics to excitionics for faster signal processing and computing will be advantaged by coherent exciton transfer at room temperature. The key feature required of exciton components for this technology is efficient and coherent transfer of long-lived excitons. We report theoretical investigations of optical properties of SiC materials having potential for high-temperature excitonics. Using Car-Parinello simulated annealing and DFT we identified low-energy SiC molecular structures. The closo-Si12C12 isomer, the most stable 12-12 isomer below 1100 C, has potential to make self-assembled chains and 2-D nanostructures to construct exciton components. Using TDDFT, we calculated the optical properties of the isomer as well as oligomers and 2-D crystal formed from the isomer as the monomer unit. This molecule has large optical oscillator strength in the visible. Its high-energy and low-energy transitions (1.15 eV and 2.56 eV) are nearly pure one-electron silicon-to-carbon transitions, while an intermediate energy transition (1.28 eV) is a nearly pure carbon-to-silicon one-electron charge transfer. These results are useful to describe resonant, coherent transfer of dark excitons in the nanostructures. Research supported by the Air Force Office of Scientific Research.

  16. Exciton laser rate equations

    Directory of Open Access Journals (Sweden)

    Garkavenko A. S.


    Full Text Available The rate equations of the exciton laser in the system of interacting excitons have been obtained and the inverted population conditions and generation have been derived. The possibility of creating radically new gamma-ray laser has been shown.

  17. Excitonic processes at organic heterojunctions (United States)

    He, ShouJie; Lu, ZhengHong


    Understanding excitonic processes at organic heterojunctions is crucial for development of organic semiconductor devices. This article reviews recent research on excitonic physics that involve intermolecular charge transfer (CT) excitons, and progress on understanding relationships between various interface energy levels and key parameters governing various competing interface excitonic processes. These interface excitonic processes include radiative exciplex emission, nonradiative recombination, Auger electron emission, and CT exciton dissociation. This article also reviews various device applications involving interface CT excitons, such as organic light-emitting diodes (OLEDs), organic photovoltaic cells, organic rectifying diodes, and ultralow-voltage Auger OLEDs.

  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


    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. Charged excitonic complexes in GaAs/Al0.35Ga0.65As p-i-n double quantum wells

    DEFF Research Database (Denmark)

    Timofeev, V. B.; Larionov, A. V.; Alessi, M. Grassi


    Photoluminescence (PL) and PL excitation measurements (PLE) have been performed in GaAs/AlxGa1-xAs double quantum well (QW) structures under different applied electric fields. An emission due to charged excitons (trions) has been identified in the PL spectra similar to 3 meV below the heavy-hole ......, as shown by (i) an analysis of the PL polarization for resonant excitation of the heavy- and the light-exciton ground state, and (ii) the analysis of the Zeeman effect for the trion PL band in the Faraday geometry, i.e., for a magnetic field normal to the QW's....

  20. Molecular variation in the Postia caesia complex. (United States)

    Yao, Yi-Jian; Pegler, David N; Chase, Mark W


    DNA sequences of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrDNA) and small-subunit of mitochondrial ribosomal DNA (mt-rDNA) were obtained from 12 different collections initially identified as either Postia caesia or P. subcaesia based on morphological criteria. Sequences of ITS from British collections separate into three clear groups, each with identical sequences, regardless of the lignicolous host and distribution. These British collections can be distinguished morphologically as two groups, (a) thick and larger basidiomata (1.5-5.0x2.0-6.0x3.0-15 cm) with a strigose to tomentose pileus and (b) thin and smaller basidiomata (0.5-2.0x1.0-2.5x1.5-4.0 cm) with a smooth pileus. The former were all collected from hardwoods and the latter from both hardwoods and coniferous woods. Group (a) corresponds to one of the sequence groups, but group (b) displays two different sequences. Two collections from Norway, one from each of the morphological groups, exhibit further sequence variation within the ITS regions, although closer to those of British group (b). Representative sequences of mt-rDNA from each of the three British ITS sequence groups remain distinct, but those from the two Norwegian collections, however, are identical to one of the British groups. Further comparison of basidiospore size revealed no clear distinction among these groups, although the ratio of spore length to spore width is generally greater in group (a). Although there is no clear separation of these collections into two species, there is a clear tendency of variation at both morphological and molecular levels, among them. Differences in morphology and DNA sequences do not warrant species recognition, but do demonstrate high variability within the species complex.

  1. Exciton circular dichroism in channelrhodopsin. (United States)

    Pescitelli, Gennaro; Kato, Hideaki E; Oishi, Satomi; Ito, Jumpei; Maturana, Andrés Daniel; Nureki, Osamu; Woody, Robert W


    Channelrhodopsins (ChRs) are of great interest currently because of their important applications in optogenetics, the photostimulation of neurons. The absorption and circular dichroism (CD) spectra of C1C2, a chimera of ChR1 and ChR2 of Chlamydomonas reinhardtii, have been studied experimentally and theoretically. The visible absorption spectrum of C1C2 shows vibronic fine structure in the 470 nm band, consistent with the relatively nonpolar binding site. The CD spectrum has a negative band at 492 nm (Δε(max) = -6.17 M(-1) cm(-1)) and a positive band at 434 nm (Δε(max) = +6.65 M(-1) cm(-1)), indicating exciton coupling within the C1C2 dimer. Time-dependent density functional theory (TDDFT) calculations are reported for three models of the C1C2 chromophore: (1) the isolated protonated retinal Schiff base (retPSB); (2) an ion pair, including the retPSB chromophore, two carboxylate side chains (Asp 292, Glu 162), modeled by acetate, and a water molecule; and (3) a hybrid quantum mechanical/molecular mechanical (QM/MM) model depicting the binding pocket, in which the QM part consists of the same ion pair as that in (2) and the MM part consists of the protein residues surrounding the ion pair within 10 Å. For each of these models, the CD of both the monomer and the dimer was calculated with TDDFT. For the dimer, DeVoe polarizability theory and exciton calculations were also performed. The exciton calculations were supplemented by calculations of the coupling of the retinal transition with aromatic and peptide group transitions. For the dimer, all three methods and three models give a long-wavelength C2-axis-polarized band, negative in CD, and a short-wavelength band polarized perpendicular to the C2 axis with positive CD, differing in wavelength by 1-5 nm. Only the retPSB model gives an exciton couplet that agrees qualitatively with experiment. The other two models give a predominantly or solely positive band. We further analyze an N-terminal truncated mutant

  2. Interwell excitons in GaAs superlattices

    DEFF Research Database (Denmark)

    Birkedal, Dan; Sayed, Karim El; Sanders, G.


    The formation of spatially indirect excitons in superlattices with narrow minibands is theoretically and experimentally investigated. We identify the experimental conditions for the observation of interwell excitons and find a distinct excitonic state energetically located between the Is exciton ...

  3. Molecular complexes of phenols with DDQ

    Indian Academy of Sciences (India)

    charge transfer (CT) complexes with p acceptors 1, we considered it interesting to investigate the CT spectra, stabilities and thermodynamic parameters of CT complexes of phenols with 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ). Literature survey revealed that DDQ forms CT complexes with phenols and produces a ...

  4. A path based approach to assessing molecular complexity. (United States)

    Proudfoot, John R


    An atom environment, path based approach to calculating molecular complexity is described. Based on Shannon's equation, the method transforms the number and diversity of paths emanating from an atom to an atom-complexity from which a number of molecular complexity measures are derived. The method is independent of explicitly predefined features such as ring membership, bond types, chirality or symmetry. These path-based measures of complexity can distinguish subtle differences in molecular structure and an application to the visualization of marketed drugs, including a number of biologics, is presented. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Positron annihilation studies of some charge transfer molecular complexes

    CERN Document Server

    El-Sayed, A; Boraei, A A A


    Positron annihilation lifetimes were measured for some solid charge transfer (CT) molecular complexes of quinoline compounds (2,6-dimethylquinoline, 6-methoxyquinoline, quinoline, 6-methylquinoline, 3-bromoquinoline and 2-chloro-4-methylquinoline) as electron donor and picric acid as an electron acceptor. The infrared spectra (IR) of the solid complexes clearly indicated the formation of the hydrogen-bonding CT-complexes. The annihilation spectra were analyzed into two lifetime components using PATFIT program. The values of the average and bulk lifetimes divide the complexes into two groups according to the non-bonding ionization potential of the donor (electron donating power) and the molecular weight of the complexes. Also, it is found that the ionization potential of the donors and molecular weight of the complexes have a conspicuous effect on the average and bulk lifetime values. The bulk lifetime values of the complexes are consistent with the formation of stable hydrogen-bonding CT-complexes as inferred...

  6. Optical second harmonic generation from Wannier excitons

    DEFF Research Database (Denmark)

    Pedersen, Thomas Garm; Cornean, Horia


    , a simplified three-band Wannier exciton model of cubic semiconductors is applied and a closed form expression for the complex second harmonic response function including broadening is derived. Our calculated spectra are found to be in excellent agreement with the measured response near the band edge...

  7. Binary Molecular Complexes and the Nature of Molecular Association

    African Journals Online (AJOL)



    Jun 15, 2004 ... computer program package13 at the second order level of. Møller-Plesset perturbation theory.14 We ... dimethyl ether, methyl fluoride, trimethyl phosphine, dimethyl sulphide and methyl chloride as proton ..... and ammonia, as electron donors, and molecular fluorine, chlorine and bromine as electron ...

  8. Synthesis and Exciton Dynamics of Triplet Sensitized Conjugated Polymers

    KAUST Repository

    Andernach, Rolf


    We report the synthesis of a novel polythiophene-based host-guest copolymer incorporating a Pt-porphyrin complex (TTP-Pt) into the backbone for efficient singlet to triplet polymer exciton sensitization. We elucidated the exciton dynamics in thin films of the material by means of Transient Absorption Spectrosopcy (TAS) on multiple timescales and investigated the mechanism of triplet exciton formation. During sensitization, single exciton diffusion is followed by exciton transfer from the polymer backbone to the complex where it undergoes intersystem crossing to the triplet state of the complex. We directly monitored the triplet exciton back transfer from the Pt-porphyrin to the polymer and find that 60% of the complex triplet excitons are transferred with a time constant of 1087 ps. We propose an equilibrium between polymer and porphyrin triplet states as a result of the low triplet diffusion length in the polymer backbone and hence an increased local triplet population resulting in increased triplet-triplet annihilation. This novel system has significant implications for the design of novel materials for triplet sensitized solar cells and up-conversion layers.

  9. Molecular Taxonomy of the Trichophyton rubrum Complex


    Gräser, Y.; Kuijpers, A.F.A.; Presber, W; de Hoog, G.S.


    The validity of taxa around Trichophyton rubrum was evaluated by a combination of phenetic and molecular methods. Morphological and physiological features were compared to results of sequencing of the internal transcribed spacer region of the ribosomal operon, PCR fingerprinting, and amplified fragment length polymorphism analysis. The 15 species and varieties investigated (Trichophyton circonvolutum, Trichophyton fischeri, Trichophyton fluviomuniense, Trichophyton glabrum, Trichophyton gourv...

  10. Mapping the exciton diffusion in semiconductor nanocrystal solids. (United States)

    Kholmicheva, Natalia; Moroz, Pavel; Bastola, Ebin; Razgoniaeva, Natalia; Bocanegra, Jesus; Shaughnessy, Martin; Porach, Zack; Khon, Dmitriy; Zamkov, Mikhail


    Colloidal nanocrystal solids represent an emerging class of functional materials that hold strong promise for device applications. The macroscopic properties of these disordered assemblies are determined by complex trajectories of exciton diffusion processes, which are still poorly understood. Owing to the lack of theoretical insight, experimental strategies for probing the exciton dynamics in quantum dot solids are in great demand. Here, we develop an experimental technique for mapping the motion of excitons in semiconductor nanocrystal films with a subdiffraction spatial sensitivity and a picosecond temporal resolution. This was accomplished by doping PbS nanocrystal solids with metal nanoparticles that force the exciton dissociation at known distances from their birth. The optical signature of the exciton motion was then inferred from the changes in the emission lifetime, which was mapped to the location of exciton quenching sites. By correlating the metal-metal interparticle distance in the film with corresponding changes in the emission lifetime, we could obtain important transport characteristics, including the exciton diffusion length, the number of predissociation hops, the rate of interparticle energy transfer, and the exciton diffusivity. The benefits of this approach to device applications were demonstrated through the use of two representative film morphologies featuring weak and strong interparticle coupling.

  11. Molecular Architecture of the Yeast Monopolin Complex

    Directory of Open Access Journals (Sweden)

    Kevin D. Corbett


    Full Text Available The Saccharomyces cerevisiae monopolin complex directs proper chromosome segregation in meiosis I by mediating co-orientation of sister kinetochores on the meiosis I spindle. The monopolin subunits Csm1 and Lrs4 form a V-shaped complex that may directly crosslink sister kinetochores. We report here biochemical characterization of the monopolin complex subunits Mam1 and Hrr25 and of the complete four-protein monopolin complex. By purifying monopolin subcomplexes with different subunit combinations, we have determined the stoichiometry and overall architecture of the full monopolin complex. We have determined the crystal structure of Csm1 bound to a Mam1 fragment, showing how Mam1 wraps around the Csm1 dimer and alters the stoichiometry of kinetochore-protein binding by Csm1. We further show that the kinase activity of Hrr25 is altered by Mam1 binding, and we identify Hrr25 phosphorylation sites on Mam1 that may affect monopolin complex stability and/or kinetochore binding in meiosis.

  12. Molecular Architecture of the Yeast Monopolin Complex

    Energy Technology Data Exchange (ETDEWEB)

    Corbett, Kevin D.; Harrison, Stephen C. (Harvard-Med); (UCSD)


    The Saccharomyces cerevisiae monopolin complex directs proper chromosome segregation in meiosis I by mediating co-orientation of sister kinetochores on the meiosis I spindle. The monopolin subunits Csm1 and Lrs4 form a V-shaped complex that may directly crosslink sister kinetochores. We report here biochemical characterization of the monopolin complex subunits Mam1 and Hrr25 and of the complete four-protein monopolin complex. By purifying monopolin subcomplexes with different subunit combinations, we have determined the stoichiometry and overall architecture of the full monopolin complex. We have determined the crystal structure of Csm1 bound to a Mam1 fragment, showing how Mam1 wraps around the Csm1 dimer and alters the stoichiometry of kinetochore-protein binding by Csm1. We further show that the kinase activity of Hrr25 is altered by Mam1 binding, and we identify Hrr25 phosphorylation sites on Mam1 that may affect monopolin complex stability and/or kinetochore binding in meiosis.

  13. Energy Gap Law for Exciton Dynamics in Gold Cluster Molecules. (United States)

    Kwak, Kyuju; Thanthirige, Viraj Dhanushka; Pyo, Kyunglim; Lee, Dongil; Ramakrishna, Guda


    The energy gap law relates the nonradiative decay rate to the energy gap separating the ground and excited states. Here we report that the energy gap law can be applied to exciton dynamics in gold cluster molecules. Size-dependent electrochemical and optical properties were investigated for a series of n-hexanethiolate-protected gold clusters ranging from Au25 to Au333. Voltammetric studies reveal that the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gaps of these clusters decrease with increasing cluster size. Combined femtosecond and nanosecond time-resolved transient absorption measurements show that the exciton lifetimes decrease with increasing cluster size. Comparison of the size-dependent exciton lifetimes with the HOMO-LUMO gaps shows that they are linearly correlated, demonstrating the energy gap law for excitons in these gold cluster molecules.

  14. Exciton multiplication from first principles. (United States)

    Jaeger, Heather M; Hyeon-Deuk, Kim; Prezhdo, Oleg V


    Third-generation photovolatics require demanding cost and power conversion efficiency standards, which may be achieved through efficient exciton multiplication. Therefore, generating more than one electron-hole pair from the absorption of a single photon has vast ramifications on solar power conversion technology. Unlike their bulk counterparts, irradiated semiconductor quantum dots exhibit efficient exciton multiplication, due to confinement-enhanced Coulomb interactions and slower nonradiative losses. The exact characterization of the complicated photoexcited processes within quantum-dot photovoltaics is a work in progress. In this Account, we focus on the photophysics of nanocrystals and investigate three constituent processes of exciton multiplication, including photoexcitation, phonon-induced dephasing, and impact ionization. We quantify the role of each process in exciton multiplication through ab initio computation and analysis of many-electron wave functions. The probability of observing a multiple exciton in a photoexcited state is proportional to the magnitude of electron correlation, where correlated electrons can be simultaneously promoted across the band gap. Energies of multiple excitons are determined directly from the excited state wave functions, defining the threshold for multiple exciton generation. This threshold is strongly perturbed in the presence of surface defects, dopants, and ionization. Within a few femtoseconds following photoexcitation, the quantum state loses coherence through interactions with the vibrating atomic lattice. The phase relationship between single excitons and multiple excitons dissipates first, followed by multiple exciton fission. Single excitons are coupled to multiple excitons through Coulomb and electron-phonon interactions, and as a consequence, single excitons convert to multiple excitons and vice versa. Here, exciton multiplication depends on the initial energy and coupling magnitude and competes with electron

  15. Molecular architecture of the yeast Mediator complex (United States)

    Robinson, Philip J; Trnka, Michael J; Pellarin, Riccardo; Greenberg, Charles H; Bushnell, David A; Davis, Ralph; Burlingame, Alma L; Sali, Andrej; Kornberg, Roger D


    The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20–40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex. DOI: PMID:26402457

  16. Organometallic chemistry: A shortcut to molecular complexity (United States)

    Murakami, Masahiro; Ishida, Naoki


    A unique transformation for the site-selective cleavage of one C-C single bond and two C-H bonds in sequence has now been developed. This enables a simple carbon skeleton to be reorganized into a significantly more complex form with remarkable efficiency.

  17. Molecular Taxonomy of the Trichophyton rubrum Complex (United States)

    Gräser, Y.; Kuijpers, A. F. A.; Presber, W.; de Hoog, G. S.


    The validity of taxa around Trichophyton rubrum was evaluated by a combination of phenetic and molecular methods. Morphological and physiological features were compared to results of sequencing of the internal transcribed spacer region of the ribosomal operon, PCR fingerprinting, and amplified fragment length polymorphism analysis. The 15 species and varieties investigated (Trichophyton circonvolutum, Trichophyton fischeri, Trichophyton fluviomuniense, Trichophyton glabrum, Trichophyton gourvilii, Trichophyton kanei, Trichophyton kuryangei, Trichophyton megninii, Trichophyton pedis, Trichophyton raubitschekii, Trichophyton rodhaini, Trichophyton rubrum var. nigricans, Trichophyton soudanense, Trichophyton violaceum var. indicum, and Trichophyton yaoundei) were reclassified or synonymized as T. rubrum or T. violaceum. PMID:10970379

  18. Excitons: Molecules in flatland (United States)

    Yao, Wang


    Forming molecules from atoms is commonplace in dense atomic gases. But it now seems that some two-dimensional materials provide a suitable environment for creating complex molecular states from the hydrogen-like electron-hole pairs that form in semiconductors.

  19. Phonon-Driven Oscillatory Plasmonic Excitonic Nanomaterials

    Energy Technology Data Exchange (ETDEWEB)

    Kirschner, Matthew S. [Department; Ding, Wendu [Department; Li, Yuxiu [Center; College; Chapman, Craig T. [Department; Lei, Aiwen [College; Lin, Xiao-Min [Center; Chen, Lin X. [Department; Chemical; Schatz, George C. [Department; Schaller, Richard D. [Department; Center


    We demonstrate that coherent acoustic phonons derived from plasmonic nanoparticles can modulate electronic interactions with proximal excitonic molecular species. A series of gold bipyramids with systematically varied aspect ratios and corresponding localized surface plasmon resonance energies, functionalized with a J-aggregated thiacarbocyanine dye molecule, produce two hybridized states that exhibit clear anti-crossing behavior with a Rabi splitting energy of 120 meV. In metal nanoparticles, photoexcitation generates coherent acoustic phonons that cause oscillations in the plasmon resonance energy. In the coupled system, these photo-generated oscillations alter the metal nanoparticle’s energetic contribution to the hybridized system and, as a result, change the coupling between the plasmon and exciton. We demonstrate that such modulations in the hybridization is consistent across a wide range of bipyramid ensembles. We also use Finite-Difference Time Domain calculations to develop a simple model describing this behavior. Such oscillatory plasmonic-excitonic nanomaterials (OPENs) offer a route to manipulate and dynamically-tune the interactions of plasmonic/excitonic systems and unlock a range of potential applications.

  20. Synthesis and molecular structure of manganese complexes with ...

    Indian Academy of Sciences (India)


    Synthesis and molecular structure of manganese complexes with hindered N3 ligand. UDAI P SINGHa, R SINGHa, S HIKICHIb and Y MORO-OKAb ... O–N distances in this complex are shorter (011-N82, 2·76(1) Å) than the range of distances expected for a hydrogen bond between the peroxide and the imidazole proton.

  1. Molecular electrostatic potential analysis of non-covalent complexes

    Indian Academy of Sciences (India)

    MP4/Aug-cc-pvDZ level to obtain the basis set super- position error (BSSE). The BSSE-corrected binding energy (Eint) of the complexes is calculated as the dif- ference between the energy of the complexes and their constituent monomers. Molecular electrostatic potential (MESP) arise due to the static charge distribution of ...

  2. Energy and Information Transfer Via Coherent Exciton Wave Packets (United States)

    Zang, Xiaoning

    Electronic excitons are bound electron-hole states that are generated when light interacts with matter. Such excitations typically entangle with phonons and rapidly decohere; the resulting electronic state dynamics become diffusive as a result. However, if the exciton-phonon coupling can be reduced, it may be possible to construct excitonic wave packets that offer a means of efficiently transmitting information and energy. This thesis is a combined theory/computation investigation to design condensed matter systems which support the requisite coherent transport. Under the idealizing assumption that exciton-phonon entanglement could be completely suppressed, the majority of this thesis focuses on the creation and manipulation of exciton wave packets in quasi-one-dimensional systems. While each site could be a silicon quantum dot, the actual implementation focused on organic molecular assemblies for the sake of computational simplicity, ease of experimental implementation, potential for coherent transport, and promise because of reduced structural uncertainty. A laser design was derived to create exciton wave packets with tunable shape and speed. Quantum interference was then exploited to manipulate these packets to block, pass, and even dissociate excitons based on their energies. These developments allow exciton packets to be considered within the arena of quantum information science. The concept of controllable excitonic wave packets was subsequently extended to consider molecular designs that allow photons with orbital angular momentum to be absorbed to create excitons with a quasi-angular momentum of their own. It was shown that a well-defined measure of topological charge is conserved in such light-matter interactions. Significantly, it was also discovered that such molecules allow photon angular momenta to be combined and later emitted. This amounts to a new way of up/down converting photonic angular momentum without relying on nonlinear optical materials. The

  3. Soft x-ray excitonics (United States)

    Moulet, A.; Bertrand, J. B.; Klostermann, T.; Guggenmos, A.; Karpowicz, N.; Goulielmakis, E.


    The dynamic response of excitons in solids is central to modern condensed-phase physics, material sciences, and photonic technologies. However, study and control have hitherto been limited to photon energies lower than the fundamental band gap. Here we report application of attosecond soft x-ray and attosecond optical pulses to study the dynamics of core-excitons at the L2,3 edge of Si in silicon dioxide (SiO2). This attosecond x-ray absorption near-edge spectroscopy (AXANES) technique enables direct probing of the excitons’ quasiparticle character, tracking of their subfemtosecond relaxation, the measurement of excitonic polarizability, and observation of dark core-excitonic states. Direct measurement and control of core-excitons in solids lay the foundation of x-ray excitonics.

  4. Tunable excitons in bilayer graphene (United States)

    Ju, Long; Wang, Lei; Cao, Ting; Taniguchi, Takashi; Watanabe, Kenji; Louie, Steven G.; Rana, Farhan; Park, Jiwoong; Hone, James; Wang, Feng; McEuen, Paul L.


    Excitons, the bound states of an electron and a hole in a solid material, play a key role in the optical properties of insulators and semiconductors. Here, we report the observation of excitons in bilayer graphene (BLG) using photocurrent spectroscopy of high-quality BLG encapsulated in hexagonal boron nitride. We observed two prominent excitonic resonances with narrow line widths that are tunable from the mid-infrared to the terahertz range. These excitons obey optical selection rules distinct from those in conventional semiconductors and feature an electron pseudospin winding number of 2. An external magnetic field induces a large splitting of the valley excitons, corresponding to a g-factor of about 20. These findings open up opportunities to explore exciton physics with pseudospin texture in electrically tunable graphene systems​.

  5. Exciton dephasing and biexciton binding in CdSe/ZnSe islands

    DEFF Research Database (Denmark)

    Wagner, Hans Peter; Tranitz, H.-P.; Preis, H


    The dephasing of excitons and the formation of biexcitons in self-organized CdSe/ZnSe islands grown by molecular-beam epitaxy is investigated using spectrally resolved four-wave mixing. A distribution of exciton-exciton scattering efficiencies and dephasing times in the range of 0.5-10 ps are obs...... energy slightly increases from 21.5 to 23 meV, while its broadening decreases from 5.5 to 3 meV. This is attributed to a strong three-dimensional confinement with improving shape uniformity for decreasing exciton energy. [S0163-1829(99)04739-6]....

  6. The Molecular Universe from Simple Diatomics to Complex Organics (United States)

    Cecchi-Pestellini, C.


    From distant galaxies to diffuse interstellar matter in our galaxy, from molecular clouds where stars are formed together with protoplanetary disks and planets to comets and meteorites the chemestry displays its whole richness and complexity. I shall present an outline of the ubiquitous presence of molecules in various astrophysical environments.

  7. Fischer and Schrock Carbene Complexes: A Molecular Modeling Exercise (United States)

    Montgomery, Craig D.


    An exercise in molecular modeling that demonstrates the distinctive features of Fischer and Schrock carbene complexes is presented. Semi-empirical calculations (PM3) demonstrate the singlet ground electronic state, restricted rotation about the C-Y bond, the positive charge on the carbon atom, and hence, the electrophilic nature of the Fischer…

  8. The molecular architecture of the nuclear pore complex

    NARCIS (Netherlands)

    Alber, Frank; Dokudovskaya, Svetlana; Veenhoff, Liesbeth M.; Zhang, Wenzhu; Kipper, Julia; Devos, Damien; Suprapto, Adisetyantari; Karni-Schmidt, Orit; Williams, Rosemary; Chait, Brian T.; Sali, Andrej; Rout, Michael P.


    Nuclear pore complexes (NPCs) are proteinaceous assemblies of approximately 50 MDa that selectively transport cargoes across the nuclear envelope. To determine the molecular architecture of the yeast NPC, we collected a diverse set of biophysical and proteomic data, and developed a method for using

  9. Resolving ultrafast exciton migration in organic solids at the nanoscale (United States)

    Penwell, Samuel B.; Ginsberg, Lucas D. S.; Noriega, Rodrigo; Ginsberg, Naomi S.


    Effectiveness of molecular-based light harvesting relies on transport of excitons to charge-transfer sites. Measuring exciton migration, however, has been challenging because of the mismatch between nanoscale migration lengths and the diffraction limit. Instead of using bulk substrate quenching methods, here we define quenching boundaries all-optically with sub-diffraction resolution, thus characterizing spatiotemporal exciton migration on its native nanometre and picosecond scales. By transforming stimulated emission depletion microscopy into a time-resolved ultrafast approach, we measure a 16-nm migration length in poly(2,5-di(hexyloxy)cyanoterephthalylidene) conjugated polymer films. Combined with Monte Carlo exciton hopping simulations, we show that migration in these films is essentially diffusive because intrinsic chromophore energetic disorder is comparable to chromophore inhomogeneous broadening. Our approach will enable previously unattainable correlation of local material structure to exciton migration character, applicable not only to photovoltaic or display-destined organic semiconductors but also to explaining the quintessential exciton migration exhibited in photosynthesis.

  10. Hydroxyflavone metal complexes - molecular structure, antioxidant activity and biological effects. (United States)

    Samsonowicz, Mariola; Regulska, Ewa; Kalinowska, Monika


    High content of hydroxyflavones in fruits, vegetables, cereals and herbs makes them a common component of the human diet. Because of their antioxidant, antiviral, antibacterial, anti-inflammatory, anticancer properties they still pay an attention of many scientific centers. Hydroxyflavones may form complexes with metal cations, and their chelating properties differ significantly depending on the number and position of hydroxyl substituents in the ring. Synthesis of new complexes of hydroxyflavones allows for improvement biological properties, stability, water-solubility, hydrophilicity, bioavailability comparing with the parent hydroxyflavones. It expands the applicability of hydroxyflavones as food additives, diet supplements, preservatives or drug. This paper reviews on the procedures of synthesis of metal complexes with hydroxyflavones, their molecular structure, mode of coordinations, spectroscopic properties and their biological activity. The dependency between the biological activity of these compounds and their molecular structure is discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Exciton dynamics in cuprous oxide

    NARCIS (Netherlands)

    Fishman, D. A.; Revcolevschi, A.; van Loosdrecht, P. H. M.; Stutzmann, M


    This work addresses the mid-infrared properties of cuprous oxide and in particular induced absorption due to the presence of excitons. We probe the population of the non-radiative ground state of para-excitons via laser-induced changes of the transmission in the "hydrogenic" 1s-2p/1s-3p transition

  12. Exciton Formation in Disordered Semiconductors

    DEFF Research Database (Denmark)

    Klochikhin, A.; Reznitsky, A.; Permogorov, S.


    Stationary luminescence spectra of disordered solid solutions can be accounted by the model of localized excitons. Detailed analysis of the long time decay kinetics of luminescence shows that exciton formation in these systems is in great extent due to the bimolecular reaction of separated carrie...

  13. Excitons in solid C60

    Energy Technology Data Exchange (ETDEWEB)

    Shirley, Eric L.; Benedict, Lorin X.; Louie, Steven G.


    Exciton levels in undoped, solid C60 are calculated using a model Hamiltonian. We find excitation energies of 1.58 and 1.30 eV for the lowest singlet and triplet exciton, respectively, in comparison with the measured energies of 1.83 and 1.55 eV. Singlet and triplet states have similar energy diagrams, wherein exciton states having T{sub 2g}, T{sub 1g},G{sub g}, and H{sub g} symmetries are separated by up to several tenths of an electron volt. As a function of crystal momentum, exciton energies exhibit dispersion from 20 to 40 meV. Theoretical pressure derivatives of exciton energies are presented.

  14. Molecular Signatures of Membrane Protein Complexes Underlying Muscular Dystrophy* (United States)

    Turk, Rolf; Hsiao, Jordy J.; Smits, Melinda M.; Ng, Brandon H.; Pospisil, Tyler C.; Jones, Kayla S.; Campbell, Kevin P.; Wright, Michael E.


    Mutations in genes encoding components of the sarcolemmal dystrophin-glycoprotein complex (DGC) are responsible for a large number of muscular dystrophies. As such, molecular dissection of the DGC is expected to both reveal pathological mechanisms, and provides a biological framework for validating new DGC components. Establishment of the molecular composition of plasma-membrane protein complexes has been hampered by a lack of suitable biochemical approaches. Here we present an analytical workflow based upon the principles of protein correlation profiling that has enabled us to model the molecular composition of the DGC in mouse skeletal muscle. We also report our analysis of protein complexes in mice harboring mutations in DGC components. Bioinformatic analyses suggested that cell-adhesion pathways were under the transcriptional control of NFκB in DGC mutant mice, which is a finding that is supported by previous studies that showed NFκB-regulated pathways underlie the pathophysiology of DGC-related muscular dystrophies. Moreover, the bioinformatic analyses suggested that inflammatory and compensatory mechanisms were activated in skeletal muscle of DGC mutant mice. Additionally, this proteomic study provides a molecular framework to refine our understanding of the DGC, identification of protein biomarkers of neuromuscular disease, and pharmacological interrogation of the DGC in adult skeletal muscle PMID:27099343

  15. High molecular weight forms of mammalian respiratory chain complex II.

    Directory of Open Access Journals (Sweden)

    Nikola Kovářová

    Full Text Available Mitochondrial respiratory chain is organised into supramolecular structures that can be preserved in mild detergent solubilisates and resolved by native electrophoretic systems. Supercomplexes of respiratory complexes I, III and IV as well as multimeric forms of ATP synthase are well established. However, the involvement of complex II, linking respiratory chain with tricarboxylic acid cycle, in mitochondrial supercomplexes is questionable. Here we show that digitonin-solubilised complex II quantitatively forms high molecular weight structures (CIIhmw that can be resolved by clear native electrophoresis. CIIhmw structures are enzymatically active and differ in electrophoretic mobility between tissues (500 - over 1000 kDa and cultured cells (400-670 kDa. While their formation is unaffected by isolated defects in other respiratory chain complexes, they are destabilised in mtDNA-depleted, rho0 cells. Molecular interactions responsible for the assembly of CIIhmw are rather weak with the complexes being more stable in tissues than in cultured cells. While electrophoretic studies and immunoprecipitation experiments of CIIhmw do not indicate specific interactions with the respiratory chain complexes I, III or IV or enzymes of the tricarboxylic acid cycle, they point out to a specific interaction between CII and ATP synthase.

  16. Production and sympathetic cooling of complex molecular ions

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Chaobo


    This thesis reports on experimental and theoretical studies of the sympathetic cooling of complex molecular ions demonstrating that this general method for cooling atomic and molecular ions is reliable and efficient. For this purpose, complex molecular ions and barium ions have been confined simultaneously in a linear Paul trap. The complex molecular ions are generated in an electrospray ionization system and transferred to the trap via a 2 m long octopole ion guide. These molecular ions are pre-cooled by room temperature helium buffer gas so that they can be captured by the trap. The atomic barium ions are loaded from a barium evaporator oven and are laser-cooled by a 493 nm cooling laser and a 650 nm repumping laser. Due to the mutual Coulomb interaction among these charged particles, the kinetic energy of the complex molecular ions can be reduced significantly. In our experiments we have demonstrated the sympathetic cooling of various molecules (CO{sub 2}, Alexa Fluor 350, glycyrrhetinic acid, cytochrome c) covering a wide mass range from a few tens to 13000 amu. In every case the molecular ions could be cooled down to millikelvin temperatures. Photo-chemical reactions of the {sup 138}Ba{sup +} ions in the ({sup 2}P{sub 1/2}) excited state with gases such as O{sub 2}, CO{sub 2}, or N{sub 2}O, could be observed. If the initial {sup 138}Ba{sup +} ion ensemble is cold, the produced {sup 138}BaO{sup +} ions are cold as well, with a similar temperature as the laser-cooled barium ions (a few tens of millikelvin). The back-reaction of {sup 138}BaO{sup +} ions with neutral CO to {sup 138}Ba{sup +} is possible and was observed in our experiments as well. A powerful molecular dynamics (MD) simulation program has been developed. With this program dynamic properties of ion ensembles, such as sympathetic interactions or heating effects, have been investigated and experimental results have been analyzed to obtain, for example, ion numbers and temperatures. Additionally, the

  17. Exciton condensation in strongly correlated electron bilayers

    NARCIS (Netherlands)

    Rademaker, Louk; van den Brink, J.; Zaanen, Jan; Hilgenkamp, H.


    We studied the possibility of exciton condensation in Mott insulating bilayers. In these strongly correlated systems, an exciton is the bound state of a double occupied and empty site. In the strong coupling limit, the exciton acts as a hard-core boson. Its physics is captured by the exciton t -J

  18. Counting constituents in molecular complexes by fluorescence photon antibunching

    Energy Technology Data Exchange (ETDEWEB)

    Fore, S; Laurence, T; Hollars, C; Huser, T


    Modern single molecule fluorescence microscopy offers new, highly quantitative ways of studying the systems biology of cells while keeping the cells healthy and alive in their natural environment. In this context, a quantum optical technique, photon antibunching, has found a small niche in the continuously growing applications of single molecule techniques to small molecular complexes. Here, we review some of the most recent applications of photon antibunching in biophotonics, and we provide a guide for how to conduct photon antibunching experiments at the single molecule level by applying techniques borrowed from time-correlated single photon counting. We provide a number of new examples for applications of photon antibunching to the study of multichromophoric molecules and small molecular complexes.

  19. Dephasing and interaction of excitons CdSe/ZnSe islands

    DEFF Research Database (Denmark)

    Wagner, H. P.; Tranitz, H.-P.; Preis, H.


    The dephasing of excitons in self-organized CdSe/ZnSe islands grown by molecular-beam epitaxy is investigated using spectrally resolved four-wave mixing. A distribution of dephasing times is observed, indicating the existence of localized excitons with different relaxation times at comparable tra...... transition energies. Polarization-dependent measurements identify the formation of biexcitons. The observed large biexciton binding energy of 22meV increases with decreasing exciton energy, which is attributed to an increasing three-dimensional confinement.......The dephasing of excitons in self-organized CdSe/ZnSe islands grown by molecular-beam epitaxy is investigated using spectrally resolved four-wave mixing. A distribution of dephasing times is observed, indicating the existence of localized excitons with different relaxation times at comparable...

  20. Editorial on indirect excitons: Physics and applications (United States)


    This special issue contains 9 original review papers, research papers and discussion papers on indirect excitons. An exciton is a Coulomb-correlated electron-hole pair. Frenkel excitons dominate optical properties of organic semiconductors, while Wannier-Mott excitons are responsible for the hydrogen-like absorption spectra of inorganic semiconductors at low temperatures. The interest to the physics of excitons has strongly increased in the new century. This interest is motivated by unique bosonic properties of excitons that lead to the phenomena of exciton-polariton lasing and stimulated scattering, build-up of the spontaneous coherence and polarisation in cold exciton gases. In addition to the rich fundamental physics, excitons offer the perspective of applications in opto-electronic devices such as exciton transistors, switches, optical integrated circuits, etc.

  1. Exciton formation and dissociation in mass-asymmetric electron-hole plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Fehske, H [Institut fuer Physik, Ernst-Moritz-Arndt-Universitaet Greifswald, Domstrasse 10a, D-17489 Greifswald (Germany); Filinov, V [Institute for High Energy Density, Russian Academy of Sciences, Izhorskay 13/19, Moscow 127412 (Russian Federation); Bonitz, M [Christian-Albrechts-Universitaet zu Kiel, Institut fuer Theoretische Physik und Astrophysik, Lehrstuhl Statistische Physik, Leibnizstrasse 15, 24098 Kiel (Germany); Fortov, V [Institute for High Energy Density, Russian Academy of Sciences, Izhorskay 13/19, Moscow 127412 (Russian Federation); Levashov, P [Institute for High Energy Density, Russian Academy of Sciences, Izhorskay 13/19, Moscow 127412 (Russian Federation)


    First-principle path integral Monte Carlo simulations were performed in order to analyze correlation effects in complex electron-hole plasmas, particularly with regard to the appearance of excitonic bound states. Results are discussed in relation to exciton formation in unconventional semiconductors with large electron hole mass asymmetry.

  2. Optics of exciton-plasmon nanomaterials (United States)

    Sukharev, Maxim; Nitzan, Abraham


    This review provides a brief introduction to the physics of coupled exciton-plasmon systems, the theoretical description and experimental manifestation of such phenomena, followed by an account of the state-of-the-art methodology for the numerical simulations of such phenomena and supplemented by a number of FORTRAN codes, by which the interested reader can introduce himself/herself to the practice of such simulations. Applications to CW light scattering as well as transient response and relaxation are described. Particular attention is given to so-called strong coupling limit, where the hybrid exciton-plasmon nature of the system response is strongly expressed. While traditional descriptions of such phenomena usually rely on analysis of the electromagnetic response of inhomogeneous dielectric environments that individually support plasmon and exciton excitations, here we explore also the consequences of a more detailed description of the molecular environment in terms of its quantum density matrix (applied in a mean field approximation level). Such a description makes it possible to account for characteristics that cannot be described by the dielectric response model: the effects of dephasing on the molecular response on one hand, and nonlinear response on the other. It also highlights the still missing important ingredients in the numerical approach, in particular its limitation to a classical description of the radiation field and its reliance on a mean field description of the many-body molecular system. We end our review with an outlook to the near future, where these limitations will be addressed and new novel applications of the numerical approach will be pursued.

  3. Carbon nanotubes as excitonic insulators. (United States)

    Varsano, Daniele; Sorella, Sandro; Sangalli, Davide; Barborini, Matteo; Corni, Stefano; Molinari, Elisa; Rontani, Massimo


    Fifty years ago Walter Kohn speculated that a zero-gap semiconductor might be unstable against the spontaneous generation of excitons-electron-hole pairs bound together by Coulomb attraction. The reconstructed ground state would then open a gap breaking the symmetry of the underlying lattice, a genuine consequence of electronic correlations. Here we show that this excitonic insulator is realized in zero-gap carbon nanotubes by performing first-principles calculations through many-body perturbation theory as well as quantum Monte Carlo. The excitonic order modulates the charge between the two carbon sublattices opening an experimentally observable gap, which scales as the inverse of the tube radius and weakly depends on the axial magnetic field. Our findings call into question the Luttinger liquid paradigm for nanotubes and provide tests to experimentally discriminate between excitonic and Mott insulators.

  4. Excitonic insulator transition in the conjugated polymer polyacene

    NARCIS (Netherlands)

    Rice, MJ; Gartstein, YN


    According to molecular orbital theory, the symmetrically positioned one-dimensional (I-D) conduction and valence bands of polyacene touch at the X point. Clearly, the exciton binding energy of this semimetal exceeds the band gap so that polyacene should be a textbook case of a semimetal undergoing a

  5. Disorder-induced exciton localization and violation of optical selection rules in supramolecular nanotubes

    NARCIS (Netherlands)

    Vlaming, S. M.; Bloemsma, E. A.; Nietiadi, M. Linggarsari; Knoester, J.


    Using numerical simulations, we study the effect of disorder on the optical properties of cylindrical aggregates of molecules with strong excitation transfer interactions. The exciton states and the energy transport properties of such molecular nanotubes attract considerable interest for application

  6. The CaMKII/NMDAR complex as a molecular memory

    Directory of Open Access Journals (Sweden)

    Sanhueza Magdalena


    Full Text Available Abstract CaMKII is a major synaptic protein that is activated during the induction of long-term potentiation (LTP by the Ca2+ influx through NMDARs. This activation is required for LTP induction, but the role of the kinase in the maintenance of LTP is less clear. Elucidating the mechanisms of maintenance may provide insights into the molecular processes that underlie the stability of stored memories. In this brief review, we will outline the criteria for evaluating an LTP maintenance mechanism. The specific hypothesis evaluated is that LTP is maintained by the complex of activated CaMKII with the NMDAR. The evidence in support of this hypothesis is substantial, but further experiments are required, notably to determine the time course and persistence of complex after LTP induction. Additional work is also required to elucidate how the CaMKII/NMDAR complex produces the structural growth of the synapse that underlies late LTP. It has been proposed by Frey and Morris that late LTP involves the setting of a molecular tag during LTP induction, which subsequently allows the activated synapse to capture the proteins responsible for late LTP. However, the molecular processes by which this leads to the structural growth that underlies late LTP are completely unclear. Based on known binding reactions, we suggest the first molecularly specific version of tag/capture hypothesis: that the CaMKII/NMDAR complex, once formed, serves as a tag, which then leads to a binding cascade involving densin, delta-catenin, and N-cadherin (some of which are newly synthesized. Delta-catenin binds AMPA-binding protein (ABP, leading to the LTP-induced increase in AMPA channel content. The addition of postsynaptic N-cadherin, and the complementary increase on the presynaptic side, leads to a trans-synaptically coordinated increase in synapse size (and more release sites. It is suggested that synaptic strength is stored stably through the combined actions of the Ca

  7. Interfacial charge separation and recombination in InP and quasi-type II InP/CdS core/shell quantum dot-molecular acceptor complexes. (United States)

    Wu, Kaifeng; Song, Nianhui; Liu, Zheng; Zhu, Haiming; Rodríguez-Córdoba, William; Lian, Tianquan


    Recent studies of group II-VI colloidal semiconductor heterostuctures, such as CdSe/CdS core/shell quantum dots (QDs) or dot-in-rod nanorods, show that type II and quasi-type II band alignment can facilitate electron transfer and slow down charge recombination in QD-molecular electron acceptor complexes. To explore the general applicability of this wave function engineering approach for controlling charge transfer properties, we investigate exciton relaxation and dissociation dynamics in InP (a group III-V semiconductor) and InP/CdS core/shell (a heterostructure beween group III-V and II-VI semiconductors) QDs by transient absorption spectroscopy. We show that InP/CdS QDs exhibit a quasi-type II band alignment with the 1S electron delocalized throughout the core and shell and the 1S hole confined in the InP core. In InP-methylviologen (MV(2+)) complexes, excitons in the QD can be dissociated by ultrafast electron transfer to MV(2+) from the 1S electron level (with an average time constant of 11.4 ps) as well as 1P and higher electron levels (with a time constant of 0.39 ps), which is followed by charge recombination to regenerate the complex in its ground state (with an average time constant of 47.1 ns). In comparison, InP/CdS-MV(2+) complexes show similar ultrafast charge separation and 5-fold slower charge recombination rates, consistent with the quasi-type II band alignment in these heterostructures. This result demonstrates that wave function engineering in nanoheterostructures of group III-V and II-VI semiconductors provides a promising approach for optimizing their light harvesting and charge separation for solar energy conversion applications.

  8. Clinical and molecular complexity of breast cancer metastases. (United States)

    Kimbung, Siker; Loman, Niklas; Hedenfalk, Ingrid


    Clinical oncology is advancing toward a more personalized treatment orientation, making the need to understand the biology of metastasis increasingly acute. Dissecting the complex molecular, genetic and clinical phenotypes underlying the processes involved in the development of metastatic disease, which remains the principal cause of cancer-related deaths, could lead to the identification of more effective prognostication and targeted approaches to prevent and treat metastases. The past decade has witnessed significant progress in the field of cancer metastasis research. Clinical and technological milestones have been reached which have tremendously enriched our understanding of the complex pathways undertaken by primary tumors to progress into lethal metastases and how some of these processes might be amenable to therapy. The aim of this review article is to highlight the recent advances toward unraveling the clinical and molecular complexity of breast cancer metastases. We focus on genes mediating breast cancer metastases and organ-specific tropism, and discuss gene signatures for prediction of metastatic disease. The challenges of translating this information into clinically applicable tools for improving the prognostication of the metastatic potential of a primary breast tumor, as well as for therapeutic interventions against latent and active metastatic disease are addressed. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. A complex systems approach to computational molecular biology

    Energy Technology Data Exchange (ETDEWEB)

    Lapedes, A. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States)


    We report on the containing research program at Santa Fe Institute that applies complex systems methodology to computational molecular biology. Two aspects are stressed here are the use of co-evolving adaptive neutral networks for determining predictable protein structure classifications, and the use of information theory to elucidate protein structure and function. A ``snapshot`` of the current state of research in these two topics is presented, representing the present state of two major research thrusts in the program of Genetic Data and Sequence Analysis at the Santa Fe Institute.

  10. Scaling laws of Rydberg excitons (United States)

    Heckötter, J.; Freitag, M.; Fröhlich, D.; Aßmann, M.; Bayer, M.; Semina, M. A.; Glazov, M. M.


    Rydberg atoms have attracted considerable interest due to their huge interaction among each other and with external fields. They demonstrate characteristic scaling laws in dependence on the principal quantum number n for features such as the magnetic field for level crossing or the electric field of dissociation. Recently, the observation of excitons in highly excited states has allowed studying Rydberg physics in cuprous oxide crystals. Fundamentally different insights may be expected for Rydberg excitons, as the crystal environment and associated symmetry reduction compared to vacuum give not only optical access to many more states within an exciton multiplet but also extend the Hamiltonian for describing the exciton beyond the hydrogen model. Here we study experimentally and theoretically the scaling of several parameters of Rydberg excitons with n , for some of which we indeed find laws different from those of atoms. For others we find identical scaling laws with n , even though their origin may be distinctly different from the atomic case. At zero field the energy splitting of a particular multiplet n scales as n-3 due to crystal-specific terms in the Hamiltonian, e.g., from the valence band structure. From absorption spectra in magnetic field we find for the first crossing of levels with adjacent principal quantum numbers a Br∝n-4 dependence of the resonance field strength, Br, due to the dominant paramagnetic term unlike for atoms for which the diamagnetic contribution is decisive, resulting in a Br∝n-6 dependence. By contrast, the resonance electric field strength shows a scaling as Er∝n-5 as for Rydberg atoms. Also similar to atoms with the exception of hydrogen we observe anticrossings between states belonging to multiplets with different principal quantum numbers at these resonances. The energy splittings at the avoided crossings scale roughly as n-4, again due to crystal specific features in the exciton Hamiltonian. The data also allow us to

  11. The molecular architecture of the plant nuclear pore complex. (United States)

    Tamura, Kentaro; Hara-Nishimura, Ikuko


    The nucleus contains the cell's genetic material, which directs cellular activity via gene regulation. The physical barrier of the nuclear envelope needs to be permeable to a variety of macromolecules and signals. The most prominent gateways for the transport of macromolecules are the nuclear pore complexes (NPCs). The NPC is the largest multiprotein complex in the cell, and is composed of multiple copies of ~30 different proteins called nucleoporins. Although much progress has been made in dissecting the NPC structure in vertebrates and yeast, the molecular architecture and physiological function of nucleoporins in plants remain poorly understood. In this review, we summarize the current knowledge regarding the plant NPC proteome and address structural and functional aspects of plant nucleoporins, which support the fundamental cellular machinery.

  12. Unequivocal determination of complex molecular structures using anisotropic NMR measurements. (United States)

    Liu, Yizhou; Saurí, Josep; Mevers, Emily; Peczuh, Mark W; Hiemstra, Henk; Clardy, Jon; Martin, Gary E; Williamson, R Thomas


    Assignment of complex molecular structures from nuclear magnetic resonance (NMR) data can be prone to interpretational mistakes. Residual dipolar couplings and residual chemical shift anisotropy provide a spatial view of the relative orientations between bonds and chemical shielding tensors, respectively, regardless of separation. Consequently, these data constitute a reliable reporter of global structural validity. Anisotropic NMR parameters can be used to evaluate investigators' structure proposals or structures generated by computer-assisted structure elucidation. Application of the method to several complex structure assignment problems shows promising results that signal a potential paradigm shift from conventional NMR data interpretation, which may be of particular utility for compounds not amenable to x-ray crystallography. Copyright © 2017, American Association for the Advancement of Science.

  13. Plasmonic, excitonic and exciton-plasmonic photoinduced nanocomposites (United States)

    Bityurin, N.; Ermolaev, N.; Smirnov, A. A.; Afanasiev, A.; Agareva, N.; Koryukina, T.; Bredikhin, V.; Kamensky, V.; Pikulin, A.; Sapogova, N.


    UV irradiation of materials consisting of a polymer matrix that possesses precursors of different kinds can result in creation of nanoparticles within the irradiated domains. Such photoinduced nanocomposites are promising for photonic applications due to the strong alteration of their optical properties compared to initial non-irradiated materials. We report our results on the synthesis and investigation of plasmonic, excitonic and exciton-plasmonic photoinduced nanocomposites. Plasmonic nanocomposites contain metal nanoparticles of noble metals with a pronounced plasmon resonance. Excitonic nanocomposites possess semiconductor nanoclusters (quantum dots). We consider the CdS-Au pair because the luminescent band of CdS nanoparticles enters the plasmon resonance band of gold nanoparticles. The obtaining of such particles within the same composite materials is promising for the creation of media with exciton-plasmon resonance. We demonstrate that it is possible to choose appropriate precursor species to obtain the initially transparent poly(methyl methacrylate) (PMMA) films containing both types of these molecules either separately or together. Proper irradiation of these materials by a light-emitting diode operating at the wavelength of 365 nm provides material alteration demonstrating light-induced optical absorption and photoluminescent properties typical for the corresponding nanoparticles. Thus, an exciton-plasmonic photoinduced nanocomposite is obtained. It is important that here we use the precursors that are different from those usually employed.

  14. Molecular epidemiology of Mycobacterium abscessus complex isolates in Ireland. (United States)

    O'Driscoll, C; Konjek, J; Heym, B; Fitzgibbon, M M; Plant, B J; Ní Chróinín, M; Mullane, D; Lynch-Healy, M; Corcoran, G D; Schaffer, K; Rogers, T R; Prentice, M B


    The Mycobacterium abscessus complex are the rapidly growing mycobacteria (RGM) most commonly causing lung disease, especially in cystic fibrosis (CF) patients. Ireland has the world's highest CF incidence. The molecular epidemiology of M. abscessus complex in Ireland is unreported. We performed rpoB gene sequencing and multi-locus sequence typing (MLST) on M. abscessus complex strains isolated from thirty-six patients in 2006-2012 (eighteen known CF patients). Twenty-eight strains (78%) were M. abscessus subsp. abscessus, eight M. abscessus subsp. massiliense, none were M. abscessus subsp. bolletii. Sequence type 1 (ST1) and ST26 (M. abscessus subsp. abscessus) were commonest. Seven M. abscessus subsp. abscessus STs (25%) were novel (two with novel alleles). Seven M. abscessus subsp. massiliense STs were previously reported (88%), including two ST23, the globally successful clone. In 2012, of 552 CF patients screened, eleven were infected with M. abscessus complex strains (2%). The most prevalent M. abscessus subsp. abscessus and M. abscessus subsp. massiliense strains in Ireland belong to widely-distributed STs, but there is evidence of high M. abscessus subsp. abscessus diversity. Copyright © 2015 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

  15. Structural characterization of polymorphs and molecular complexes of finasteride (United States)

    Wawrzycka, Irena; Stȩpniak, Krystyna; Matyjaszczyk, Sławomir; Kozioł, Anna E.; Lis, Tadeusz; Abboud, Khalil A.


    The molecular structure of finasteride, 17 β-( N-tert-butylcarbamoyl)-4-aza-5 α-androst-1-en-3-one, and structures of three related crystalline forms have been determined by X-ray analysis. The rigid steroid skeleton of the molecule adopts a half-chair/chair/chair/half-chair conformation. Two peptide groups, one cyclic (lactam) in the ring A and a second being a part of the substituent at C17, are the main factors influencing intermolecular contacts. Different hydrogen-bond interactions of these hydrophilic groups are observed in the crystal structures. An infinite ribbon of finasteride molecules is formed between lactam groups in the orthorhombic homomolecular crystal ( 1) obtained from an ethanol solution. The linear molecular complex finasteride-acetic acid ( 1a) is connected by hydrogen bonds between the lactam of finasteride and the carboxyl group of acetic acid. The crystallization from an ethyl acetate solution gives a complex structure of bis-finasteride monohydrate ethyl acetate clathrate ( 1b) with guest molecule disordered in channels. Crystals of a second (monoclinic) finasteride polymorph ( 2) were obtained during thermal decomposition of 1a, and sublimation of 1, 1a and 1b. Two polymorphic forms show different IR spectra.

  16. Submillimeter Array reveals molecular complexity of dying stars (United States)



    The unique capabilities of the Submillimeter Array (SMA) have allowed unprecedented studies of cool evolved stars at submillimeter wavelengths. In particular, the SMA now offers the possibility to image multiple molecular transitions at once, owing to the 32-GHz wide instantaneous bandwidth of SWARM, the SMA’s new correlator. Molecular gas located far and very close to the photosphere of an asymptotic-giant branch (AGB) star, a red supergiant, or a pre-planetary nebula can now be examined in transitions observed simultaneously from a wide range of energy levels. This allows a very detailed quantitative investigation of physical and chemical conditions around these variable objects. Several imaging line surveys have been obtained with the SMA to reveal the beautiful complexity of these evolved systems. The surveys resulted in first submillimeter-wave identifications of molecules of prime astrophysical interest, e.g. of TiO, TiO2, and of rotational transitions at excited vibrational states of CO. An overview of recent SMA observations of cool evolved stars will be given with an emphasize on the interferometric line surveys. We will demonstrate their importance in unraveling the mass-loss phenomena, propagation of shocks in the circumstellar medium, and production of dust at elevated temperatures. The SMA studies of these molecular factories have a direct impact on our understanding of the chemical evolution of the Galaxy and stellar evolution at low and high masses.

  17. Molecular simulations of drug-receptor complexes in anticancer research. (United States)

    Gago, Federico


    Molecular modeling and computer simulation techniques have matured significantly in recent years and proved their value in the study of drug-DNA, drug-DNA-protein, drug-protein and protein-protein interactions. Evolution in this area has gone hand-in-hand with an increased availability of structural data on biological macromolecules, major advances in molecular mechanics force fields and considerable improvements in computer technologies, most significantly processing speeds, multiprocessor programming and data-storage capacity. The information derived from molecular simulations of drug-receptor complexes can be used to extract structural and energetic information that is usually beyond current experimental possibilities, provide independent accounts of experimentally observed behavior, help in the interpretation of biochemical or pharmacological results, and open new avenues for research by posing novel relevant questions that can guide the design of new experiments. As drug-screening tools, ligand- and fragment-docking platforms stand out as powerful techniques that can provide candidate molecules for hit and lead development. This review provides an overall perspective of the main methods and focuses on some selected applications to both classical and novel anticancer targets.

  18. Exciton dynamics in solid-state green fluorescent protein (United States)

    Dietrich, Christof P.; Siegert, Marie; Betzold, Simon; Ohmer, Jürgen; Fischer, Utz; Höfling, Sven


    We study the decay characteristics of Frenkel excitons in solid-state enhanced green fluorescent protein (eGFP) dried from solution. We further monitor the changes of the radiative exciton decay over time by crossing the phase transition from the solved to the solid state. Complex interactions between protonated and deprotonated states in solid-state eGFP can be identified from temperature-dependent and time-resolved fluorescence experiments that further allow the determination of activation energies for each identified process.

  19. Band Gap, Excitons, and Coulomb Interaction in Solid C60

    NARCIS (Netherlands)

    Lof, R.W.; Veenendaal, M.A. van; Jonkman, H.T.; Sawatzky, G.A.; Koopmans, H.


    The band gap of solid C60 is found to be 2.3 ± 0.1 eV. The on-site molecular C60 Coulomb interaction (U) as determined from the KVV C60 Auger spectrum is found to be 1.6 ± 0.2 eV. This value of U is shown to lead to Frenkel-type molecular excitons in the 1.5-2 eV range. These results lead us to

  20. Molecular architecture and mechanism of the anaphase-promoting complex (United States)

    Yang, Jing; McLaughlin, Stephen H.; Barford, David


    The ubiquitination of cell cycle regulatory proteins by the anaphase-promoting complex/cyclosome (APC/C) controls sister chromatid segregation, cytokinesis and the establishment of G1. The APC/C is an unusually large multimeric cullin-RING ligase. Its activity is strictly dependent on regulatory coactivator subunits that promote APC/C – substrate interactions and stimulate its catalytic reaction. Because the structures of many APC/C subunits and their organization within the assembly are unknown, the molecular basis for these processes is poorly understood. Here, from a cryo-EM reconstruction of a human APC/C-coactivator-substrate complex at 7.4 Å resolution, we have determined the complete secondary structural architecture of the complex. With this information we identified protein folds for structurally uncharacterized subunits, and the definitive location of all 20 APC/C subunits within the 1.2 MDa assembly. Comparison with apo APC/C shows that coactivator promotes a profound allosteric transition involving displacement of the cullin-RING catalytic subunits relative to the degron recognition module of coactivator and Apc10. This transition is accompanied by increased flexibility of the cullin-RING subunits and enhanced affinity for UbcH10~ubiquitin, changes which may contribute to coactivator-mediated stimulation of APC/C E3 ligase activity. PMID:25043029

  1. Mapping the Orion Molecular Cloud Complex in Radio Frequencies (United States)

    Castelaz, Michael W.; Lemly, C.


    The purpose of this research project was to create a large-scale intensity map of the Orion Molecular Cloud Complex at a radio frequency of 1420 MHz. A mapping frequency of 1420 MHz was chosen because neutral hydrogen, which is the primary component of the Orion Molecular Complex, naturally emits radio waves at this frequency. The radio spectral data for this project were gathered using a 4.6-m radio telescope whose spectrometer was tuned to 1420 MHz and whose beam width was 2.7 degrees. The map created for this project consisted of an eight-by-eight grid centered on M42 spanning 21.6 degrees per side. The grid consisted of 64 individual squares spanning 2.7 degrees per side (corresponding to the beam width of the telescope). Radio spectra were recorded for each of these individual squares at an IF gain of 18. Each spectrum consisted of intensity on an arbitrary scale from 0 to 10 plotted as a function frequencies ranging from -400 kHz to +100 kHz around the origin of 1420 MHz. The data from all 64 radio spectra were imported into Wolfram Alpha, which was used to fit Gaussian functions to the data. The peak intensity and the frequency at which this peak intensity occurs could then be extracted from the Gaussian functions. Other helpful quantities that could be calculated from the Gaussian functions include flux (integral of Gaussian function over frequency range), average value of intensity (flux integral divided by frequency range), and half maximum of intensity. Because all of the radio spectra were redshifted, the velocities of the hydrogen gas clouds of the Orion Molecular Cloud Complex could be calculated using the Doppler equation. The data extracted from the Gaussian functions were then imported into Mathcad to create 2D grayscale maps with right ascension (RA) on the x-axis, declination on the y-axis, and intensity (or flux, etc.) represented on a scale from black to white (with white representing the highest intensities). These 2D maps were then imported

  2. Interwell excitons in GaAs superlattices

    DEFF Research Database (Denmark)

    Birkedal, Dan; Sayed, Karim El; Sanders, G.


    The formation of spatially indirect excitons in superlattices with narrow minibands is investigated experimentally. The interwell exciton is similar to the first Wannier-Stark localized exciton of an electrically biased superlattice. However, in the present case the localization is mediated by th...

  3. Molecular model for annihilation rates in positron complexes

    Energy Technology Data Exchange (ETDEWEB)

    Assafrao, Denise [Laboratorio de Atomos e Moleculas Especiais, Departamento de Fisica, ICEx, Universidade Federal de Minas Gerais, P.O. Box 702, 30123-970 Belo Horizonte, MG (Brazil); Department of Applied Mathematics and Theoretical Physics, Queen' s University of Belfast, Belfast BT7 1NN, Northern Ireland (United Kingdom); Walters, H.R. James [Department of Applied Mathematics and Theoretical Physics, Queen' s University of Belfast, Belfast BT7 1NN, Northern Ireland (United Kingdom); Mohallem, Jose R. [Laboratorio de Atomos e Moleculas Especiais, Departamento de Fisica, ICEx, Universidade Federal de Minas Gerais, P.O. Box 702, 30123-970 Belo Horizonte, MG (Brazil); Department of Applied Mathematics and Theoretical Physics, Queen' s University of Belfast, Belfast BT7 1NN, Northern Ireland (United Kingdom)], E-mail:


    The molecular approach for positron interaction with atoms is developed further. Potential energy curves for positron motion are obtained. Two procedures accounting for the nonadiabatic effective positron mass are introduced for calculating annihilation rate constants. The first one takes the bound-state energy eigenvalue as an input parameter. The second is a self-contained and self-consistent procedure. The methods are tested with quite different states of the small complexes HPs, e{sup +}He (electronic triplet) and e{sup +}Be (electronic singlet and triplet). For states yielding the positronium cluster, the annihilation rates are quite stable, irrespective of the accuracy in binding energies. For the e{sup +}Be states, annihilation rates are larger and more consistent with qualitative predictions than previously reported ones.

  4. Lanthanide Complexes in Molecular Magnetic Resonance Imaging and Theranostics. (United States)

    Lacerda, Sara; Tóth, Éva


    Lanthanide complexes have attracted much attention in the biomedical field, and today various imaging applications make use of their versatile magnetic and luminescence properties. In this minireview, we give insight into the mechanistic aspects that allow modulation of the relaxation or chemical exchange saturation transfer (CEST) features, and thus the magnetic resonance imaging (MRI) efficiency of paramagnetic lanthanide chelates in order to create agents that are capable of providing an MRI response as a function of a specific biomarker. We focus on the detection of neurotransmitters, enzymatic activities, and amyloid peptides. We also describe two selected theranostic strategies: 1) a novel approach directed at monitoring drug release from liponanoparticles and 2) molecular or nanoparticle probes for the MRI visualization of photosensitizer delivery in photodynamic therapy. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.


    Energy Technology Data Exchange (ETDEWEB)

    Athanassios Z. Panagiotopoulos


    The general area of this project was the development and application of novel molecular simulation methods for prediction of thermodynamic and structural properties of complex polymeric, surfactant and ionic fluids. Over this project period, we have made considerable progress in developing novel algorithms to meet the computational challenges presented by the strong or long-range interactions in these systems and have generated data for well-defined mod-els that can be used to test theories and compare to experimental data. Overall, 42 archival papers and many invited and contributed presentations and lectures have been based on work supported by this project. 6 PhD, 1 M.S. and 2 postdoctoral students have been associated with this work, as listed in the body of the report.

  6. Conserved Molecular Mechanisms Underlying Homeostasis of the Golgi Complex

    Directory of Open Access Journals (Sweden)

    Cathal Wilson


    Full Text Available The Golgi complex performs a central function in the secretory pathway in the sorting and sequential processing of a large number of proteins destined for other endomembrane organelles, the plasma membrane, or secretion from the cell, in addition to lipid metabolism and signaling. The Golgi apparatus can be regarded as a self-organizing system that maintains a relatively stable morphofunctional organization in the face of an enormous flux of lipids and proteins. A large number of the molecular players that operate in these processes have been identified, their functions and interactions defined, but there is still debate about many aspects that regulate protein trafficking and, in particular, the maintenance of these highly dynamic structures and processes. Here, we consider how an evolutionarily conserved underlying mechanism based on retrograde trafficking that uses lipids, COPI, SNAREs, and tethers could maintain such a homeodynamic system.

  7. Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase

    Directory of Open Access Journals (Sweden)

    Beata Szefler


    Full Text Available Glucose oxidase (GOx is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H2O2. GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI. The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD study of the PEI ligand (C14N8_07_B22 and the GOx enzyme (3QVR was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1 of −5.8 kcal/mol and (LIG2 of −4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1 and on its surface (LIG2 were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase.

  8. Molecular recognition in complexes of TRF proteins with telomeric DNA.

    Directory of Open Access Journals (Sweden)

    Miłosz Wieczór

    Full Text Available Telomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1 and TRF2. These two homologous proteins are therefore essential for the formation and normal function of telomeres. Indeed, TRF1 and TRF2 are implicated in a plethora of different cellular functions and their depletion leads to telomere dysfunction with chromosomal fusions, followed by apoptotic cell death. More specifically, it was found that TRF1 acts as a negative regulator of telomere length, and TRF2 is involved in stabilizing the loop structure. Consequently, these proteins are of great interest, not only because of their key role in telomere maintenance and stability, but also as potential drug targets. In the current study, we investigated the molecular basis of telomeric sequence recognition by TRF1 and TRF2 and their DNA binding mechanism. We used molecular dynamics (MD to calculate the free energy profiles for binding of TRFs to telomeric DNA. We found that the predicted binding free energies were in good agreement with experimental data. Further, different molecular determinants of binding, such as binding enthalpies and entropies, the hydrogen bonding pattern and changes in surface area, were analyzed to decompose and examine the overall binding free energies at the structural level. With this approach, we were able to draw conclusions regarding the consecutive stages of sequence-specific association, and propose a novel aspartate-dependent mechanism of sequence recognition. Finally, our work demonstrates the applicability of computational MD-based methods to studying protein-DNA interactions.

  9. Molecular paleontology and complexity in the last eukaryotic common ancestor. (United States)

    Koumandou, V Lila; Wickstead, Bill; Ginger, Michael L; van der Giezen, Mark; Dacks, Joel B; Field, Mark C


    Eukaryogenesis, the origin of the eukaryotic cell, represents one of the fundamental evolutionary transitions in the history of life on earth. This event, which is estimated to have occurred over one billion years ago, remains rather poorly understood. While some well-validated examples of fossil microbial eukaryotes for this time frame have been described, these can provide only basic morphology and the molecular machinery present in these organisms has remained unknown. Complete and partial genomic information has begun to fill this gap, and is being used to trace proteins and cellular traits to their roots and to provide unprecedented levels of resolution of structures, metabolic pathways and capabilities of organisms at these earliest points within the eukaryotic lineage. This is essentially allowing a molecular paleontology. What has emerged from these studies is spectacular cellular complexity prior to expansion of the eukaryotic lineages. Multiple reconstructed cellular systems indicate a very sophisticated biology, which by implication arose following the initial eukaryogenesis event but prior to eukaryotic radiation and provides a challenge in terms of explaining how these early eukaryotes arose and in understanding how they lived. Here, we provide brief overviews of several cellular systems and the major emerging conclusions, together with predictions for subsequent directions in evolution leading to extant taxa. We also consider what these reconstructions suggest about the life styles and capabilities of these earliest eukaryotes and the period of evolution between the radiation of eukaryotes and the eukaryogenesis event itself.

  10. Hunting complex differential gene interaction patterns across molecular contexts. (United States)

    Song, Mingzhou; Zhang, Yang; Katzaroff, Alexia J; Edgar, Bruce A; Buttitta, Laura


    Heterogeneity in genetic networks across different signaling molecular contexts can suggest molecular regulatory mechanisms. Here we describe a comparative chi-square analysis (CPχ(2)) method, considerably more flexible and effective than other alternatives, to screen large gene expression data sets for conserved and differential interactions. CPχ(2) decomposes interactions across conditions to assess homogeneity and heterogeneity. Theoretically, we prove an asymptotic chi-square null distribution for the interaction heterogeneity statistic. Empirically, on synthetic yeast cell cycle data, CPχ(2) achieved much higher statistical power in detecting differential networks than alternative approaches. We applied CPχ(2) to Drosophila melanogaster wing gene expression arrays collected under normal conditions, and conditions with overexpressed E2F and Cabut, two transcription factor complexes that promote ectopic cell cycling. The resulting differential networks suggest a mechanism by which E2F and Cabut regulate distinct gene interactions, while still sharing a small core network. Thus, CPχ(2) is sensitive in detecting network rewiring, useful in comparing related biological systems.

  11. Molecular Genotype Identification of Different Chickens: Major Histocompatibility Complex

    Directory of Open Access Journals (Sweden)

    Hongzhi Wang


    Full Text Available Chicken is a main poultry in China. Molecular breeding for disease resistance plays an important role in the control of diseases, especially infectious diseases. Choice of genes for disease resistance is the key technology of molecular breeding. The major histocompatibility complex (MHC is of great interest to poultry breeding scientists for its extraordinary polymorphism and close relation with traits of resistance against infectious diseases. The MHC-B haplotype plays an important role in the study of disease resistance in chicken. The traditional chicken MHC-B haplotype is commonly defined by serologic reactions of erythrocytes and the majority of studies have been conducted in Leghorn and broiler but study about other chicken breeds is little. In this study, firstly, the microsatellite marker LEI0258 which is located within the MHC was sequenced by using target sequence capture assay in different chicken breeds, and then according to the number of repeated structures and polymorphic sequences in microsatellite, sequence information for the region defined by LEI0258 was obtained for different haplotypes. Afterwards, we identified the relation between MHC-B haplotypes and disease resistance. Collectively, these observed results provided the reference data for disease-resistant breeding association with blood type and for further study of MHC gene function in poultry.

  12. Bosonic cascades of indirect excitons (United States)

    Nalitov, A. V.; De Liberato, S.; Lagoudakis, P.; Savvidis, P. G.; Kavokin, A. V.


    Recently, the concept of the terahertz bosonic cascade laser (BCL) based on a parabolic quantum well (PQW) embedded in a microcavity was proposed. We refine this proposal by suggesting transitions between indirect exciton (IX) states as a source of terahertz emission. We explicitly propose a structure containing a narrow-square QW and a wide-parabolic QW for the realisation of a bosonic cascade. Advantages of this type of structures are in large dipole matrix elements for terahertz transitions and in long exciton radiative lifetimes which are crucial for realisation of threshold and quantum efficiency BCLs.

  13. Proposal of highly efficient photoemitter with strong photon-harvesting capability and exciton superradiance (United States)

    Matsuda, Takuya; Ishihara, Hajime


    We propose a system of highly efficient photoemitters comprising metal-molecule multilayered structures. In the proposed structure, the absorption in the molecular layer is greatly enhanced through quantum interference between the split modes arising from the coupling of the layered excitons and the plasmons sustained by the metal layer. Furthermore, the large interaction volume between surface plasmons and excitons causes exciton superradiance, which results in the extremely efficient photoemission. This finding indicates the possibility of designing highly efficient photoemitters based on simple layered structures.

  14. Dynamic Control of Plasmon-Exciton Coupling in Au Nanodisk–J-Aggregate Hybrid Nanostructure Arrays

    KAUST Repository

    Zheng, Yue Bing


    We report the dynamic control of plasmon-exciton coupling in Au nanodisk arrays adsorbed with J-aggregate molecules by incident angle of light. The angle-resolved spectra of an array of bare Au nanodisks exhibit continuous shifting of localized surface plasmon resonances. This characteristic enables the production of real-time, controllable spectral overlaps between molecular and plasmonic resonances, and the efficient measurement of plasmon-exciton coupling as a function of wavelength with one or fewer nanodisk arrays. Experimental observations of varying plasmon-exciton coupling match with coupled dipole approximation calculations.

  15. Molecular Analyzer for Complex Refractory Organic-Rich Surfaces (MACROS) (United States)

    Getty, Stephanie A.; Cook, Jamie E.; Balvin, Manuel; Brinckerhoff, William B.; Li, Xiang; Grubisic, Andrej; Cornish, Timothy; Ferrance, Jerome; Southard, Adrian


    The Molecular Analyzer for Complex Refractory Organic-rich Surfaces, MACROS, is a novel instrument package being developed at NASA Goddard Space Flight Center. MACROS enables the in situ characterization of a sample's composition by coupling two powerful techniques into one compact instrument package: (1) laser desorption/ionization time-of-flight mass spectrometry (LDMS) for broad detection of inorganic mineral composition and non-volatile organics, and (2) liquid-phase extraction methods to gently isolate the soluble organic and inorganic fraction of a planetary powder for enrichment and detailed analysis by liquid chromatographic separation coupled to LDMS. The LDMS is capable of positive and negative ion detection, precision mass selection, and fragment analysis. Two modes are included for LDMS: single laser LDMS as the broad survey mode and two step laser mass spectrometry (L2MS). The liquid-phase extraction will be done in a newly designed extraction module (EM) prototype, providing selectivity in the analysis of a complex sample. For the sample collection, a diamond drill front end will be used to collect rock/icy powder. With all these components and capabilities together, MACROS offers a versatile analytical instrument for a mission targeting an icy moon, carbonaceous asteroid, or comet, to fully characterize the surface composition and advance our understanding of the chemical inventory present on that body.

  16. Exciton Localization in Extended {\\pi}-electron Systems: Comparison of Linear and Cyclic Structures

    CERN Document Server

    Thiessen, Alexander; Jester, Stefan-S; Aggarwal, A Vikas; Idelson, Alissa; Bange, Sebastian; Vogelsang, Jan; Höger, Sigurd; Lupton, John M


    We employ five {\\pi}-conjugated model materials of different molecular shape --- oligomers and cyclic structures --- to investigate the extent of exciton self-trapping and torsional motion of the molecular framework following optical excitation. Our studies combine steady-state and transient fluorescence spectroscopy in the ensemble with measurements of polarization anisotropy on single molecules, supported by Monte Carlo simulations. The dimer exhibits a significant spectral red-shift within $\\sim$ 100 ps after photoexcitation which is attributed to torsional relaxation. This relaxation mechanism is inhibited in the structurally rigid macrocyclic analogue. However, both systems show a high degree of exciton localization but with very different consequences: while in the macrocycle the exciton localizes randomly on different parts of the ring, scrambling polarization memory, in the dimer, localization leads to a deterministic exciton position with luminescence characteristics of a dipole. Monte Carlo simulati...

  17. Exciton size and quantum transport in nanoplatelets

    Energy Technology Data Exchange (ETDEWEB)

    Pelzer, Kenley M., E-mail:; Gray, Stephen K. [Center for Nanoscale Materials, Argonne National Laboratory, 9700 Cass Ave., Argonne, Illinois 60439 (United States); Darling, Seth B. [Center for Nanoscale Materials, Argonne National Laboratory, 9700 Cass Ave., Argonne, Illinois 60439 (United States); Institute for Molecular Engineering, University of Chicago, 5747 S. Ellis Ave., Chicago, Illinois 60637 (United States); Schaller, Richard D. [Center for Nanoscale Materials, Argonne National Laboratory, 9700 Cass Ave., Argonne, Illinois 60439 (United States); Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208 (United States)


    Two-dimensional nanoplatelets (NPLs) are an exciting class of materials with promising optical and energy transport properties. The possibility of efficient energy transport between nanoplatelets raises questions regarding the nature of energy transfer in these thin, laterally extended systems. A challenge in understanding exciton transport is the uncertainty regarding the size of the exciton. Depending on the material and defects in the nanoplatelet, an exciton could plausibly extend over an entire plate or localize to a small region. The variation in possible exciton sizes raises the question how exciton size impacts the efficiency of transport between nanoplatelet structures. Here, we explore this issue using a quantum master equation approach. This method goes beyond the assumptions of Förster theory to allow for quantum mechanical effects that could increase energy transfer efficiency. The model is extremely flexible in describing different systems, allowing us to test the effect of varying the spatial extent of the exciton. We first discuss qualitative aspects of the relationship between exciton size and transport and then conduct simulations of exciton transport between NPLs for a range of exciton sizes and environmental conditions. Our results reveal that exciton size has a strong effect on energy transfer efficiency and suggest that manipulation of exciton size may be useful in designing NPLs for energy transport.

  18. Magnetic exciton dispersion in praseodymium

    DEFF Research Database (Denmark)

    Rainford, B. D.; Houmann, Jens Christian Gylden


    Measurements of the dispersion of magnetic excitons have been made in a single crystal of praseodymium metal using inelastic neutron scattering. A preliminary analysis of the data yields the first detailed information about the exchange interactions and the crystal field splittings in the light...

  19. Imaging heterogeneous ultrafast exciton dynamics in organic semiconducting thin films (United States)

    Ginsberg, Naomi S.


    In solid state semiconducting molecular materials used in electro-optical applications, relatively long exciton diffusion lengths hold the promise to boost device performance by relaxing proximity constraints on the locations for light absorption and interfacial charge separation. The architecture of such materials determines their optical and electronic properties as a result of spacing- and orientation-dependent Coulomb couplings between adjacent molecules. Exciton character and dynamics are generally inferred from bulk optical measurements, which can present a severe limitation on our understanding of these films because their constituent molecules are not perfectly ordered. Rather, films of small organic molecules are composed of multiple microcrystalline domains, and this deposition-dependent microstructure can have profound impacts on transport properties. Using ultrafast transient absorption microscopy, we track the time evolution of excitons, domain by domain, in solid state thin films of TIPS-pentacene, a small soluble molecule that has recently been used in organic semiconducting devices because of its high hole mobility. The results from this spatially-resolved nonlinear optical spectroscopy support our hypothesis that bulk optical measurements deleteriously average over heterogeneities in both spatial and electronic structure; we have revealed significant inhomogeneity in exciton dynamics. Domains that appear homogeneous in linear optical microscopy are shown to have spatial variation and defects, and notable differences in exciton character and behavior are observed at domain boundaries. To interpret the contrast we observe with ultrafast dynamics, we correlate our data to local linear absorption, polarization analysis, profilometry, and atomic force microscopy. With this combined approach, we aim to ultimately understand fundamental structure-function relationship in molecular materials to provide predictive power to material development and device

  20. Disassembled DJ-1 high molecular weight complex in cortex mitochondria from Parkinson's disease patients

    Directory of Open Access Journals (Sweden)

    Adler Charles


    Full Text Available Abstract Correction to Nural H, He P, Beach T, Sue L, Xia W, Shen Y. Disassembled DJ-1 high molecular weight complex in cortex mitochondria from Parkinson's disease patients Molecular Neurodegeneration 2009, 4:23.

  1. Synthetic Control of Exciton Behavior in Colloidal Quantum Dots. (United States)

    Pu, Chaodan; Qin, Haiyan; Gao, Yuan; Zhou, Jianhai; Wang, Peng; Peng, Xiaogang


    Colloidal quantum dots are promising optical and optoelectronic materials for various applications, whose performance is dominated by their excited-state properties. This article illustrates synthetic control of their excited states. Description of the excited states of quantum-dot emitters can be centered around exciton. We shall discuss that, different from conventional molecular emitters, ground-state structures of quantum dots are not necessarily correlated with their excited states. Synthetic control of exciton behavior heavily relies on convenient and affordable monitoring tools. For synthetic development of ideal optical and optoelectronic emitters, the key process is decay of band-edge excitons, which renders transient photoluminescence as important monitoring tool. On the basis of extensive synthetic developments in the past 20-30 years, synthetic control of exciton behavior implies surface engineering of quantum dots, including surface cation/anion stoichiometry, organic ligands, inorganic epitaxial shells, etc. For phosphors based on quantum dots doped with transition metal ions, concentration and location of the dopant ions within a nanocrystal lattice are found to be as important as control of the surface states in order to obtain bright dopant emission with monoexponential yet tunable photoluminescence decay dynamics.

  2. Lifetimes and stabilities of familiar explosives molecular adduct complexes during ion mobility measurements (United States)

    McKenzie, Alan; DeBord, John Daniel; Ridgeway, Mark; Park, Melvin; Eiceman, Gary; Fernandez-Lima, Francisco


    Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) was utilized for the separation and identification of familiar explosives in complex mixtures. For the first time, molecular adduct complex lifetimes, relative stability, binding energies and candidate structures are reported for familiar explosives. Experimental and theoretical results showed that the adduct size and reactivity, complex binding energy and the explosive structure tailors the stability of the molecular adduct complex. TIMS flexibility to adapt the mobility separation as a function of the molecular adduct complex stability (i.e., short or long IMS experiments / low or high IMS resolution) permits targeted measurements of explosives in complex mixtures with higher confidence levels. PMID:26153567

  3. Sporothrix schenckii complex in Iran: Molecular identification and antifungal susceptibility. (United States)

    Mahmoudi, Shahram; Zaini, Farideh; Kordbacheh, Parivash; Safara, Mahin; Heidari, Mansour


    Sporotrichosis is a global subcutaneous fungal infection caused by the Sporothrix schenckii complex. Sporotrichosis is an uncommon infection in Iran, and there have been no phenotypic, molecular typing or antifungal susceptibility studies of Sporothrix species. This study aimed to identify nine Iranian isolates of the S. schenckii complex to the species level using colony morphology, carbohydrate assimilation tests, and PCR-sequencing of the calmodulin gene. The antifungal susceptibilities of these Sporothrix isolates to five antifungal agents (amphotericin B (AMB), voriconazole (VRC), itraconazole (ITC), fluconazole (FLC), and terbinafine (TRB)) were also evaluated according to the M27-A3 and M38-A2 protocols of the Clinical and Laboratory Standards Institute for yeast and mycelial phases, respectively. Five of seven clinical isolates were identified as S. schenckii, and two clinical and two environmental isolates were identified as S. globosa. This is the first report of S. globosa in Iran. There was significant agreement (73%) between the results of the phenotypic and genotypic identification methods. TRB and ITC were the most effective antifungals against the Sporothrix isolates. The minimum inhibitory concentration (MIC) values of TRB for the yeast and mycelial phases of S. schenckii differed significantly. There was also a significant difference in the minimum fungicidal concentration (MFC) values of AMB and TRB for the two phases. Considering the low efficacy of VRC and FLC and the wide MIC ranges of AMB (1-16 μg/ml and 1-8 μg/ml for yeast and mycelial forms, respectively) observed in the present study, in vitro antifungal susceptibility testing should be performed to determine appropriate therapeutic regimens. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail:

  4. Low temperature exciton-exciton annihilation in amphi-PIPE J-aggregates

    Directory of Open Access Journals (Sweden)

    C. Spitz


    Full Text Available The mobility of optically excited excitons on J-aggregates can be demonstrated by the phenomena of exciton-exciton annihilation. In this intensity-dependent process the collision of two excitons results in their annihilation and hence in a shortening of the mean excitation lifetime. By measuring the intensity-dependent fluorescent lifetime in contrast to the predicted immobilization of the excitons at low temperature we could prove the excellent mobility of the excitons at a temperature (4K, which is far below their expected freezing point.

  5. Plasmonic band gap engineering of plasmon-exciton coupling. (United States)

    Karademir, Ertugrul; Balci, Sinan; Kocabas, Coskun; Aydinli, Atilla


    Controlling plasmon-exciton coupling through band gap engineering of plasmonic crystals is demonstrated in the Kretschmann configuration. When the flat metal surface is textured with a sinusoidal grating only in one direction, using laser interference lithography, it exhibits a plasmonic band gap because of the Bragg scattering of surface plasmon polaritons on the plasmonic crystals. The contrast of the grating profile determines the observed width of the plasmonic band gap and hence allows engineering of the plasmonic band gap. In this work, resonant coupling between the molecular resonance of a J-aggregate dye and the plasmonic resonance of a textured metal film is extensively studied through plasmonic band gap engineering. Polarization dependent spectroscopic reflection measurements probe the spectral overlap occurring between the molecular resonance and the plasmonic resonance. The results indicate that plasmon-exciton interaction is attenuated in the band gap region along the grating direction.

  6. Mechanistic modeling confronts the complexity of molecular cell biology. (United States)

    Phair, Robert D


    Mechanistic modeling has the potential to transform how cell biologists contend with the inescapable complexity of modern biology. I am a physiologist-electrical engineer-systems biologist who has been working at the level of cell biology for the past 24 years. This perspective aims 1) to convey why we build models, 2) to enumerate the major approaches to modeling and their philosophical differences, 3) to address some recurrent concerns raised by experimentalists, and then 4) to imagine a future in which teams of experimentalists and modelers build-and subject to exhaustive experimental tests-models covering the entire spectrum from molecular cell biology to human pathophysiology. There is, in my view, no technical obstacle to this future, but it will require some plasticity in the biological research mind-set. © 2014 Phair. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (

  7. Molecular differentiation of sibling species in the Galactomyces geotrichum complex. (United States)

    Naumova, E S; Smith MTh; Boekhout, T; de Hoog, G S; Naumov, G I


    PCR-analysis, multilocus enzyme electrophoresis and molecular karyotyping were used to characterize 52 strains belonging to the genus Galactomyces. The resultant data revealed that a PCR method employing the universal primer N21 and microsatellite primer (CAC)5 is appropriate for the distinction of four Ga. geotrichum sibling species, Ga. citri-aurantii and Ga. reessii. Better separation was achieved with the UP primer N21; each species displayed a specific pattern with very low intraspecific variation. We propose to use the primer N21 for the differentiation of the six taxa composing the genus Galactomyces. Multilocus enzyme electrophoresis revealed genetic homogeneity of each sibling species within the Ga. geotrichum complex. On the other hand, the four sibling species, having from 41 to 59% of nDNA homology and similar phenotypic characteristics, are clearly distinguished based on their electrophoretic profiles using two enzymes: mannose-6-phosphate isomerase (MPI) and phosphoglucomutase (PGM). Despite the same number of chromosomal bands, different karyotype patterns were found in Ga. geotrichum sensu stricto and its two sibling species A and B. Within each sibling species, chromosome length polymorphism was observed, in particular for small bands, allowing discrimination to the strain level.

  8. Protein corona - from molecular adsorption to physiological complexity. (United States)

    Treuel, Lennart; Docter, Dominic; Maskos, Michael; Stauber, Roland H


    In biological environments, nanoparticles are enshrouded by a layer of biomolecules, predominantly proteins, mediating its subsequent interactions with cells. Detecting this protein corona, understanding its formation with regards to nanoparticle (NP) and protein properties, and elucidating its biological implications were central aims of bio-related nano-research throughout the past years. Here, we discuss the mechanistic parameters that are involved in the protein corona formation and the consequences of this corona formation for both, the particle, and the protein. We review consequences of corona formation for colloidal stability and discuss the role of functional groups and NP surface functionalities in shaping NP-protein interactions. We also elaborate the recent advances demonstrating the strong involvement of Coulomb-type interactions between NPs and charged patches on the protein surface. Moreover, we discuss novel aspects related to the complexity of the protein corona forming under physiological conditions in full serum. Specifically, we address the relation between particle size and corona composition and the latest findings that help to shed light on temporal evolution of the full serum corona for the first time. Finally, we discuss the most recent advances regarding the molecular-scale mechanistic role of the protein corona in cellular uptake of NPs.

  9. Protein corona – from molecular adsorption to physiological complexity (United States)

    Docter, Dominic; Maskos, Michael


    Summary In biological environments, nanoparticles are enshrouded by a layer of biomolecules, predominantly proteins, mediating its subsequent interactions with cells. Detecting this protein corona, understanding its formation with regards to nanoparticle (NP) and protein properties, and elucidating its biological implications were central aims of bio-related nano-research throughout the past years. Here, we discuss the mechanistic parameters that are involved in the protein corona formation and the consequences of this corona formation for both, the particle, and the protein. We review consequences of corona formation for colloidal stability and discuss the role of functional groups and NP surface functionalities in shaping NP–protein interactions. We also elaborate the recent advances demonstrating the strong involvement of Coulomb-type interactions between NPs and charged patches on the protein surface. Moreover, we discuss novel aspects related to the complexity of the protein corona forming under physiological conditions in full serum. Specifically, we address the relation between particle size and corona composition and the latest findings that help to shed light on temporal evolution of the full serum corona for the first time. Finally, we discuss the most recent advances regarding the molecular-scale mechanistic role of the protein corona in cellular uptake of NPs. PMID:25977856

  10. The Fractal Dimension of the ρ Ophiucus Molecular Cloud Complex (United States)

    Lee, Yongung; Yi, Di; Kim, Y. S.; Jung, J. H.; Kang, H. W.; Lee, C. H.; Yim, I. S.; Kim, H. G.


    We estimate the fractal dimension of the ρ Ophiuchus Molecular Cloud Complex, associated with star forming regions. We selected a cube (v, l, b) database, obtained with J=1-0 transition lines of \\coand tco at a resolution of 22'' using a multibeam receiver system on the 14-m telescope of the Five College Radio Astronomy Observatory. Using a code developed within IRAF, we identified slice-clouds with two threshold temperatures to estimate the fractal dimension. With threshold temperatures of 2.25 K (3σ) and 3.75 K (5σ), the fractal dimension of the target cloud is estimated to be D = 1.52-1.54, where P ∝ A^{D/2} , which is larger than previous results. We suggest that the sampling rate (spatial resolution) of observed data must be an important parameter when estimating the fractal dimension, and that narrower or wider dispersion around an arbitrary fit line and the intercepts at NP = 100 should be checked whether they relate to rms noise level or characteristic structure of the target cloud. This issue could be investigated by analysing several high resolution databases with different quality (low or moderate sensitivity).

  11. Protein corona – from molecular adsorption to physiological complexity

    Directory of Open Access Journals (Sweden)

    Lennart Treuel


    Full Text Available In biological environments, nanoparticles are enshrouded by a layer of biomolecules, predominantly proteins, mediating its subsequent interactions with cells. Detecting this protein corona, understanding its formation with regards to nanoparticle (NP and protein properties, and elucidating its biological implications were central aims of bio-related nano-research throughout the past years. Here, we discuss the mechanistic parameters that are involved in the protein corona formation and the consequences of this corona formation for both, the particle, and the protein. We review consequences of corona formation for colloidal stability and discuss the role of functional groups and NP surface functionalities in shaping NP–protein interactions. We also elaborate the recent advances demonstrating the strong involvement of Coulomb-type interactions between NPs and charged patches on the protein surface. Moreover, we discuss novel aspects related to the complexity of the protein corona forming under physiological conditions in full serum. Specifically, we address the relation between particle size and corona composition and the latest findings that help to shed light on temporal evolution of the full serum corona for the first time. Finally, we discuss the most recent advances regarding the molecular-scale mechanistic role of the protein corona in cellular uptake of NPs.

  12. Molecular Dynamics of Mouse Acetylcholinesterase Complexed with Huperzine A

    Energy Technology Data Exchange (ETDEWEB)

    Tara, Sylvia; Helms, Volkhard H.; Straatsma, TP; Mccammon, J Andrew A.


    Two molecular dynamics simulations were performed for a modeled complex of mouse acetylcholinesterase liganded with huperzine A (HupA). Analysis of these simulations shows that HupA shifts in the active site toward Tyr 337 and Phe 338, and that several residues in the active site area reach out to make hydrogen bonds with the inhibitor. Rapid fluctuations of the gorge width are observed, ranging from widths that allow substrate access to the active site, to pinched structures that do not allow access of molecules as small as water. Additional openings or channels to the active site are found. One opening is formed in the side wall of the active site gorge by residues Val 73, Asp 74, Thr 83, Glu 84, and Asn 87. Another opening is formed at the base of the gorge by residues Trp 86, Val 132, Glu 202, Gly 448, and Ile 451. Both of these openings have been observed separately in the Torpedo californica form of the enzyme. These channels could allow transport of waters and ions to and from the bulk solution.

  13. Spatially indirect excitons in coupled quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Lai, Chih-Wei Eddy [Univ. of California, Berkeley, CA (United States)


    Microscopic quantum phenomena such as interference or phase coherence between different quantum states are rarely manifest in macroscopic systems due to a lack of significant correlation between different states. An exciton system is one candidate for observation of possible quantum collective effects. In the dilute limit, excitons in semiconductors behave as bosons and are expected to undergo Bose-Einstein condensation (BEC) at a temperature several orders of magnitude higher than for atomic BEC because of their light mass. Furthermore, well-developed modern semiconductor technologies offer flexible manipulations of an exciton system. Realization of BEC in solid-state systems can thus provide new opportunities for macroscopic quantum coherence research. In semiconductor coupled quantum wells (CQW) under across-well static electric field, excitons exist as separately confined electron-hole pairs. These spatially indirect excitons exhibit a radiative recombination time much longer than their thermal relaxation time a unique feature in direct band gap semiconductor based structures. Their mutual repulsive dipole interaction further stabilizes the exciton system at low temperature and screens in-plane disorder more effectively. All these features make indirect excitons in CQW a promising system to search for quantum collective effects. Properties of indirect excitons in CQW have been analyzed and investigated extensively. The experimental results based on time-integrated or time-resolved spatially-resolved photoluminescence (PL) spectroscopy and imaging are reported in two categories. (i) Generic indirect exciton systems: general properties of indirect excitons such as the dependence of exciton energy and lifetime on electric fields and densities were examined. (ii) Quasi-two-dimensional confined exciton systems: highly statistically degenerate exciton systems containing more than tens of thousands of excitons within areas as small as (10 micrometer)2 were

  14. Molecular species delimitation in the Racomitrium canescens complex (Grimmiaceae and implications for DNA barcoding of species complexes in mosses.

    Directory of Open Access Journals (Sweden)

    Michael Stech

    Full Text Available In bryophytes a morphological species concept is still most commonly employed, but delimitation of closely related species based on morphological characters is often difficult. Here we test morphological species circumscriptions in a species complex of the moss genus Racomitrium, the R. canescens complex, based on variable DNA sequence markers from the plastid (rps4-trnT-trnL region and nuclear (nrITS genomes. The extensive morphological variability within the complex has led to different opinions about the number of species and intraspecific taxa to be distinguished. Molecular phylogenetic reconstructions allowed to clearly distinguish all eight currently recognised species of the complex plus a ninth species that was inferred to belong to the complex in earlier molecular analyses. The taxonomic significance of intraspecific sequence variation is discussed. The present molecular data do not support the division of the R. canescens complex into two groups of species (subsections or sections. Most morphological characters, albeit being in part difficult to apply, are reliable for species identification in the R. canescens complex. However, misidentification of collections that were morphologically intermediate between species questioned the suitability of leaf shape as diagnostic character. Four partitions of the molecular markers (rps4-trnT, trnT-trnL, ITS1, ITS2 that could potentially be used for molecular species identification (DNA barcoding performed almost equally well concerning amplification and sequencing success. Of these, ITS1 provided the highest species discrimination capacity and should be considered as a DNA barcoding marker for mosses, especially in complexes of closely related species. Molecular species identification should be complemented by redefining morphological characters, to develop a set of easy-to-use molecular and non-molecular identification tools for improving biodiversity assessments and ecological research

  15. Coherent exciton-polariton devices (United States)

    Fraser, Michael D.


    The Bose-Einstein condensate of exciton-polaritons has emerged as a unique, coherent system for the study of non-equilibrium, macroscopically coherent Bose gases, while the full confinement of this coherent state to a semiconductor chip has also generated considerable interest in developing novel applications employing the polariton condensate, possibly even at room temperature. Such devices include low-threshold lasers, precision inertial sensors, and circuits based on superfluidity with ultra-fast non-linear elements. While the demonstration and development of such devices are at an early stage, rapid progress is being made. In this review, an overview of the exciton-polariton condensate system and the established and emerging material systems and fabrication techniques are presented, followed by a critical, in-depth assessment of the ability of the coherent polariton system to deliver on its promise of devices offering either new functionality and/or room-temperature operation.

  16. Analytic derivative couplings and first-principles exciton/phonon coupling constants for an ab initio Frenkel-Davydov exciton model: Theory, implementation, and application to compute triplet exciton mobility parameters for crystalline tetracene (United States)

    Morrison, Adrian F.; Herbert, John M.


    Recently, we introduced an ab initio version of the Frenkel-Davydov exciton model for computing excited-state properties of molecular crystals and aggregates. Within this model, supersystem excited states are approximated as linear combinations of excitations localized on molecular sites, and the electronic Hamiltonian is constructed and diagonalized in a direct-product basis of non-orthogonal configuration state functions computed for isolated fragments. Here, we derive and implement analytic derivative couplings for this model, including nuclear derivatives of the natural transition orbital and symmetric orthogonalization transformations that are part of the approximation. Nuclear derivatives of the exciton Hamiltonian's matrix elements, required in order to compute the nonadiabatic couplings, are equivalent to the "Holstein" and "Peierls" exciton/phonon couplings that are widely discussed in the context of model Hamiltonians for energy and charge transport in organic photovoltaics. As an example, we compute the couplings that modulate triplet exciton transport in crystalline tetracene, which is relevant in the context of carrier diffusion following singlet exciton fission.

  17. Analytic derivative couplings and first-principles exciton/phonon coupling constants for an ab initio Frenkel-Davydov exciton model: Theory, implementation, and application to compute triplet exciton mobility parameters for crystalline tetracene. (United States)

    Morrison, Adrian F; Herbert, John M


    Recently, we introduced an ab initio version of the Frenkel-Davydov exciton model for computing excited-state properties of molecular crystals and aggregates. Within this model, supersystem excited states are approximated as linear combinations of excitations localized on molecular sites, and the electronic Hamiltonian is constructed and diagonalized in a direct-product basis of non-orthogonal configuration state functions computed for isolated fragments. Here, we derive and implement analytic derivative couplings for this model, including nuclear derivatives of the natural transition orbital and symmetric orthogonalization transformations that are part of the approximation. Nuclear derivatives of the exciton Hamiltonian's matrix elements, required in order to compute the nonadiabatic couplings, are equivalent to the "Holstein" and "Peierls" exciton/phonon couplings that are widely discussed in the context of model Hamiltonians for energy and charge transport in organic photovoltaics. As an example, we compute the couplings that modulate triplet exciton transport in crystalline tetracene, which is relevant in the context of carrier diffusion following singlet exciton fission.

  18. Probing the Role of the Eighth Bacteriochlorophyll in holo-FMO Complex by Simulated Two-Dimensional Electronic Spectroscopy

    CERN Document Server

    Yeh, Shu-Hao


    The Fenna-Matthews-Olson (FMO) protein-pigment complex acts as a molecular wire between the outer antenna system and the reaction center (RC); it is an important model system to study the excitonic energy transfer. Recent crystallographic studies report the existence of an additional (eighth) bacteriochlorophyll a (BChl a). To understand the functionality of this eighth BChl, we simulated the two-dimensional electronic spectra of both the 7-site (apo form) and the 8-site (holo form) variant of the FMO complex from green sulfur bacteria, Prosthecochloris aestuarii. By comparing the difference between the spectrum, it was found that the eighth BChl can affect two different excitonic energy transfer pathways, these being: (1) directly involve in the first pathway 6 $\\rightarrow$ 3 $\\rightarrow$ 1 of the apo form model by passing the excitonic energy to exciton 6; and (2) increase the excitonic wave function overlap between excitons 4 and 5 in the second pathway (7 $\\rightarrow$ 4,5 $\\rightarrow$ 2 $\\rightarrow$ ...

  19. Cleavage and formation of molecular dinitrogen in a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine. (United States)

    Miyazaki, Takamasa; Tanaka, Hiromasa; Tanabe, Yoshiaki; Yuki, Masahiro; Nakajima, Kazunari; Yoshizawa, Kazunari; Nishibayashi, Yoshiaki


    The N≡N bond of molecular dinitrogen bridging two molybdenum atoms in the pentamethylcyclopentadienyl molybdenum complexes that bear ferrocenyldiphosphine as an auxiliary ligand is homolytically cleaved under visible light irradiation at room temperature to afford two molar molybdenum nitride complexes. Conversely, the bridging molecular dinitrogen is reformed by the oxidation of the molybdenum nitride complex at room temperature. This result provides a successful example of the cleavage and formation of molecular dinitrogen induced by a pair of two different external stimuli using a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine under ambient conditions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. The interplay between excitons and trions in a monolayer of MoSe2 (United States)

    Lundt, N.; Cherotchenko, E.; Iff, O.; Fan, X.; Shen, Y.; Bigenwald, P.; Kavokin, A. V.; Höfling, S.; Schneider, C.


    The luminescence and absorption properties of transition metal dichalcogenide monolayers are widely determined by neutral and charged excitonic complexes. Here, we focus on the impact of a free carrier reservoir on the optical properties of excitonic and trionic complexes in a MoSe2 monolayer at cryogenic temperatures. By applying photodoping via a non-resonant pump laser, the electron density can be controlled in our sample, which is directly reflected in the contribution of excitons and trions to the luminescence signal. We find significant shifts of both the exciton and trion energies in the presence of an induced electron gas both in power- and in time evolution (on the second to minute scale) in our photoluminescence spectra. In particular, in the presence of the photo-doped carrier reservoir, we observe that the splitting between excitons and trions can be enhanced by up to 4 meV. This behaviour is phenomenologically explained by an interplay between an increased screening of excitons via electrons in our system and a modification of the Fermi level. We introduce a simple but still quantitative treatment of these effects within a variational approach that takes into account both screening and phase space filling effects.

  1. Influence of exciton-phonons coupling on the exciton binding energy in monolayer transition metal dichalcogenides (United States)

    Wang, Zi-Wu; Li, Wei-Ping; Xiao, Yao; Li, Run-Ze; Li, Zhi-Qing


    We theoretically investigate the correction of exciton binding energy arising from the exciton-optical phonon coupling in monolayer transition metal dichalcogenides (TMDs) using the linear operator and Lee-Low-Pines unitary transformation methods. We take into account not only the exciton coupling with intrinsic longitudinal optical phonon modes but also the surface optical phonon modes induced by polar substrates supporting monolayer TMDs. We find that the exciton binding energies are corrected on a large scale due to these exciton-optical phonon couplings. We discuss the dependences of exciton binding energy on the cut-off wave vector of optical phonon modes, the polarization strength of substrate materials, and the distance between polar substrates and TMDs. These results provide potential explanations for the divergence of the exciton binding energy between the experiment and theory in TMDs.

  2. Charged Frenkel biexcitons in organic molecular crystals

    CERN Document Server

    Agranovich, V M; Kamchatnov, A M


    It is known that the energy of the lowest electronic transition in neutral molecules of anthracene, tetracene and other polyacenes is blue shifted in comparison with the corresponding transition energy in mono-valent molecular ions. This effect in molecular crystal may be responsible for the attraction between molecular (Frenkel) exciton and charge carrier. Due to this attraction the bound state of Frenkel exciton and free charge (charged Frenkel exciton) may be formed. The same mechanism can be responsible for formation of charged biexcitons (bound state of two Frenkel excitons and a charge carrier). Calculations are performed for molecular crystals like tetracene by means of one-dimensional lattice model

  3. Fractal dimension method for exciton in cylindrical GaAs/AlxGa1‑xAs core-shell-cap nanowires (United States)

    Sun, Hui; Wu, Zhenhua; Tian, Qiang


    By use of the fractal dimension method, the binding energies of heavy-hole exciton and light-hole exciton in cylindrical GaAs/AlxGa1‑xAs core-shell-cap nanowire are explored. In this study, the exciton is confined in GaAs shell of the GaAs/AlxGa1‑xAs core-shell-cap nanowire for a given aluminum concentration of x=0.3. The numerical results of heavy-hole exciton binding energy, light-hole exciton binding energy and fractal dimension parameter are worked out as functions of shell width and core radius. It has been shown by the calculated results that heavy-hole exciton binding energy and light-hole exciton binding energy firstly increase and then decrease as the shell width increases. When the core radius increases, both the heavy-hole exciton binding energy and light-hole exciton binding energy increase gradually. Exciton problems in GaAs shell of the cylindrical GaAs/AlxGa1‑xAs core-shell-cap nanowire are solved in a simple manner to avoid complex and lengthy calculations by using the fractal dimension method.

  4. From HAMLET to XAMLET: The molecular complex selectively ...

    African Journals Online (AJOL)

    HAMLET (human α-lactalbumin made lethal to tumor cells) is a complex consisting of decalcinated α-lactalbumin and oleic acid. It has been shown to induce massive cell death in various cancers without serious damage to normal tissues in both in vitro and in vivo experiments. The complexity of the mechanism in the ...

  5. Molecular electrostatic potential analysis of non-covalent complexes

    Indian Academy of Sciences (India)

    PADINJARE VEETIL BIJINA CHERUMUTTATHU H SURESH ... The electronic changes associated with the non-covalent complex formation is monitored in terms of MESP minimum (Vmin) in the free and complexed states of the donor and acceptor molecules as well as in terms ofMESP at the donor and acceptor atoms ...

  6. (Molecular cloning and structural characteristics of the R complex of maize)

    Energy Technology Data Exchange (ETDEWEB)


    Studies on the R complex in Maize continued Progress is discussed in the following areas: Establishing identity of R components and cloning of R components; CO allele origin; molecular organization of R-r complex; NCO allele origin; genetic analysis of R-r complex; studies of the Sn locus and reverse paramutation.

  7. [Molecular cloning and structural characteristics of the R complex of maize]. Annual progress report

    Energy Technology Data Exchange (ETDEWEB)


    Studies on the R complex in Maize continued Progress is discussed in the following areas: Establishing identity of R components and cloning of R components; CO allele origin; molecular organization of R-r complex; NCO allele origin; genetic analysis of R-r complex; studies of the Sn locus and reverse paramutation.

  8. Transient terahertz spectroscopy of excitons and unbound carriers in quasi two-dimensional electron-hole gases

    Energy Technology Data Exchange (ETDEWEB)

    Kaindl, Robert A.; Hagele, D.; Carnahan, M. A.; Chemla, D. S.


    We report a comprehensive experimental study and detailed model analysis of the terahertz (THz) dielectric response and density kinetics of excitons and unbound electron-hole pairs in GaAs quantum wells. A compact expression is given, in absolute units, for the complex-valued THz dielectric function of intra-excitonic transitions between the 1s and higher-energy exciton and continuum levels. It closely describes the THz spectra of resonantly generated excitons. Exciton ionization and formation are further explored, where the THz response exhibits both intra-excitonic and Drude features. Utilizing a two-component dielectric function, we derive the underlying exciton and unbound pair densities. In the ionized state, excellent agreement is found with the Saha thermodynamic equilibrium, which provides experimental verification of the two-component analysis and density scaling. During exciton formation, in turn, the pair kinetics is quantitatively described by a Saha equilibrium that follows the carrier cooling dynamics. The THz-derived kinetics is, moreover, consistent with time-resolved luminescence measured for comparison. Our study establishes a basis for tracking pair densities via transient THz spectroscopy of photoexcited quasi-2D electron-hole gases.

  9. 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: [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)


    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.

  10. Excitonic magnetism in d6 perovskites (United States)

    Afonso, J. Fernández; Kuneš, J.


    We use the LDA+U method to study the possibility of exciton condensation in perovskites of transition metals with the d6 electronic configuration such as LaCoO3. For realistic interaction parameters we find several distinct solutions exhibiting a spin-triplet exciton condensate, which gives rise to a local spin density distribution while the ordered moments are vanishingly small. Rhombohedral distortion from the ideal cubic structure suppresses the ordered state, contrary to the spin-orbit coupling which enhances the excitonic condensation energy. We explain the trends observed in the numerical simulations with the help of a simplified strong-coupling model. Our results indicate that LaCoO3 is close to the excitonic instability and suggest ways how to achieve the exciton condensation.

  11. Non-Markovian quantum jumps in excitonic energy transfer

    Energy Technology Data Exchange (ETDEWEB)

    Rebentrost, Patrick; Chakraborty, Rupak; Aspuru-Guzik, Alan


    We utilize the novel non-Markovian quantum jump (NMQJ) approach to stochastically simulate exciton dynamics derived from a time-convolutionless master equation. For relevant parameters and time scales, the time-dependent, oscillatory decoherence rates can have negative regions, a signature of non-Markovian behavior and of the revival of coherences. This can lead to non-Markovian population beatings for a dimer system at room temperature. We show that strong exciton-phonon coupling to low frequency modes can considerably modify transport properties. We observe increased excitontransport, which can be seen as an extension of recent environment-assisted quantum transport concepts to the non-Markovian regime. Within the NMQJ method, the Fenna–Matthew–Olson protein is investigated as a prototype for larger photosynthetic complexes.

  12. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    Energy Technology Data Exchange (ETDEWEB)

    Nagaoka, Masataka [Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan); Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Honmachi, Kawaguchi 332-0012 (Japan); ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520 (Japan)


    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  13. Mre11-Rad50 complex crystals suggest molecular calisthenics

    NARCIS (Netherlands)

    C. Wyman (Claire); J.H.G. Lebbink (Joyce); R. Kanaar (Roland)


    textabstractRecently published crystal structures of different Mre11 and Rad50 complexes show the arrangement of these proteins and imply dramatic ligand-induced rearrangements with important functional consequences.

  14. Mre11-Rad50 complex crystals suggest molecular calisthenics


    Wyman, Claire; Lebbink, Joyce; Kanaar, Roland


    Recently published crystal structures of different Mre11 and Rad50 complexes show the arrangement of these proteins and imply dramatic ligand-induced rearrangements with important functional consequences.

  15. Atomistic model for excitons: Capturing Strongly Bound Excitons in Monolayer Transition-Metal Dichalcogenides (United States)

    Tseng, Frank; Simsek, Ergun; Gunlycke, Daniel


    Monolayer transition-metal dichalcogenides form a direct bandgap predicted in the visible regime making them attractive host materials for various electronic and optoelectronic applications. Due to a weak dielectric screening in these materials, strongly bound electron-hole pairs or excitons have binding energies up to at least several hundred meV's. While the conventional wisdom is to think of excitons as hydrogen-like quasi-particles, we show that the hydrogen model breaks down for these experimentally observed strongly bound, room-temperature excitons. To capture these non-hydrogen-like photo-excitations, we introduce an atomistic model for excitons that predicts both bright excitons and dark excitons, and their broken degeneracy in these two-dimensional materials. For strongly bound exciton states, the lattice potential significantly distorts the envelope wave functions, which affects predicted exciton peak energies. The combination of large binding energies and non-degeneracy of exciton states in monolayer transition metal dichalogendies may furthermore be exploited in room temperature applications where prolonged exciton lifetimes are necessary. This work has been funded by the Office of Naval Research (ONR), directly and through the Naval Research Laboratory (NRL). F.T and E.S acknowledge support from NRL through the NRC Research Associateship Program and ONR Summer Faculty Program, respectively.

  16. High-resolution overtone spectra of molecular complexes (United States)

    Didriche, K.; Földes, T.


    A high-resolution spectrum of the acetylene-water complex has been recorded in the overtone range. Two bands of C2H2-D2O were analysed, corresponding to the overtone excitations of either the acetylene or the water units. The vibrational shifts and the upper states rotational constants were retrieved, demonstrating that the geometry of the complex is only slightly modified by the excitation. A larger linewidth was observed for the 2CH band than for the 2OD + DOD band, probably due to the direct coupling of the 2CH excitation with the dissociation coordinate.

  17. Molecular dynamic simulation of complex NS2B-NS3 DENV2 ...

    African Journals Online (AJOL)

    In many researches, several models of peptides inhibitor were generated in complexes with the NS2B-NS3 DENV2 protease by performing molecular docking. The goal of this research was to study the interaction of ligands as inhibitors for protein (enzyme) in solvent explicit condition by performing molecular dynamics ...

  18. Molecular dynamic simulation of complex NS2B-NS3 DENV2 ...

    African Journals Online (AJOL)



    Jul 10, 2013 ... many researches, several models of peptides inhibitor were generated in complexes with the NS2B-NS3. DENV2 protease by performing molecular docking. The goal of this research was to study the interaction of ligands as inhibitors for protein (enzyme) in solvent explicit condition by performing molecular ...

  19. Resonant Scattering of Muonic Hydrogen Atoms and Dynamics of the Muonic Molecular Complex

    Energy Technology Data Exchange (ETDEWEB)

    Fujiwara, M. C., E-mail: [University of British Columbia (Canada); Adamczak, A. [Institute Nuclear Physics (Poland); Bailey, J. M. [Chester Technology (United Kingdom); Beer, G. A. [University of Victoria (Canada); Beveridge, J. L. [TRIUMF (Canada); Faifman, M. P. [Kurchatov Institute (Russian Federation); Huber, T. M. [Gustavus Adolphus College (United States); Kammel, P. [University of Illinois at Urbana-Champaign (United States); Kim, S. K. [Jeonbuk National University (Korea, Republic of); Knowles, P. E. [Universite de Fribourg (Switzerland); Kunselman, A. R. [University of Wyoming (United States); Markushin, V. E. [Paul Scherrer Institute (Switzerland); Marshal, G. M. [TRIUMF (Canada); Mason, G. R. [University of Victoria (Canada); Mulhauser, F. [Universite de Fribourg (Switzerland); Olin, A. [TRIUMF (Canada); Petitjean, C. [Paul Scherrer Institute (Switzerland); Porcelli, T. A. [University of Northern British Columbia (Canada); Wozniak, J. [Institute Physics and Nuclear Techniques (Poland); Zmeskal, J. [Austrian Academy of Sciences (Austria)


    Resonant scattering of muonic hydrogen atoms via back decay of the molecular complex, a key process in the understanding of epithermal muonic molecular formation, is analyzed. The limitations of the effective rate approximation are discussed and the importance of the explicit treatment of the back decay is stressed. An expression of the energy distribution for the back-decayed atoms is given.

  20. Modification of the luminescent characteristics belonging to the molecule that interacts with the exciton states of the J-aggregate (United States)

    Ropakova, I. Yu.; Sorokin, A. V.; Zvyagin, A. A.; Malyukin, Yu. V.


    A quantum theory for the light absorption and photoluminescence of a molecule (luminophore) interacting with a J-aggregate linear molecular chain is constructed. It is shown that together with the band states of Frenkel excitons in the molecular chain the contribution to light absorption and luminescence comes from local levels that split off from the exciton band as a result of the interaction between the molecular chain and the luminophore. It is also demonstrated that the contribution to light absorption and photoluminescence from local levels is non-linearly dependent on the coupling parameter between the luminophore and the J-aggregate molecular chain.

  1. The Binary Boron Trifluoride-Hydroxylamine Molecular Complex: N ...

    African Journals Online (AJOL)


    type suggest that hydroxylamine would bind to boron trifluoride preferentially through its nitrogen atom. Whether such a complex adopts ... nitrogen atoms in the sp hybrid state (O-bound CO2 and. N-bound N2O6) tend to take part ..... are strongly coupled with the B…N or B…O stretching vibration, so the assignments of the.

  2. Excitonic quasimolecules in nanosystems of quantum dots (United States)

    Pokutnyi, Sergey I.


    The theory of excitonic quasimolecules (biexcitons) (formed of spatially separated electrons and holes) in a nanosystem that consists of semiconductor quantum dots synthesized in a borosilicate glass matrix is presented. It is shown that exciton quasimolecule formation is of a threshold character and is possible in nanosystem, if the spacing between the quantum dots surfaces is larger than a certain critical spacing. It was found that the binding energy of the singlet ground state of an exciton quasimolecule, consisting of two semiconductor quantum dots is a significant large values, larger than the binding energy of the biexciton in a semiconductor single crystal by almost two orders of magnitude.

  3. Characterizing the molecular architectures of chromatin-modifying complexes. (United States)

    Setiaputra, Dheva T; Yip, Calvin K


    Eukaryotic cells package their genome in the form of a DNA-protein complex known as chromatin. This organization not only condenses the genome to fit within the confines of the nucleus, but also provides a platform for a cell to regulate accessibility to different gene sequences. The basic packaging element of chromatin is the nucleosome, which consists of 146 base pairs of DNA wrapped around histone proteins. One major means that a cell regulates chromatin structure is by depositing post-translational modifications on nucleosomal histone proteins, and thereby altering internucleosomal interactions and/or binding to different chromatin associated factors. These chromatin modifications are often catalyzed by multi-subunit enzyme complexes, whose large size, sophisticated composition, and inherent conformational flexibility pose significant technical challenges to their biochemical and structural characterization. Multiple structural approaches including nuclear magnetic resonance spectroscopy, X-ray crystallography, single-particle electron microscopy, and crosslinking coupled to mass spectrometry are often used synergistically to probe the overall architecture, subunit organization, and catalytic mechanisms of these macromolecular assemblies. In this review, we highlight several recent chromatin-modifying complexes studies that embodies this multipronged structural approach, and explore common themes amongst them. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Role of many-body effects in the coherent dynamics of excitons in low-temperature-grown GaAs

    Energy Technology Data Exchange (ETDEWEB)

    Webber, D.; Hacquebard, L.; Hall, K. C. [Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia B3H 4R2 (Canada); Liu, X.; Dobrowolska, M.; Furdyna, J. K. [Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556 (United States)


    Femtosecond four-wave mixing experiments on low-temperature-grown (LT-) GaAs indicate a polarization-dependent nonlinear optical response at the exciton, which we attribute to Coulomb-mediated coupling between excitons and electron-hole pairs simultaneously excited by the broad-bandwidth laser pulses. Strong suppression of the exciton response through screening by carriers injected by a third pump pulse was observed, an effect that is transient due to rapid carrier trapping. Our findings highlight the need to account for the complex interplay of disorder and many-body effects in the design of ultrafast optoelectronic devices using this material.

  5. Nanoporous carbon sorbent for molecular-sieve chromatography of lipoprotein complex (United States)

    Kerimkulova, A. R.; Mansurova, B. B.; Gil'manov, M. K.; Mansurov, Z. A.


    The physicochemical characteristics of carbon sorbents are investigated. Electron microscopy data for the sorbent and separated lipoprotein complex are presented. It is found that the obtained carbon sorbent possess high porosity. Nanoporous carbon sorbents for the chromatography of molecular-sieve markers are obtained and tested. The applicability of nanoporous carbon sorbents for separation of lipoprotein complexes (LPC) is investigated.

  6. Studies on cluster, salt and molecular complex of zinc-quinolinate

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 127; Issue 2. Studies on cluster ... Keywords. Zinc-clusters; molecular complex; hydrolytic equilibrium; zinc oxide; porous material. ... Complex 5 is formed from a hydrolytic equilibrium of water with zinc chloride yielding tetrachloro zinc anion and zinc hydroxide. Taking ...

  7. Visualization of complex processes in lipid systems using computer simulations and molecular graphics. (United States)

    Telenius, Jelena; Vattulainen, Ilpo; Monticelli, Luca


    Computer simulation has become an increasingly popular tool in the study of lipid membranes, complementing experimental techniques by providing information on structure and dynamics at high spatial and temporal resolution. Molecular visualization is the most powerful way to represent the results of molecular simulations, and can be used to illustrate complex transformations of lipid aggregates more easily and more effectively than written text. In this chapter, we review some basic aspects of simulation methodologies commonly employed in the study of lipid membranes and we describe a few examples of complex phenomena that have been recently investigated using molecular simulations. We then explain how molecular visualization provides added value to computational work in the field of biological membranes, and we conclude by listing a few molecular graphics packages widely used in scientific publications.

  8. Doing molecular biophysics: finding, naming, and picturing signal within complexity. (United States)

    Richardson, Jane S; Richardson, David C


    A macromolecular structure, as measured data or as a list of coordinates or even on-screen as a full atomic model, is an extremely complex and confusing object. The underlying rules of how it folds, moves, and interacts as a biological entity are even less evident or intuitive to the human mind. To do science on such molecules, or to relate them usefully to higher levels of biology, we need to start with a natural history that names their features in meaningful ways and with multiple representations (visual or algebraic) that show some aspect of their organizing principles. The two of us have jointly enjoyed a highly varied and engrossing career in biophysical research over nearly 50 years. Our frequent changes of emphasis are tied together by two threads: first, by finding the right names, visualizations, and methods to help both ourselves and others to better understand the 3D structures of protein and RNA molecules, and second, by redefining the boundary between signal and noise for complex data, in both directions-sometimes identifying and promoting real signal up out of what seemed just noise, and sometimes demoting apparent signal into noise or systematic error. Here we relate parts of our scientific and personal lives, including ups and downs, influences, anecdotes, and guiding principles such as the title theme.

  9. Increase in Complexity and Information through Molecular Evolution

    Directory of Open Access Journals (Sweden)

    Peter Schuster


    Full Text Available Biological evolution progresses by essentially three different mechanisms: (I optimization of properties through natural selection in a population of competitors; (II development of new capabilities through cooperation of competitors caused by catalyzed reproduction; and (III variation of genetic information through mutation or recombination. Simplified evolutionary processes combine two out of the three mechanisms: Darwinian evolution combines competition (I and variation (III and is represented by the quasispecies model, major transitions involve cooperation (II of competitors (I, and the third combination, cooperation (II and variation (III provides new insights in the role of mutations in evolution. A minimal kinetic model based on simple molecular mechanisms for reproduction, catalyzed reproduction and mutation is introduced, cast into ordinary differential equations (ODEs, and analyzed mathematically in form of its implementation in a flow reactor. Stochastic aspects are investigated through computer simulation of trajectories of the corresponding chemical master equations. The competition-cooperation model, mechanisms (I and (II, gives rise to selection at low levels of resources and leads to symbiontic cooperation in case the material required is abundant. Accordingly, it provides a kind of minimal system that can undergo a (major transition. Stochastic effects leading to extinction of the population through self-enhancing oscillations destabilize symbioses of four or more partners. Mutations (III are not only the basis of change in phenotypic properties but can also prevent extinction provided the mutation rates are sufficiently large. Threshold phenomena are observed for all three combinations: The quasispecies model leads to an error threshold, the competition-cooperation model allows for an identification of a resource-triggered bifurcation with the transition, and for the cooperation-mutation model a kind of stochastic threshold for

  10. Exciton in closed and opened quantum dot

    Directory of Open Access Journals (Sweden)



    Full Text Available The theory of exciton spectrum in spherically symmetric states for the three- shell closed spherical quantum dot is proposed. The evolution of the exciton spectrum while varying the outer well thickness from zero (stationary spectrum of single closed spherical quantum dot to infinity (quasistationary spectrum of a single open spherical quantum dot is investigated. The mechanism of damping (semiwidth of quasistationary states due to the redistribution over the energy levels of probability of exciton location in the space of two inner shells of nanosystem is studied. It is shown that the three shell closed spherical quantum dot of a rather big thickness of the outer well quite sufficiently and exactly reflects the basic properties of the quasistationary exciton spectrum in a single open spherical quantum dot.

  11. Exciton absorption in narrow armchair graphene nanoribbons

    Energy Technology Data Exchange (ETDEWEB)

    Monozon, B.S. [Physics Department, Marine Technical University, 3 Lotsmanskaya Str., 190008 St. Petersburg (Russian Federation); Schmelcher, P., E-mail: [Zentrum für Optische Quantentechnologien, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany)


    We develop an analytical approach to the exciton optical absorption for narrow gap armchair graphene nanoribbons (AGNR). We focus on the regime of dominant size quantization in combination with the attractive electron–hole interaction. An adiabatic separation of slow and fast motions leads via the two-body Dirac equation to the isolated and coupled subband approximations. Discrete and continuous exciton states are in general coupled and form quasi-Rydberg series of purely discrete and resonance type character. The corresponding oscillator strengths and widths are derived. We show that the exciton peaks are blue-shifted, become broader and increase in magnitude upon narrowing the ribbon. At the edge of a subband the singularity related to the 1D density of states is transformed into finite absorption via the presence of the exciton. Our analytical results are in good agreement with those obtained by other methods including numerical approaches. Estimates of the expected experimental values are provided for realistic AGNR.

  12. Excitonic physics in a Dirac quantum dot (United States)

    Raca, V.; Milovanović, M. V.


    We present a description of vacuum polarization in a circular Dirac quantum dot in two spatial dimensions assuming α —the relative strength of the Coulomb interaction small enough to render an approximation with a single electron (hole) lowest energy level relevant. Applying this approximation, we find that for αc≈1.05 the lowest level is half filled irrespective of the number of flavors that are present. The ground state can be represented as a superposition of particular (even number) excitonic states which constitute an excitonic cloud that evolves in a crossover manner. The ground state is degenerate with an intervalley excitonic state at αc≈1.05 , a critical strength, that in our approximation marks a point with single electron and exciton resonances.

  13. Atomic lattice excitons: from condensates to crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kantian, A [Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, A-6020 Innsbruck (Austria); Daley, A J [Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, A-6020 Innsbruck (Austria); Toermae, P [Nanoscience Center, Department of Physics, University of Jyvaeskylae, PO Box 35, FIN-40014 (Finland); Zoller, P [Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, A-6020 Innsbruck (Austria)


    We discuss atomic lattice excitons (ALEs), bound particle-hole pairs formed by fermionic atoms in two bands of an optical lattice. Such a system provides a clean set-up, with tunable masses and interactions, to study fundamental properties of excitons including exciton condensation. We also find that for a large effective mass ratio between particles and holes, effective long-range interactions can mediate the formation of an exciton crystal, for which superfluidity is suppressed. Using a combination of mean-field treatments, bosonized theory based on a Born-Oppenheimer approximation, and one-dimensional (1D) numerical computation, we discuss the properties of ALEs under varying conditions, and discuss in particular their preparation and measurement.

  14. Gate controlled Aharonov-Bohm-type oscillations from single neutral excitons in quantum rings

    NARCIS (Netherlands)

    Ding, F.; Akopian, N.; Li, B.; Perinetti, U.; Govorov, A.; Peeters, F.M.; Bof Bufon, C.C.; Deneke, C.; Chen, Y.H.; Rastelli, A.; Schmidt, O.G.; Zwiller, V.


    We report on a magnetophotoluminescence study of single self-assembled semiconductor nanorings which are fabricated by molecular-beam epitaxy combined with AsBr3 in situ etching. Oscillations in the neutral exciton radiative recombination energy and in the emission intensity are observed under an

  15. Exciton-polariton wakefields in semiconductor microcavities

    Energy Technology Data Exchange (ETDEWEB)

    Terças, H., E-mail: [Physics of Information Group, Instituto de Telecomunicações, Lisbon (Portugal); Institute for Theoretical Physics, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck (Austria); Mendonça, J.T., E-mail: [Instituto de Física, Universidade de São Paulo, São Paulo SP, 05508-090 Brazil (Brazil); IPFN, Instituto Superior Técnico, 1049-001 Lisboa (Portugal)


    We consider the excitation of polariton wakefields due to a propagating light pulse in a semiconductor microcavity. We show that two kinds of wakes are possible, depending on the constituents fraction (either exciton or photon) of the polariton wavefunction. The nature of the wakefields (pure excitonic or polaritonic) can be controlled by changing the speed of propagation of the external pump. This process could be used as a diagnostic for the internal parameters of the microcavity.

  16. Strong coupling in porphyrin J-aggregate excitons and plasmons in nano-void arrays (United States)

    Ferdele, Stefano; Jose, Bincy; Foster, Robert; Keyes, Tia E.; Rice, James H.


    Active plasmonic nano-void arrays made through colloidal lithography (a cost effective and rapid process) potentially offers opportunities for scalable device design. In this work we demonstrate strong coupling between Bragg-like quadrupole surface plasmon modes in nano-void substrate designs with Frankel excitons in a molecular J-aggregate layer though angular tuning. The enhanced exciton-plasmon coupling creates a Fano like line shape in the differential reflection spectra associated with the formation of new hybrid states, leading to anti-crossing of the upper and lower polaritons with a Rabi frequency of 120 meV.

  17. Intrinsic dynamics of weakly and strongly confined excitons in nonpolar nitride-based heterostructures


    Corfdir, Pierre; Levrat, Jacques; Dussaigne, Amélie; Lefebvre, Pierre; Teisseyre, Henryk; Grzegory, Izabella; Suski, Tadeusz; Ganière, Jean-Daniel; Grandjean, Nicolas; Deveaud-Plédran, Benoît


    Both weakly and strongly confined excitons are studied by time-resolved photoluminescence in a nonpolar nitride-based heterostructure grown by molecular beam epitaxy on the a-facet of a bulk GaN crystal, with an ultralow dislocation density of 2 × 105 cm-2. Strong confinement is obtained in a 4 nm thick Al0.06Ga0.94N/GaN quantum well (QW), whereas weakly confined exciton-polaritons are observed in a 200 nm thick GaN epilayer. Thanks to the low dislocation density, the effective lifetime of st...


    Directory of Open Access Journals (Sweden)

    R. E. Khoma


    Full Text Available The literature data on the synthesis, stoichiometry, structure and relative stability of molecular  complexes of sulphur dioxide with N,O-containing organic bases have been systematized and  generalized. It was shown that the yield of the reaction product of sulfur dioxide with organic  bases (such as amines are strongly influenced by the conditions of synthesis: the nature of  the solvent (basicity, polarity, the temperature and SO2:L ratio in the reaction medium. The stoichiometry of SO2*nL molecular complexes depends on ligand denticity, as well as its  ability to H-bonding. The reaction of the sulfur oxide (IV with organic bases can give S←N and S←O complexes. With the increase of the value of base proton affinity the decrease ΔrSN values has been marked. Characteristic parameter Δr SN = r SN – a1(rS+ rN (where rSNis the S←N donor-acceptor bond length has been determined by microwave spectroscopy and X-ray analysis, rSand rNwere the tabulated values of the homopolar covalent radii of sulphur and nitrogen heteroatoms. The dependence of formation enthalpy of molecular complexes of basic amines and spectral characteristics has been noted; enthalpy-entropy compensation for S←N and S←O complex-es has been stated. Despite the limited experimental data on the thermodynamics of complex formation and the lengths of donor-acceptor bonds for the same compounds it has been found bond S←N strength in SO2 molecular complexes to depend on the intrinsic value of ΔrSN. The contribution of van der Waals forces and charge transfer forces to the formation of molecular complexes of sulphur dioxide has been stated.

  19. Complexation and molecular modeling studies of europium(III)-gallic acid-amino acid complexes. (United States)

    Taha, Mohamed; Khan, Imran; Coutinho, João A P


    With many metal-based drugs extensively used today in the treatment of cancer, attention has focused on the development of new coordination compounds with antitumor activity with europium(III) complexes recently introduced as novel anticancer drugs. The aim of this work is to design new Eu(III) complexes with gallic acid, an antioxida'nt phenolic compound. Gallic acid was chosen because it shows anticancer activity without harming health cells. As antioxidant, it helps to protect human cells against oxidative damage that implicated in DNA damage, cancer, and accelerated cell aging. In this work, the formation of binary and ternary complexes of Eu(III) with gallic acid, primary ligand, and amino acids alanine, leucine, isoleucine, and tryptophan was studied by glass electrode potentiometry in aqueous solution containing 0.1M NaNO3 at (298.2 ± 0.1) K. Their overall stability constants were evaluated and the concentration distributions of the complex species in solution were calculated. The protonation constants of gallic acid and amino acids were also determined at our experimental conditions and compared with those predicted by using conductor-like screening model for realistic solvation (COSMO-RS) model. The geometries of Eu(III)-gallic acid complexes were characterized by the density functional theory (DFT). The spectroscopic UV-visible and photoluminescence measurements are carried out to confirm the formation of Eu(III)-gallic acid complexes in aqueous solutions. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes

    Directory of Open Access Journals (Sweden)

    Le Novère Nicolas


    Full Text Available Abstract Background Most cellular signal transduction mechanisms depend on a few molecular partners whose roles depend on their position and movement in relation to the input signal. This movement can follow various rules and take place in different compartments. Additionally, the molecules can form transient complexes. Complexation and signal transduction depend on the specific states partners and complexes adopt. Several spatial simulator have been developed to date, but none are able to model reaction-diffusion of realistic multi-state transient complexes. Results Meredys allows for the simulation of multi-component, multi-feature state molecular species in two and three dimensions. Several compartments can be defined with different diffusion and boundary properties. The software employs a Brownian dynamics engine to simulate reaction-diffusion systems at the reactive particle level, based on compartment properties, complex structure, and hydro-dynamic radii. Zeroth-, first-, and second order reactions are supported. The molecular complexes have realistic geometries. Reactive species can contain user-defined feature states which can modify reaction rates and outcome. Models are defined in a versatile NeuroML input file. The simulation volume can be split in subvolumes to speed up run-time. Conclusions Meredys provides a powerful and versatile way to run accurate simulations of molecular and sub-cellular systems, that complement existing multi-agent simulation systems. Meredys is a Free Software and the source code is available at

  1. Computational study of the molecular mechanisms of caffeine action: Caffeine complexes with adenosine receptors (United States)

    Poltev, V. I.; Rodríguez, E.; Grokhlina, T. I.; Deriabina, A.; Gonzalez, E.

    To understand the molecular basis of the principal biological action of the caffeine (CAF), the molecular mechanics calculations of possible complexes between CAF and the fragments of human A1 adenosine receptor were performed. The fragments were selected after considerations of the CAF molecular structure and its possible interactions, as well as after an analysis of the extensive bibliography on the structure, biological role, site-directed mutagenesis, and the modeling of the adenosine receptors. The minimum energy configurations of these complexes were obtained using two different computer programs with different force fields. The most favorable configurations correspond to the formation of two hydrogen bonds between the CAF molecule and hydrophilic amino acid residues of the fragments of transmembrane domains of the receptor. These configurations are supposed to contribute to CAF blocking of the adenosine receptors. They will be used later for the construction of model CAF complexes with two transmembrane domains simultaneously.

  2. Soliton physics with semiconductor exciton-polaritons in confined systems (United States)

    Sich, Maksym; Skryabin, Dmitry V.; Krizhanovskii, Dmitry N.


    In the past decade, there has been a significant progress in the study of non-linear polariton phenomena in semiconductor microcavities. One of the key features of non-linear systems is the emergence of solitons. The complexity and the inherently strong nonlinearity of the polariton system made it a perfect sandpit for observing solitonic effects in half-light half-matter environment. This review focuses on the theory and the latest experimental elucidating physics as well as potential applications of conservative and dissipative solitons in exciton-polariton systems. xml:lang="fr"

  3. In good company: association between fungal glycans generates molecular complexes with unique functions. (United States)

    Rodrigues, Marcio L; Nimrichter, Leonardo


    The biological properties of fungal immunogens have historically utilized testing of isolated molecules. Recent findings, however, indicate that fungal glycans differing in structure and function can interact to form hybrid complexes with unique properties. In the pathogenic yeast Cryptococcus neoformans, chitin-like molecules associate with capsular glucuronoxylomannan (GXM) to form functionally distinct glycan complexes. Such interactions between glycans that result in the formation of structures with different functions strongly suggest that additional molecular complexes with unknown properties may exist in fungal pathogens. Moreover, the identification of these novel complexes has stimulated the search of new immunogens with potential to protect human and animal hosts against systemic mycoses.

  4. Cellular Uptake Properties of the Complex Derived from Quantum Dots and G8 Molecular Transporter

    Energy Technology Data Exchange (ETDEWEB)

    Im, Jung Kyun; Maiti, Kaustabh K.; Kim, Wan Il; Kim, Kyong Tai; Chung, Sung Kee [Pohang University of Science and Technology, Pohang (Korea, Republic of)


    The biotin-attached G8 molecular transporter (5) was synthesized and used together with quantum dots in preparing the complexes (QD-MT). The QD-MT complexes were studied in terms of the cellular uptake and the internalization mechanism in live HeLa cells with the aid of various known endocytosis inhibitors. It has been concluded that the QD-MT complex is internalized largely by macropinocytosis. The mouse tissue distribution of the QD-MT complex by i.p. and i.v. routes showed some organ selectivity and a good ability to cross the BBB.

  5. A rhenium complex doped in a silica molecular sieve for molecular oxygen sensing: Construction and characterization (United States)

    Yang, Xiaozhou; Li, Yanxiao


    This paper reported a diamine ligand and its Re(I) complex for potential application in oxygen sensing. The novelty of this diamine ligand localized at its increased conjugation chain which had a typical electron-withdrawing group of 1,3,4-oxadiazole. Electronic distribution of excited electrons and their lifetime were supposed to be increased, favoring oxygen sensing collision. This hypothesis was confirmed by single crystal analysis, theoretical calculation and photophysical measurement. It was found that this Re(I) complex had a long-lived emission peaking at 545 nm, favoring sensing application. By doping this complex into a silica matrix MCM-41, oxygen sensing performance and mechanism of the resulting composites were discussed in detail. Non-linear Stern-Volmer working curves were observed with maximum sensitivity of 5.54 and short response time of 6 s.

  6. Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants. (United States)

    Kujur, Alice; Saxena, Maneesha S; Bajaj, Deepak; Laxmi; Parida, Swarup K


    The enormous population growth, climate change and global warming are now considered major threats to agriculture and world's food security. To improve the productivity and sustainability of agriculture, the development of highyielding and durable abiotic and biotic stress-tolerant cultivars and/climate resilient crops is essential. Henceforth, understanding the molecular mechanism and dissection of complex quantitative yield and stress tolerance traits is the prime objective in current agricultural biotechnology research. In recent years, tremendous progress has been made in plant genomics and molecular breeding research pertaining to conventional and next-generation whole genome, transcriptome and epigenome sequencing efforts, generation of huge genomic, transcriptomic and epigenomic resources and development of modern genomics-assisted breeding approaches in diverse crop genotypes with contrasting yield and abiotic stress tolerance traits. Unfortunately, the detailed molecular mechanism and gene regulatory networks controlling such complex quantitative traits is not yet well understood in crop plants. Therefore, we propose an integrated strategies involving available enormous and diverse traditional and modern -omics (structural, functional, comparative and epigenomics) approaches/resources and genomics-assisted breeding methods which agricultural biotechnologist can adopt/utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in crop plants. This would provide clues and much needed inputs for rapid selection of novel functionally relevant molecular tags regulating such complex traits to expedite traditional and modern marker-assisted genetic enhancement studies in target crop species for developing high-yielding stress-tolerant varieties.

  7. Excitonic polaritons of zinc diarsenide single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Syrbu, N.N., E-mail: [Technical University of Moldova, Chisinau, Republic of Moldova (Moldova, Republic of); Stamov, I.G. [T.G. Shevchenko State University of Pridnestrovie, Tiraspol, Republic of Moldova (Moldova, Republic of); Zalamai, V.V. [Institute of Applied Physics, Academy of Sciences of Moldova, Chisinau, Republic of Moldova (Moldova, Republic of); Dorogan, A. [Technical University of Moldova, Chisinau, Republic of Moldova (Moldova, Republic of)


    Excitonic polaritons of ZnAs{sub 2} single crystals had been investigated. Parameters of singlet excitons with Г{sub 2}¯(z) symmetry and orthoexcitons 2Г{sub 1}¯(y)+Г{sub 2}¯(x) had been determined. Spectral dependencies of ordinary and extraordinary dispersion of refractive index had been calculated using interferential reflection and transmittance spectra. It was shown, that A excitonic series were due to hole (V{sub 1}) and electron (C{sub 1}) bands. The values of effective masses of electrons (m{sub c}{sup *}=0.10 m{sub 0}) and holes (m{sub v1}{sup *}=0.89 m{sub 0}) had been estimated. It was revealed that the hole mass m{sub v1}{sup *} changes from 1.03 m{sub 0} to 0.55 m{sub 0} at temperature increasing from 10 K up to 230 K and that the electron mass m{sub c}{sup *} does not depend on temperature. The integral absorption A (eV cm{sup −1}) of the states n=1, 2 and 3 of Г{sub 2}¯(z) excitons depends on the A{sub n}≈n{sup −3} equality, which it is characteristic for S-type excitonic functions. Temperature dependences of the integral absorption of ground states for Г{sub 2}¯(z) and Г{sub 2}¯(Ñ…) excitons differ. The ground states of B and C excitons formed by V{sub 3} – C{sub 1} and V{sub 4} – C{sub 1} bands and its parameters had been determined.

  8. Spectroscopic study of molecular structure, antioxidant activity and biological effects of metal hydroxyflavonol complexes (United States)

    Samsonowicz, Mariola; Regulska, Ewa


    Flavonols with varied hydroxyl substitution can act as strong antioxidants. Thanks to their ability to chelate metals as well as to donate hydrogen atoms they have capacity to scavenge free radicals. Their metal complexes are often more active in comparison with free ligands. They exhibit interesting biological properties, e.g. anticancer, antiphlogistic and antibacterial. The relationship between molecular structure and their biological properties was intensively studied using spectroscopic methods (UV-Vis, IR, Raman, NMR, ESI-MS). The aim of this paper is review on spectroscopic analyses of molecular structure and biological activity of hydroxyflavonol metal complexes.

  9. Spontaneous emission from large quantum dots in nanostructures: Exciton-photon interaction beyond the dipole approximation

    DEFF Research Database (Denmark)

    Stobbe, S.; Kristensen, Philip Trøst; Mortensen, Jakob E.


    the interaction between light and spatially extended excitons. In this regime, light and matter degrees of freedom cannot be separated and a complex interplay between the nanostructured optical environment and the exciton envelope function emerges. We illustrate this by specific examples and derive a series...... of important analytical relations, which are useful for applying the formalism to practical problems. In the dipole limit, the decay rate is proportional to the projected local density of optical states, and we obtain the strong and weak confinement regimes as special cases....

  10. Molecular structure in correlation with electrochemical properties of mixed-ligand cobalt(III complexes

    Directory of Open Access Journals (Sweden)



    Full Text Available Four mixed-ligand cobalt(III complexes (1–4 of the general formula [Co(Rdtccyclam](ClO42 and [Co(Raccyclam](ClO42 (cyclam = 1,4,8,11-tetraazacyclotetradecane; Rdtc = thiomorpholine-(Timdtc or 2-methylpiperidine-(2-Mepipdtc dithiocarbamates; Rac = 1,1,1,5,5,5-hexafluoro-2,4-pentanedionato (Hfac or 2,2,6,6-tetramethyl-3,5-heptanedionato (Tmhd, respectively were electro­chemically examined on a glassy carbon and an iron electrode in perchloric acid solution. The obtained results showed the influence of these complexes on hydrogen evolution, the oxygen reduction reaction and iron dissolution. The exhibited effects of the complexes on these reactions depend on structure related to the bidentate dithiocarbamato or b-diketonato ligand. The electrochemical properties of the complexes were correlated with molecular structure and parameters derived from spectral analysis and molecular modeling.

  11. Multi-excitonic emission from Stranski-Krastanov GaN/AlN quantum dots inside a nanoscale tip (United States)

    Mancini, L.; Moyon, F.; Houard, J.; Blum, I.; Lefebvre, W.; Vurpillot, F.; Das, A.; Monroy, E.; Rigutti, L.


    Single-dot time-resolved micro-photoluminescence spectroscopy and correlated electron tomography (ET) have been performed on self-assembled GaN/AlN quantum dots isolated within a field-emission nanoscale tip by focused ion beam (FIB). Despite the effect of the FIB, the system conserves the capability of emitting light through multi-excitonic complexes. The optical spectroscopy data have then been correlated with the electronic structure and lifetime parameters that could be extracted using the structural parameters obtained by ET via a 6 band k.p model. A biexciton-exciton cascade could be identified and thoroughly analysed. The biexciton-exciton states exhibit a non-negligible polarization component along the [0001] polar crystal axis, indicating a significant valence band mixing, while the relationship between exciton energy and biexciton binding energy is consistent with a hybrid character of the biexciton.

  12. DMPD: Molecular mechanisms of macrophage activation and deactivation bylipopolysaccharide: roles of the receptor complex. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 14609719 Molecular mechanisms of macrophage activation and deactivation bylipopolysaccharide...ivation and deactivation bylipopolysaccharide: roles of the receptor complex. Pub...medID 14609719 Title Molecular mechanisms of macrophage activation and deactivation bylipopolysaccharide: ro

  13. Lateral redistribution of excitons in CdSe/ZnSe quantum dots (United States)

    Strassburg, M.; Dworzak, M.; Born, H.; Heitz, R.; Hoffmann, A.; Bartels, M.; Lischka, K.; Schikora, D.; Christen, J.


    Lateral redistribution processes of excitons localized in CdSe/ZnSe quantum dot structures are investigated by time-integrated and time-resolved spectroscopy. The photoluminescence properties are governed by lateral energy transfer within a dense ensemble of quantum dots. The quantum dots differ in size and Cd concentration and provide a complex potential landscape with localization sites for excitons. At low temperatures, lateral transfer by tunneling leads to a redshift with increasing delay after pulsed excitation. The mobility edge was determined to 2.561 eV. Above 100 K, thermally activated escape and recapture of excitons cause a strong redshift of the PL maximum in the first 500 ps.

  14. [Mass spectrometry of triterpene glycosides molecular complexation with purine bases of nucleic acids]. (United States)

    Lekar', A V; Vetrova, E V; Borisenko, N I; Iakovishin, L A; Grishkovets, V I


    The molecular complexation of adenine and guanine with hederagenin 3-O-alpha-L-rhamnopyranosyl-(1-->2)-O-alpha-L-arabinopyranoside (alpha-hederin) and its 28-O-alpha-L-rhamnopyranosyl-(1-->4)-O-beta-D-glucopyranosyl-(1-->6)-O-beta-D-glucopyranosyl ester (hederasaponin C) was investigated for the first time using the method of electrospray ionization mass spectrometry. Guanine forms complexes more diverse in composition than adenine.

  15. Plasmon-excitonic polaritons in superlattices (United States)

    Kosobukin, V. A.


    A theory for propagation of polaritons in superlattices with resonant plasmon-exciton coupling is presented. A periodical superlattice consists of a finite number of cells with closely located a quantum well and a monolayer of metal nanoparticles. Under study is the spectrum of hybrid modes formed of the quasitwo- dimensional excitons of quantum wells and the dipole plasmons of metal particles. The problem of electrodynamics is solved by the method of Green's functions with taking account of the resonant polarization of quantum wells and nanoparticles in a self-consistent approximation. The effective polarizability of spheroidal particles occupying a square lattice is calculated with taking into consideration the local-field effect of dipole plasmons of the layer and their images caused by the excitonic polarization of nearest quantum well. Optical reflection spectra of superlattices with GaAs/AlGaAs quantum wells and silver particles are numerically analyzed. Special attention is paid to the superradiant regime originated in the Bragg diffraction of polaritons in superlattice. Superradiance is investigated separately for plasmons and excitons, and then for hybrid plasmonexcitonic polaritons. It is demonstrated that the broad spectrum of reflectance associated with plasmons depends on the number of cells in superlattice, and it has a narrow spectral dip in the range of plasmon-excitonic Rabi splitting.

  16. Molecular Architecture and Function of the SEA Complex, a Modulator of the TORC1 Pathway* (United States)

    Algret, Romain; Fernandez-Martinez, Javier; Shi, Yi; Kim, Seung Joong; Pellarin, Riccardo; Cimermancic, Peter; Cochet, Emilie; Sali, Andrej; Chait, Brian T.; Rout, Michael P.; Dokudovskaya, Svetlana


    The TORC1 signaling pathway plays a major role in the control of cell growth and response to stress. Here we demonstrate that the SEA complex physically interacts with TORC1 and is an important regulator of its activity. During nitrogen starvation, deletions of SEA complex components lead to Tor1 kinase delocalization, defects in autophagy, and vacuolar fragmentation. TORC1 inactivation, via nitrogen deprivation or rapamycin treatment, changes cellular levels of SEA complex members. We used affinity purification and chemical cross-linking to generate the data for an integrative structure modeling approach, which produced a well-defined molecular architecture of the SEA complex and showed that the SEA complex comprises two regions that are structurally and functionally distinct. The SEA complex emerges as a platform that can coordinate both structural and enzymatic activities necessary for the effective functioning of the TORC1 pathway. PMID:25073740

  17. Exciton-polaritons in cuprous oxide: Theory and comparison with experiment (United States)

    Schweiner, Frank; Ertl, Jan; Main, Jörg; Wunner, Günter; Uihlein, Christoph


    The observation of giant Rydberg excitons in cuprous oxide (Cu2O ) up to a principal quantum number of n =25 by T. Kazimierczuk et al. [Nature (London) 514, 343 (2014), 10.1038/nature13832] inevitably raises the question whether these quasiparticles must be described within a multipolariton framework since excitons and photons are always coupled in the solid. In this paper we present the theory of exciton-polaritons in Cu2O . To this end we extend the Hamiltonian which includes the complete valence-band structure, the exchange interaction, and the central-cell corrections effects, and which has been recently deduced by F. Schweiner et al. [Phys. Rev. B 95, 195201 (2017), 10.1103/PhysRevB.95.195201], for finite values of the exciton momentum ℏ K . We derive formulas to calculate not only dipole but also quadrupole oscillator strengths when using the complete basis of F. Schweiner et al., which has recently been proven as a powerful tool to calculate exciton spectra. Very complex polariton spectra for the three orientations of K along the axes [001 ] , [110 ] , and [111 ] of high symmetry are obtained and a strong mixing of exciton states is reported. The main focus is on the 1 S ortho-exciton-polariton, for which pronounced polariton effects have been measured in experiments. We set up a 5 ×5 matrix model, which accounts for both the polariton effect and the K -dependent splitting, and which allows treating the anisotropic polariton dispersion for any direction of K . We especially discuss the dispersions for K being oriented in the planes perpendicular to [1 1 ¯0 ] and [111 ] , for which experimental transmission spectra have been measured. Furthermore, we compare our results with experimental values of the K -dependent splitting, the group velocity, and the oscillator strengths of this exciton-polariton. The results are in good agreement. This proves the validity of the 5 ×5 matrix model as a useful theoretical model for further investigations on the 1 S

  18. Molecular simulation of N-acetylneuraminic acid analogs and molecular dynamics studies of cholera toxin-Neu5Gc complex. (United States)

    Blessy, J Jino; Sharmila, D Jeya Sundara


    Cholera toxin (CT) is an AB5 protein complex secreted by the pathogen Vibrio cholera, which is responsible for cholera infection. N-acetylneuraminic acid (NeuNAc) is a derivative of neuraminic acid with nine-carbon backbone. NeuNAc is distributed on the cell surface mainly located in the terminal components of glycoconjugates, and also plays an important role in cell-cell interaction. In our current study, molecular docking and molecular dynamic (MD) simulations were implemented to identify the potent NeuNAc analogs with high-inhibitory activity against CT protein. Thirty-four NeuNAc analogs, modified in different positions C-1/C-2/C-4/C-5/C-7/C-8/C-9, were modeled and docked against the active site of CT protein. Among the 34 NeuNAc analogs, the analog Neu5Gc shows the least extra precision glide score of -9.52 and glide energy of -44.71 kcal/mol. NeuNAc analogs block the CT active site residues HIS:13, ASN:90, LYS:91, GLN:56, GLN:61, and TRP:88 through intermolecular hydrogen bonding. The MD simulation for CT-Neu5Gc docking complex was performed using Desmond. MD simulation of CT-Neu5Gc complex reveals the stable nature of docking interaction.

  19. Bose-Einstein condensation and indirect excitons: a review. (United States)

    Combescot, Monique; Combescot, Roland; Dubin, François


    We review recent progress on Bose-Einstein condensation (BEC) of semiconductor excitons. The first part deals with theory, the second part with experiments. This Review is written at a time where the problem of exciton Bose-Einstein condensation has just been revived by the understanding that the exciton condensate must be dark because the exciton ground state is not coupled to light. Here, we theoretically discuss this missed understanding before providing its experimental support through experiments that scrutinize indirect excitons made of spatially separated electrons and holes. The theoretical part first discusses condensation of elementary bosons. In particular, the necessary inhibition of condensate fragmentation by exchange interaction is stressed, before extending the discussion to interacting bosons with spin degrees of freedom. The theoretical part then considers composite bosons made of two fermions like semiconductor excitons. The spin structure of the excitons is detailed, with emphasis on the crucial fact that ground-state excitons are dark: indeed, this imposes the exciton Bose-Einstein condensate to be not coupled to light in the dilute regime. Condensate fragmentations are then reconsidered. In particular, it is shown that while at low density, the exciton condensate is fully dark, it acquires a bright component, coherent with the dark one, beyond a density threshold: in this regime, the exciton condensate is 'gray'. The experimental part first discusses optical creation of indirect excitons in quantum wells, and the detection of their photoluminescence. Exciton thermalisation is also addressed, as well as available approaches to estimate the exciton density. We then switch to specific experiments where indirect excitons form a macroscopic fragmented ring. We show that such ring provides efficient electrostatic trapping in the region of the fragments where an essentially-dark exciton Bose-Einstein condensate is formed at sub-Kelvin bath

  20. Studies on cluster, salt and molecular complex of zinc-quinolinate

    Indian Academy of Sciences (India)

    127, No. 2, February 2015, pp. 215–223. c Indian Academy of Sciences. DOI 10.1007/s12039-015-0781-6. Studies on cluster, salt and molecular complex of zinc-quinolinate. PRITHIVIRAJ KHAKHLARY and JUBARAJ B BARUAH∗. Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781 039, India.

  1. Molecular details of ovalbumin-pectin complexes at the air/water interface: a spectroscopic study.

    NARCIS (Netherlands)

    Kudryashova, E.V.; Visser, A.J.W.G.; Hoek, van A.; Jongh, de H.H.J.


    To stabilize air-water interfaces, as in foams, the adsorption of surface-active components is a prerequisite. An approach to controlling the surface activity of proteins is noncovalent complex formation with a polyelectrolyte in the bulk phase. The molecular properties of egg white ovalbumin in a

  2. Molecular details of ovalbumin-pectin complexes at the air/water interface: A spectroscopic study

    NARCIS (Netherlands)

    Kudryashova, E.V.; Visser, A.J.W.G.; Hoek, A. van; Jongh, H.H.J. de


    To stabilize air-water interfaces, as in foams, the adsorption of surface-active components is a prerequisite. An approach to controlling the surface activity of proteins is noncovalent complex formation with a polyelectrolyte in the bulk phase. The molecular properties of egg white ovalbumin in a

  3. Magnetic resonance and fluorescence studies on pyruvate dehydrogenase complexes and their small molecular weight constituents

    NARCIS (Netherlands)

    Grande, H.J.


    The articles presented in this thesis do not describe at first glance one well-defined subject. They are, however, in fact connected by one central theme: the study of large enzyme aggregates by molecular physical methods. Chosen was the pyruvate dehydrogenase complex (PDC) because of its

  4. Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer

    DEFF Research Database (Denmark)

    Solov'yov, Ilia A.; Korol, Andrei V.; Solov'yov, Andrey V.

    efficiency of MBN Explorer is comparable to that of other, more specialized software packages, making it a viable multi-purpose alternative for the computational modeling of complex molecular systems. A number of detailed case studies presented in the second part of this book demonstrate MBN Explorer......This book introduces readers to MesoBioNano (MBN) Explorer - a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface - the MBN Studio - which enables the set......, and guides readers through its applications in numerous areas of research in bio- and chemical physics and material science - ranging from the nano- to the mesoscale. MBN Explorer is particularly suited to computing the system's energy, to optimizing molecular structure, and to exploring the various facets...

  5. Low Molecular Weight Chitosan–Insulin Polyelectrolyte Complex: Characterization and Stability Studies

    Directory of Open Access Journals (Sweden)

    Zakieh I. Al-Kurdi


    Full Text Available The aim of the work reported herein was to investigate the effect of various low molecular weight chitosans (LMWCs on the stability of insulin using USP HPLC methods. Insulin was found to be stable in a polyelectrolyte complex (PEC consisting of insulin and LMWC in the presence of a Tris-buffer at pH 6.5. In the presence of LMWC, the stability of insulin increased with decreasing molecular weight of LMWC; 13 kDa LMWC was the most efficient molecular weight for enhancing the physical and chemical stability of insulin. Solubilization of insulin-LMWC polyelectrolyte complex (I-LMWC PEC in a reverse micelle (RM system, administered to diabetic rats, results in an oral delivery system for insulin with acceptable bioactivity.

  6. Coarse-grained molecular dynamics simulations for giant protein-DNA complexes (United States)

    Takada, Shoji

    Biomolecules are highly hierarchic and intrinsically flexible. Thus, computational modeling calls for multi-scale methodologies. We have been developing a coarse-grained biomolecular model where on-average 10-20 atoms are grouped into one coarse-grained (CG) particle. Interactions among CG particles are tuned based on atomistic interactions and the fluctuation matching algorithm. CG molecular dynamics methods enable us to simulate much longer time scale motions of much larger molecular systems than fully atomistic models. After broad sampling of structures with CG models, we can easily reconstruct atomistic models, from which one can continue conventional molecular dynamics simulations if desired. Here, we describe our CG modeling methodology for protein-DNA complexes, together with various biological applications, such as the DNA duplication initiation complex, model chromatins, and transcription factor dynamics on chromatin-like environment.

  7. Excitonic superfluid phase in double bilayer graphene (United States)

    Li, J. I. A.; Taniguchi, T.; Watanabe, K.; Hone, J.; Dean, C. R.


    A spatially indirect exciton is created when an electron and a hole, confined to separate layers of a double quantum well system, bind to form a composite boson. Such excitons are long-lived, and in the limit of strong interactions are predicted to undergo a Bose-Einstein condensate-like phase transition into a superfluid ground state. Here, we report evidence of an exciton condensate in the quantum Hall effect regime of double-layer structures of bilayer graphene. Interlayer correlation is identified by quantized Hall drag at matched layer densities, and the dissipationless nature of the phase is confirmed in the counterflow geometry. A selection rule for the condensate phase is observed involving both the orbital and valley indices of bilayer graphene. Our results establish double bilayer graphene as an ideal system for studying the rich phase diagram of strongly interacting bosonic particles in the solid state.

  8. Exciton diffusion and dissociation in conjugated polymer/fullerene heterostructures

    NARCIS (Netherlands)

    Markov, D.E.; Amsterdam, E.; Blom, P.W.M.; Sieval, A.B.; Hummelen, J.C.; Heremans, PL; Muccini, M; Hofstraat, H


    Time-resolved luminescence spectroscopy has been used to investigate exciton diffusion in thin films of poly(p-phenylene vinylene) (PPV) based derivatives. Exciton density distribution upon photoexcitation in polymer/fullerene heterostructures has been modeled and exciton diffusion length values of

  9. Emergence of hydrogen bonds from molecular dynamics simulation of substituted N-phenylthiourea-catechol oxidase complex. (United States)

    Park, Kyung-Lae


    A series of N-phenylthiourea derivatives was built starting from the X-ray structure in the molecular mechanics framework and the interaction profile in the complex with the catechol oxidase was traced using molecular dynamics simulation. The results showed that the geometry and interactions between ligand and receptor were highly related to the position of the substituted side chains of phenyl moiety. At the end of molecular dynamics run, a concentrated multicenter hydrogen bond was created between the substituted ligand and receptor. The conformation of the ligand itself were also restricted in the receptor pocket. Furthermore, the simulation time of 50 ns were found to be long enough to explore the relevant conformational space and the stationary behavior of the molecular dynamic could be observed.

  10. Thiobiuret based Ni(II) and Co(III) complexes: Synthesis, molecular structures and DFT studies (United States)

    Sherzaman, Saira; Sadiq-ur-Rehman; Ahmed, Muhammad Naeem; Khan, Bilal Ahmad; Mahmood, Tariq; Ayub, Khurshid; Tahir, Muhammad Nawaz


    Synthesis, molecular structures and DFT investigations of two new complexes of Ni(II) and Co(III) with (Z)-3-(3,3-dimethylbutanoyl)-1,1-diethyl-2-thiobiuret ligand are reported. Characterization of these complexes was achieved by spectroanalytical techniques (FT-IR, UV-vis and 1H NMR), and the structures were finally confirmed unequivocally by single crystal X-ray diffraction analysis. The obtained data of UV-vis, FT-IR and 1HNMR were compared with the literature values which satisfactorily confirmed the synthesis of ligand and their complexes. X-ray studies revealed the square planar and octahedral geometry of both Ni(II) and Co(III) complexes, respectively. Density functional theory (DFT) studies were performed to compare the theoretical results with experimental (X-ray as well as spectroanalytical) results, and good correlation was observed. Frontier molecular orbitals (FMOs) and molecular electrostatic potential (MEP) analyses revealed the reactivity and charge distribution in both complexes.

  11. Excitonic dynamical Franz-Keldysh effect

    DEFF Research Database (Denmark)

    Nordstrøm, K.B.; Johnsen, Kristinn; Allen, S.J.


    The dynamical Franz-Keldysh effect is exposed by exploring near-band-gap absorption in the presence of intense THz electric fields. It bridges the gap between the de Franz-Keldysh effect and multiphoton absorption and competes with the THz ac Stark effect in shifting the energy of the excitonic...... resonance. A theoretical model which includes the strong THz field nonperturbatively via a nonequilibrium Green functions technique is able to describe the dynamical Franz-Keldysh effect in the presence of excitonic absorption....

  12. Exciton broadening in WS2/graphene heterostructures (United States)

    Hill, Heather M.; Rigosi, Albert F.; Raja, Archana; Chernikov, Alexey; Roquelet, Cyrielle; Heinz, Tony F.


    We have used optical spectroscopy to observe spectral broadening of WS2 exciton reflectance peaks in heterostructures of monolayer WS2 capped with mono- to few-layer graphene. The broadening is found to be similar for the A and B excitons and on the order of 5-10 meV. No strong dependence on the number of graphene layers was observed within experimental uncertainty. The broadening can be attributed to charge- and energy-transfer processes between the two materials, providing an observed lower bound for the corresponding time scales of 65 fs.

  13. Preparation, characterization and molecular modeling studies of the inclusion complex of Caffeine with Beta-cyclodextrin (United States)

    Prabu, Samikannu; Swaminathan, Meenakshisundaram; Sivakumar, Krishnamoorthy; Rajamohan, Rajaram


    The formation through supramolecular interaction of a host-guest inclusion complex of caffeine (CA) with nano-hydrophobic cavity beta-cyclodextrin (β-CD) is achieved by a physical mixture, a kneading method and a co-precipitation method. The formation of the inclusion complex of CA with β-CD in solution state is confirmed by UV-visible spectrophotometer, fluorescence spectrophotometer and time-resolved fluorescence spectrophotometer. The stoichiometry of the inclusion complex is 1:1; the imidazole ring and pyrimidine ring of caffeine is deeply entrapped in the beta-cyclodextrin as confirmed by spectral shifts. The Benesi-Hildebrand plot is used to calculate the binding constant of the inclusion complex of CA with β-CD at room temperature. The Gibbs free energy change of the inclusion complex process is calculated and the process is found to be spontaneous. The thermal stability of the inclusion complex of CA with β-CD is analyzed using differential scanning calorimetry. The crystal structure modification of a solid inclusion complex is confirmed by scanning electron microscopy image analysis. The formation of the inclusion complex of CA with β-CD in the solid phase is also confirmed by FT-IR and XRD. The formation of the inclusion complex between CA and β-CD, as confirmed by molecular docking studies, is in good relationship with the results obtained through different experimental methods.

  14. Novel water-soluble fisetin/cyclodextrins inclusion complexes: Preparation, characterization, molecular docking and bioavailability. (United States)

    Zhang, Jian-Qiang; Jiang, Kun-Ming; An, Kun; Ren, Si-Hao; Xie, Xiao-Guang; Jin, Yi; Lin, Jun


    Novel water-soluble inclusion complexes for fisetin (FIT) were developed by introducing β-cyclodextrin (β-CD) and γ-CD. Properties of the obtained complexes, as well as the interactions between each component, were systematically investigated in both solution and solid states by means of ESI-MS, NMR, FT-IR, XRD, DSC, SEM etc. All characterization information demonstrated that FIT/CDs inclusion complexes were formed, and exhibited different spectroscopic features and properties from FIT. A complex with 1:1 stoichiometry of FIT and CDs was confirmed with Job's method. Meanwhile, as supported by molecular modeling calculations, we suggested that phenyl group (C ring) of FIT molecule was included in the CDs cavity from the wide side. Moreover, the water solubility of FIT/CDs was successfully improved from 2.8 mg/mL (in ethanol aqueous solution) to 4.5 mg/mL (FIT/β-CD complex) and 7.8 mg/mL (FIT/γ-CD complex), and higher thermal stability results were shown by thermal analysis for those complexes. Notably, the inclusion complexes displayed almost two times higher cytotoxicity compared to free FIT against Hela and MCF-7 cells. These results suggested that FIT/CDs complexes could be potentially useful in food industry and healthcare area. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Intercalative interaction of asymmetric copper(II) complex with DNA: experimental, molecular docking, molecular dynamics and TDDFT studies. (United States)

    Hu, Wei; Deng, Suwen; Huang, Jianyin; Lu, Yanmei; Le, Xueyi; Zheng, Wenxu


    The intercalative interactions of small molecules with DNA are important in a variety of biological processes including mutagenesis, carcinogenesis, and chemotherapy. A comprehensive research protocol including experiments and calculations was employed to investigate the intercalative interaction between metallointercalator copper(II) complex and DNA. The intercalative binding mode has been validated by UV spectra, fluorescence spectra, CD spectra and viscosity measurements. The classical molecular dynamics simulation was carried out to investigate the intercalative interaction between asymmetric copper(II) complex and DNA. An analytical method was proposed to simulate the dynamically changing absorption spectra of intercalator/DNA system. According to the established model, the changing process of the electronic absorption spectra for intercalator/DNA system can be predicted accurately. A rational explanation for the change law of absorption spectra has been proposed. Moreover, the analyses of the frontier orbital reveal that the red shift of the absorption spectra is due to the increase of π orbital energy caused by the coupling of the π orbital of the intercalated ligand with the π orbital of DNA. This cause of red shift of spectra is completely different from the previous inference. All these insights are of crucial importance for correctly analyzing the absorption spectra of intercalative interaction, as well as for explaining the macroscopic phenomena observed in experiments at the molecular level. © 2013.

  16. Anatomy of an Exciton : Vibrational Distortion and Exciton Coherence in H- and J-Aggregates

    NARCIS (Netherlands)

    Tempelaar, Roel; Stradomska, Anna; Knoester, Jasper; Spano, Frank C.


    In organic materials, coupling of electronic excitations to vibrational degrees of freedom results in polaronic excited states. Through numerical calculations, we demonstrate that the vibrational distortion field accompanying such a polaron scales as the product of the excitonic interaction field

  17. Theoretical Study of Copper Complexes: Molecular Structure, Properties, and Its Application to Solar Cells

    Directory of Open Access Journals (Sweden)

    Jesus Baldenebro-Lopez


    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.

  18. Adsorption and solution properties of bottle-brush polyelectrolyte complexes: effect of molecular weight and stoichiometry. (United States)

    Shovsky, Alexander; Varga, Imre; Makuška, Ričardas; Claesson, Per M


    Polyelectrolyte complexes (PECs) self-assembled from bottle-brush polyelectrolytes, having a cationic main chain and uncharged side chains, and linear anionic sodium polystyrenesulfonate (NaPSS) have been investigated with emphasis on (i) the charge density and side chain density of the bottle-brush polyelectrolyte, (ii) the molecular weight of NaPSS, and (iii) the charge stoichiometry of the mixture. Light scattering and electrophoretic mobility data demonstrate that small molecular complexes are formed when the PEO45 side chain density is sufficiently high to provide steric stabilization and prevent PEC aggregation. The adsorption of PECs on negatively charged silicon oxynitride was investigated using dual polarization interferometry, and the time evolution of the adsorbed amount and thickness was determined. Cationic, uncharged, and negatively charged complexes all adsorb to negatively charged silicon oxynitride, and maximum adsorption is achieved for positively charged complexes containing small amounts of PSS. The adsorbed amount and the kinetics of adsorption are reduced with increasing PSS content, and for any given stoichiometry with increasing PSS molecular weight. These findings are discussed in terms of the PEC structure and the ability of anionic polyelectrolytes to leave the PECs during adsorption.

  19. Atomic level insights into realistic molecular models of dendrimer-drug complexes through MD simulations. (United States)

    Jain, Vaibhav; Maiti, Prabal K; Bharatam, Prasad V


    Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH 2 ) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH 2 ) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH 2 ) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an

  20. Coherent quantum dynamics of excitons in monolayer transition metal dichalcogenides

    KAUST Repository

    Moody, Galan


    Transition metal dichalcogenides (TMDs) have garnered considerable interest in recent years owing to their layer thickness-dependent optoelectronic properties. In monolayer TMDs, the large carrier effective masses, strong quantum confinement, and reduced dielectric screening lead to pronounced exciton resonances with remarkably large binding energies and coupled spin and valley degrees of freedom (valley excitons). Coherent control of valley excitons for atomically thin optoelectronics and valleytronics requires understanding and quantifying sources of exciton decoherence. In this work, we reveal how exciton-exciton and exciton-phonon scattering influence the coherent quantum dynamics of valley excitons in monolayer TMDs, specifically tungsten diselenide (WSe2), using two-dimensional coherent spectroscopy. Excitation-density and temperature dependent measurements of the homogeneous linewidth (inversely proportional to the optical coherence time) reveal that exciton-exciton and exciton-phonon interactions are significantly stronger compared to quasi-2D quantum wells and 3D bulk materials. The residual homogeneous linewidth extrapolated to zero excitation density and temperature is ~1:6 meV (equivalent to a coherence time of 0.4 ps), which is limited only by the population recombination lifetime in this sample. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

  1. Exciton diffusion length in narrow bandgap polymers

    NARCIS (Netherlands)

    Mikhnenko, Oleksandr V.; Azimi, Hamed; Scharber, Markus; Morana, Mauro; Blom, Paul W. M.; Loi, Maria Antonietta

    We developed a new method to accurately extract the singlet exciton diffusion length in organic semiconductors by blending them with a low concentration of methanofullerene[6,6]-phenyl-C-61-butyric acid methyl ester (PCBM). The dependence of photoluminescence (PL) decay time on the fullerene

  2. Effective models for excitons in carbon nanotubes

    DEFF Research Database (Denmark)

    Cornean, Horia; Duclos, Pierre; Ricaud, Benjamin


    We analyse the low lying spectrum of a model of excitons in carbon nanotubes. Consider two particles with opposite charges and a Coulomb self-interaction, placed on an infinitely long cylinder. If the cylinder radius becomes small, the low lying spectrum of their relative motion is well described...

  3. Effective models for excitons in carbon nanotubes

    DEFF Research Database (Denmark)

    Cornean, Horia; Duclos, Pierre; Ricaud, Benjamin

    We analyse the low lying spectrum of a model of excitons in carbon nanotubes. Consider two particles with a Coulomb self-interaction, placed on an infinitely long cylinder. If the cylinder radius becomes small, the low lying spectrum is well described by a one-dimensional effective Hamiltonian...

  4. Excitons in van der Waals heterostructures

    DEFF Research Database (Denmark)

    Latini, Simone; Olsen, Thomas; Thygesen, Kristian Sommer


    The existence of strongly bound excitons is one of the hallmarks of the newly discovered atomically thin semiconductors. While it is understood that the large binding energy is mainly due to the weak dielectric screening in two dimensions, a systematic investigation of the role of screening on two...

  5. Including Quantum Effects in the Dynamics of Complex (i.e., Large)Molecular Systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, William H.


    The development in the 1950's and 60's of crossed molecular beam methods for studying chemical reactions at the single-collision molecular level stimulated the need and desire for theoretical methods to describe these and other dynamical processes in molecular systems. Chemical dynamics theory has made great strides in the ensuing decades, so that methods are now available for treating the quantum dynamics of small molecular systems essentially completely. For the large molecular systems that are of so much interest nowadays (e.g. chemical reactions in solution, in clusters, in nano-structures, in biological systems, etc.), however, the only generally available theoretical approach is classical molecular dynamics (MD) simulations. Much effort is currently being devoted to the development of approaches for describing the quantum dynamics of these complex systems. This paper reviews some of these approaches, especially the use of semiclassical approximations for adding quantum effects to classical MD simulations, also showing some new versions that should make these semiclassical approaches even more practical and accurate.

  6. N₂reduction and hydrogenation to ammonia by a molecular iron-potassium complex. (United States)

    Rodriguez, Meghan M; Bill, Eckhard; Brennessel, William W; Holland, Patrick L


    The most common catalyst in the Haber-Bosch process for the hydrogenation of dinitrogen (N(2)) to ammonia (NH(3)) is an iron surface promoted with potassium cations (K(+)), but soluble iron complexes have neither reduced the N-N bond of N(2) to nitride (N(3-)) nor produced large amounts of NH(3) from N(2). We report a molecular iron complex that reacts with N(2) and a potassium reductant to give a complex with two nitrides, which are bound to iron and potassium cations. The product has a Fe(3)N(2) core, implying that three iron atoms cooperate to break the N-N triple bond through a six-electron reduction. The nitride complex reacts with acid and with H(2) to give substantial yields of N(2)-derived ammonia. These reactions, although not yet catalytic, give structural and spectroscopic insight into N(2) cleavage and N-H bond-forming reactions of iron.

  7. N2 Reduction and Hydrogenation to Ammonia by a Molecular Iron-Potassium Complex (United States)

    Rodriguez, Meghan M.; Bill, Eckhard; Brennessel, William W.; Holland, Patrick L.


    The most common catalyst in the Haber-Bosch process for the hydrogenation of dinitrogen (N2) to ammonia is an iron surface promoted with K+, but soluble iron complexes have neither reduced the N-N bond of N2 to nitride nor produced large amounts of NH3 from N2. We report a molecular iron complex that reacts with N2 and a potassium reductant to give a complex with two nitrides, which are bound to iron and potassium cations. The product has a Fe3N2 core, implying that three iron atoms cooperate to break the N-N triple bond through a six-electron reduction. The nitride complex reacts with acid and with H2 to give substantial yields of N2-derived ammonia. These reactions, though not yet catalytic, give structural and spectroscopic insight into N2 cleavage and N-H bond-forming reactions of iron. PMID:22076372

  8. Impact of backbone fluorination on nanoscale morphology and excitonic coupling in polythiophenes. (United States)

    Hu, Zhongjian; Haws, Ryan T; Fei, Zhuping; Boufflet, Pierre; Heeney, Martin; Rossky, Peter J; Vanden Bout, David A


    Fluorination represents an important strategy in developing high-performance conjugated polymers for photovoltaic applications. Here, we use regioregular poly(3-ethylhexylthiophene) (P3EHT) and poly(3-ethylhexyl-4-fluorothiophene) (F-P3EHT) as simplified model materials, using single-molecule/aggregate spectroscopy and molecular dynamic simulations, to elucidate the impacts of backbone fluorination on morphology and excitonic coupling on the molecular scale. Despite its high regioregularity, regioregular P3EHT exhibits a rather broad distribution in polymer chain conformation due to the strong steric hindrance of bulky ethylhexyl side chains. This conformational variability results in disordered interchain morphology even between a few chains, prohibiting long-range effective interchain coupling. In stark contrast, the experimental and molecular dynamic calculations reveal that backbone fluorination of F-P3EHT leads to an extended rod-like single-chain conformation and hence highly ordered interchain packing in aggregates. Surprisingly, the ordered and close interchain packing in F-P3EHT does not lead to strong excitonic coupling between the chains but rather to dominant intrachain excitonic coupling that greatly reduces the molecular energetic heterogeneity.

  9. Structure of host-guest complexes between dibenzo-18-crown-6 and water, ammonia, methanol, and acetylene: evidence of molecular recognition on the complexation. (United States)

    Kusaka, Ryoji; Kokubu, Satoshi; Inokuchi, Yoshiya; Haino, Takeharu; Ebata, Takayuki


    Complexes of dibenzo-18-crown-6 (DB18C6, host) with water, ammonia, methanol, and acetylene (guest) in supersonic jets have been characterized by laser induced fluorescence (LIF), UV-UV hole-burning (UV-UV HB), and IR-UV double resonance (IR-UV DR) spectroscopy. Firstly, we reinvestigated the conformation of bare DB18C6 (species m1 and m2) and the structure of DB18C6-H(2)O (species a) [R. Kusaka, Y. Inokuchi, T. Ebata, Phys. Chem. Chem. Phys., 2008, 10, 6238] by measuring IR-UV DR spectra in the region of the methylene CH stretching vibrations. The IR spectral feature of the methylene CH stretch of DB18C6-H(2)O is clearly different from those of bare DB18C6 conformers, suggesting that DB18C6 changes its conformation when forming a complex with a water molecule. With the aid of Monte Carlo simulation for extensive conformational search and density functional calculations (M05-2X/6-31+G*), we reassigned species m1 and m2 to conformers having C(1) and C(2) symmetry, respectively. Also, we confirmed the DB18C6 part in species a of DB18C6-H(2)O to be "boat" conformation (C(2v)). Secondly, we identified nine, one, and two species for the DB18C6 complexes with ammonia, methanol, and acetylene, respectively, by the combination of LIF and UV-UV HB spectroscopy. From the IR spectroscopic measurement in the methylene CH stretching region, a similar conformational change was identified in the DB18C6-ammonia complexes, but not in the complexes with methanol or acetylene. The structures of all the complexes were determined by analyzing the electronic transition energies, exciton splitting, and IR spectra in the region of the OH, NH, and CH stretching vibrations. In DB18C6-ammonia complexes, an ammonia molecule is incorporated into the cavity of the boat conformation by forming "bifurcated" and "bidentate" hydrogen-bond (H-bond), similar to the case of the DB18C6-H(2)O complex. On the other hand, in the DB18C6-methanol and -acetylene complexes, methanol and acetylene molecules

  10. DNA binding affinity of a macrocyclic copper(II) complex: Spectroscopic and molecular docking studies. (United States)

    Shahabadi, Nahid; Hakimi, Mohammad; Morovati, Teimoor; Fatahi, Navid


    The interaction of a novel macrocyclic copper(II) complex, ([CuL(ClO 4 ) 2 ] that L is 1,3,6,10,12,15-hexaazatricyclo[ 6,10 ]eicosane) with calf thymus DNA (ct-DNA) was investigated by various physicochemical techniques and molecular docking at simulated physiological conditions (pH = 7.4). The absorption spectra of the Cu(II) complex with ct-DNA showed a marked hyperchroism with 10 nm blue shift. The intrinsic binding constant (K b ) was determined as 1.25 × 10 4 M -1 , which is more in keeping with the groove binding with DNA. Furthermore, competitive fluorimetric studies with Hoechst33258 have shown that Cu(II) complex exhibits the ability to displace the ct-DNA-bound Hoechst33258 indicating that it binds to ct-DNA in strong competition with Hoechst33258 for the groove binding. Also, no change in the relative viscosity of ct-DNA and fluorescence intensity of ct-DNA-MB complex in the present of Cu(II) complex is another evidence to groove binding. The thermodynamic parameters are calculated by van't Hoff equation, which demonstrated that hydrogen bonds and van der Waals interactions played major roles in the binding reaction. The experimental results were in agreement with the results obtained via molecular docking study.

  11. Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Makino, Debora Lika, E-mail:; Conti, Elena [Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany)


    The crystallographic steps towards the structure determination of a complete eukaryotic exosome complex bound to RNA are presented. Phasing of this 11-protein subunit complex was carried out via molecular replacement. The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3′ degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryotic exosome-like complexes are known, but how the complete assembly is organized to fulfil processive RNA degradation has been unclear. An atomic snapshot of a Saccharomyces cerevisiae 420 kDa exosome complex bound to an RNA substrate in the pre-cleavage state of a hydrolytic reaction has been determined. Here, the crystallographic steps towards the structural elucidation, which was carried out by molecular replacement, are presented.

  12. Structural insights into the molecular mechanism of the m(6)A writer complex. (United States)

    Śledź, Paweł; Jinek, Martin


    Methylation of adenosines at the N(6) position (m(6)A) is a dynamic and abundant epitranscriptomic mark that regulates critical aspects of eukaryotic RNA metabolism in numerous biological processes. The RNA methyltransferases METTL3 and METTL14 are components of a multisubunit m(6)A writer complex whose enzymatic activity is substantially higher than the activities of METTL3 or METTL14 alone. The molecular mechanism underpinning this synergistic effect is poorly understood. Here we report the crystal structure of the catalytic core of the human m(6)A writer complex comprising METTL3 and METTL14. The structure reveals the heterodimeric architecture of the complex and donor substrate binding by METTL3. Structure-guided mutagenesis indicates that METTL3 is the catalytic subunit of the complex, whereas METTL14 has a degenerate active site and plays non-catalytic roles in maintaining complex integrity and substrate RNA binding. These studies illuminate the molecular mechanism and evolutionary history of eukaryotic m(6)A modification in post-transcriptional genome regulation.

  13. Symposium GC: Nanoscale Charge Transport in Excitonic Solar Cells

    Energy Technology Data Exchange (ETDEWEB)

    Bommisetty, Venkat [Univ. of South Dakota, Vermillion, SD (United States)


    This paper provides a summary only and table of contents of the sessions. Excitonic solar cells, including all-organic, hybrid organic-inorganic and dye-sensitized solar cells (DSSCs), offer strong potential for inexpensive and large-area solar energy conversion. Unlike traditional inorganic semiconductor solar cells, where all the charge generation and collection processes are well understood, these excitonic solar cells contain extremely disordered structures with complex interfaces which results in large variations in nanoscale electronic properties and has a strong influence on carrier generation, transport, dissociation and collection. Detailed understanding of these processes is important for fabrication of highly efficient solar cells. Efforts to improve efficiency are underway at a large number of research groups throughout the world focused on inorganic and organic semiconductors, photonics, photophysics, charge transport, nanoscience, ultrafast spectroscopy, photonics, semiconductor processing, device physics, device structures, interface structure etc. Rapid progress in this multidisciplinary area requires strong synergetic efforts among researchers from diverse backgrounds. Such effort can lead to novel methods for development of new materials with improved photon harvesting and interfacial treatments for improved carrier transport, process optimization to yield ordered nanoscale morphologies with well defined electronic structures.

  14. Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer

    DEFF Research Database (Denmark)

    Solov'yov, Ilia A.; Korol, Andrei V.; Solov'yov, Andrey V.

    This book introduces readers to MesoBioNano (MBN) Explorer - a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface - the MBN Studio - which enables the set......-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science...... practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational...

  15. Synthesis, electron paramagnetic resonance studies and molecular calculations of N-aminopyrimidine salicylaldiminato copper (II) complex (United States)

    Yalçın, Şerife Pınar; Ceylan, Ümit; Sönmez, Mehmet; Hacıyusufoğlu, Mehmet Emin; Karavelioğlu, Hatice


    In this study, Cu(II) complex, C52H40CuN6O10, was synthesized and the molecular structure was characterized by experimental Electron Paramagnetic Resonance (EPR), vibrational frequencies, absorption wavelengths and compared with theoretical methods. The molecular geometry was calculated and optimized by using Gaussian 09 software and DFT-B3LYP and B3PW91 methods with the LanL2DZ basis sets in ground state. The theoretical vibrational frequencies, was optimized geometric parameters such as bond lengths, bond angles and torsion angles and absorption wavelengths, NBO, FMO analysis, HOMO-LUMO energy and nonlinear optical properties, molecular electrostatic potential, spin density have been calculated via quantum chemical methods. Theoretically calculated data were compared with experimentally measured data. Also, the results obtained by using the two basis sets were compared with each other.

  16. Computational Molecular Nanoscience Study of the Properties of Copper Complexes for Dye-Sensitized Solar Cells (United States)

    Baldenebro-López, Jesús; Castorena-González, José; Flores-Holguín, Norma; Almaral-Sánchez, Jorge; Glossman-Mitnik, Daniel


    In this work, we studied a copper complex-based dye, which is proposed for potential photovoltaic applications and is named Cu (I) biquinoline dye. Results of electron affinities and ionization potentials have been used for the correlation between different levels of calculation used in this study, which are based on The Density Functional Theory (DFT) and time-dependent (TD) DFT. Further, the maximum absorption wavelengths of our theoretical calculations were compared with the experimental data. It was found that the M06/LANL2DZ + DZVP level of calculation provides the best approximation. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT. PMID:23443107

  17. Computational Molecular Nanoscience Study of the Properties of Copper Complexes for Dye-Sensitized Solar Cells

    Directory of Open Access Journals (Sweden)

    Jorge Almaral-Sánchez


    Full Text Available In this work, we studied a copper complex-based dye, which is proposed for potential photovoltaic applications and is named Cu (I biquinoline dye. Results of electron affinities and ionization potentials have been used for the correlation between different levels of calculation used in this study, which are based on The Density Functional Theory (DFT and time-dependent (TD DFT. Further, the maximum absorption wavelengths of our theoretical calculations were compared with the experimental data. It was found that the M06/LANL2DZ + DZVP level of calculation provides the best approximation. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT.

  18. Species Identification of Mycobacterium avium Complex Isolates by a Variety of Molecular Techniques


    Beggs, Marjorie L.; Stevanova, Rossina; Eisenach, Kathleen D.


    Organisms in the Mycobacterium avium complex (MAC; M. avium, M. intracellulare, and “nonspecific or X” MAC) are emerging pathogens among individual organisms of which significant genetic variability is displayed. The objective of the present study was to evaluate various molecular methods for the rapid and definitive identification of MAC species. Isolates were obtained from both human immunodeficiency virus (HIV)-positive patients and HIV-negative patients with and without known predisposing...

  19. PhytoAuthent: Molecular authentication of complex herbal food supplements for safety and efficacy

    Directory of Open Access Journals (Sweden)

    Mihael Ichim


    Full Text Available The PhytoAuthent project was structured to gather, test, develop and apply, in real life case scenarios, molecular techniques, such as biochemical fingerprinting and DNA sequence-based methods, for plant identification of constituents in complex herbal products. The project had a strong focus on applied aspects like protecting consumers from health risks associated with product substitution and contamination of herbal products.

  20. Hydrogen storage in C3Ti complex using quantum chemical methods and molecular dynamics simulations. (United States)

    Kalamse, Vijayanand; Wadnerkar, Nitin; Chaudhari, Ajay


    The hydrogen storage capacity of C(3)Ti and C(3)Ti(+) complex was studied using second order Møller-Plesset (MP2) and density functional theory (DFT) methods with different exchange and correlation functionals. Four and five H(2) molecules can be adsorbed on C(3)Ti and C(3)Ti(+) complex respectively at all the levels of theory used. This corresponds to the gravimetric H(2) uptake capacity of 8.77 and 10.73 wt % for the former and the latter respectively. The nature of interactions between different molecules in H(2) adsorbed complexes is also studied using many-body analysis approach. In the case of C(3)Ti(4H(2)) complex, total five-body interactions is negligible whereas for C(3)Ti(+)(5H(2)) relaxation energy is negligible. All the many-body energies have significant contribution to the binding energy of a respective complex. Atom-centered density matrix propagation molecular dynamics simulations were carried out using different methods to confirm whether H(2) molecules remain adsorbed on C(3)Ti and C(3)Ti(+) complex at room temperature. Adsorption Gibbs free energies show that four and five H(2) molecule adsorption on C(3)Ti and C(3)Ti(+) at room temperature is energetically favorable and unfavorable respectively using MP2 as well as DFT methods used here. H(2) adsorption is thermodynamically favorable over a wide range of temperature on the C(3)Ti than C(3)Ti(+)complex.

  1. Synthesis and molecular structures of hydrotris(dimethylpyrazolyl)borate complexes of the lanthanides

    Energy Technology Data Exchange (ETDEWEB)

    Liu, S.Y.; Maunder, G.H.; Sella, A. [Christopher Ingold Labs., London (United Kingdom)] [and others


    The reaction of lanthanide triflates with 2 equiv of potassium hydrotris(dimethylpyrazoly)borate (Tp{sup Me}{sub 2}) gives good yields of complexes of composition Ln(Tp{sup Me}{sub 2})OTf. For La (2), Ce (3), Pr (4), and Nd (5) the complexes are seven-coordinate in the solid state with the triflate group coordinated to the metal in unidentate fashion. Complex 5 crystallizes in the monoclinic space group P2/c with a = 17.629(3) {angstrom}, b = 12.740(2) {angstrom}, c = 18.163(3) {angstrom}, {beta} = 107.34(1){degrees}, V = 3893(1) {angstrom}{sup 3}, Z = 4, and R{sub w} = 0.0458. For the complexes of Y (1), Sm (6), Eu (7), Gd (8), Dy (9), Ho (10), and Yb (11), the smaller size of the metal ion leads to ejection of the triflate from the coordination sphere and the complexes are ionic in the solid state with a six-coordinate metal center. Complex 11 crystallizes in the monoclinic space group C2/m with a = 16.593(7) {angstrom}, b = 13.671(5) {angstrom}, c = 8.746(2) {angstrom}, {beta} = 91.66(3){degrees}, V = 1983(1) {angstrom}{sup 3}, Z = 2, and R{sub w} = 0.0416. In solution, however, complex 6 adopts a seven-coordinate molecular structure with the triflate ion within the first coordination sphere.

  2. Charge-Transfer Dynamics in the Lowest Excited State of a Pentacene–Fullerene Complex: Implications for Organic Solar Cells

    KAUST Repository

    Joseph, Saju


    We characterize the dynamic nature of the lowest excited state in a pentacene/C60 complex on the femtosecond time scale, via a combination of ab initio molecular dynamics and time-dependent density functional theory. We analyze the correlations between the molecular vibrations of the complex and the oscillations in the electron-transfer character of its lowest excited state, which point to vibration-induced coherences between the (pentacene-based) local-excitation (LE) state and the complex charge-transfer (CT) state. We discuss the implications of our results on this model system for the exciton-dissociation process in organic solar cells.

  3. Fine structure of the exciton electroabsorption in semiconductor superlattices

    Energy Technology Data Exchange (ETDEWEB)

    Monozon, B.S., E-mail: [Physics Department, Marine Technical University, 3 Lotsmanskaya Str., 190008 St.Petersburg (Russian Federation); Schmelcher, P. [Zentrum für Optische Quantentechnologien, The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany)


    Wannier-Mott excitons in a semiconductor layered superlattice (SL) are investigated analytically for the case that the period of the superlattice is much smaller than the 2D exciton Bohr radius. Additionally we assume the presence of a longitudinal external static electric field directed parallel to the SL axis. The exciton states and the optical absorption coefficient are derived in the tight-binding and adiabatic approximations. Strong and weak electric fields providing spatially localized and extended electron and hole states, respectively, are studied. The dependencies of the exciton states and the exciton absorption spectrum on the SL parameters and the electric field strength are presented in an explicit form. We focus on the fine structure of the ground quasi-2D exciton level formed by the series of closely spaced energy levels adjacent from the high frequencies. These levels are related to the adiabatically slow relative exciton longitudinal motion governed by the potential formed by the in-plane exciton state. It is shown that the external electric fields compress the fine structure energy levels, decrease the intensities of the corresponding optical peaks and increase the exciton binding energy. A possible experimental study of the fine structure of the exciton electroabsorption is discussed.

  4. Relaxation of nonthermal hh and lh excitons in ZnSe quantum wells

    DEFF Research Database (Denmark)

    Kalt, H.; Hoffmann, J.; Umlauff, M.


    The strong exciton-LO phonon coupling in ZnSe QWs gives a direct access to the relaxation dynamics of nonthermal, free heavy-hole and light-hole excitons. Narrow hot-exciton distributions can be generated by LO-phonon assisted exciton formation. The thermalization of these excitons is monitored b...

  5. Effect of Spectral Density Shapes on the Excitonic Structure and Dynamics of the Fenna-Matthews-Olson Trimer from Chlorobaculum tepidum. (United States)

    Kell, Adam; Blankenship, Robert E; Jankowiak, Ryszard


    The Fenna-Matthews-Olson (FMO) trimer (composed of identical subunits) from the green sulfur bacterium Chlorobaculum tepidum is an important protein model system to study exciton dynamics and excitation energy transfer (EET) in photosynthetic complexes. In addition, FMO is a popular model for excitonic calculations, with many theoretical parameter sets reported describing different linear and nonlinear optical spectra. Due to fast exciton relaxation within each subunit, intermonomer EET results predominantly from the lowest energy exciton states (contributed to by BChl a 3 and 4). Using experimentally determined shapes for the spectral densities, simulated optical spectra are obtained for the entire FMO trimer. Simultaneous fits of low-temperature absorption, fluorescence, and hole-burned spectra place constraints on the determined pigment site energies, providing a new Hamiltonian that should be further tested to improve modeling of 2D electronic spectroscopy data and our understanding of coherent and dissipation effects in this important protein complex.

  6. Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory. (United States)

    Mrugalla, Florian; Kast, Stefan M


    Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

  7. AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics. (United States)

    Labbé, Céline M; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O; Pajeva, Ilza; Miteva, Maria A


    AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein-ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein-ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein-ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Saturation behaviour of colloidal PbSe quantum dot exciton emission coupled into silicon photonic circuits. (United States)

    Foell, Charles A; Schelew, Ellen; Qiao, Haijun; Abel, Keith A; Hughes, Stephen; van Veggel, Frank C J M; Young, Jeff F


    We report coupling of the excitonic photon emission from photoexcited PbSe colloidal quantum dots (QDs) into an optical circuit that was fabricated in a silicon-on-insulator wafer using a CMOS-compatible process. The coupling between excitons and sub-μm sized silicon channel waveguides was mediated by a photonic crystal microcavity. The intensity of the coupled light saturates rapidly with the optical excitation power. The saturation behaviour was quantitatively studied using an isolated photonic crystal cavity with PbSe QDs site-selectively located at the cavity mode antinode position. Saturation occurs when a few μW of continuous wave HeNe pump power excites the QDs with a Gaussian spot size of 2 μm. By comparing the results with a master equation analysis that rigorously accounts for the complex dielectric environment of the QD excitons, the saturation is attributed to ground state depletion due to a non-radiative exciton decay channel with a trap state lifetime ~ 3 μs.

  9. Molecular polypyridine-based metal complexes as catalysts for the reduction of CO2. (United States)

    Elgrishi, Noémie; Chambers, Matthew B; Wang, Xia; Fontecave, Marc


    Polypyridyl transition metal complexes represent one of the more thoroughly studied classes of molecular catalysts towards CO2 reduction to date. Initial reports in the 1980s began with an emphasis on 2nd and 3rd row late transition metals, but more recently the focus has shifted towards earlier metals and base metals. Polypyridyl platforms have proven quite versatile and amenable to studying various parameters that govern product distribution for CO2 reduction. However, open questions remain regarding the key mechanistic steps that govern product selectivity and efficiency. Polypyridyl complexes have also been immobilized through a variety of methods to afford active catalytic materials for CO2 reductions. While still an emerging field, materials incorporating molecular catalysts represent a promising strategy for electrochemical and photoelectrochemical devices capable of CO2 reduction. In general, this class of compounds remains the most promising for the continued development of molecular systems for CO2 reduction and an inspiration for the design of related non-polypyridyl catalysts.

  10. Multiple Exciton Generation in Colloidal Nanocrystals

    Directory of Open Access Journals (Sweden)

    Charles Smith


    Full Text Available In a conventional solar cell, the energy of an absorbed photon in excess of the band gap is rapidly lost as heat, and this is one of the main reasons that the theoretical efficiency is limited to ~33%. However, an alternative process, multiple exciton generation (MEG, can occur in colloidal quantum dots. Here, some or all of the excess energy is instead used to promote one or more additional electrons to the conduction band, potentially increasing the photocurrent of a solar cell and thereby its output efficiency. This review will describe the development of this field over the decade since the first experimental demonstration of multiple exciton generation, including the controversies over experimental artefacts, comparison with similar effects in bulk materials, and the underlying mechanisms. We will also describe the current state-of-the-art and outline promising directions for further development.

  11. Exciton Polaritons in Microcavities New Frontiers

    CERN Document Server

    Sanvitto, Daniele


    In the past decade, there has been a burst of new and fascinating physics associated to the unique properties of two-dimensional exciton polaritons, their recent demonstration of condensation under non-equilibrium conditions and all the related quantum phenomena, which have stimulated extensive research work. This monograph summarizes the current state of the art of research on exciton polaritons in microcavities: their interactions, fast dynamics, spin-dependent phenomena, temporal and spatial coherence, condensation under non-equilibrium conditions, related collective quantum phenomena and most advanced applications. The monograph is written by the most active authors who have strongly contributed to the advances in this area. It is of great interests to both physicists approaching this subject for the first time, as well as a wide audience of experts in other disciplines who want to be updated on this fast moving field.

  12. Excitonic and photonic processes in materials

    CERN Document Server

    Williams, Richard


    This book is expected to present state-of-the-art understanding of a selection of excitonic and photonic processes in useful materials from semiconductors to insulators to metal/insulator nanocomposites, both inorganic and organic.  Among the featured applications are components of solar cells, detectors, light-emitting devices, scintillators, and materials with novel optical properties.  Excitonic properties are particularly important in organic photovoltaics and light emitting devices, as also in questions of the ultimate resolution and efficiency of new-generation scintillators for medical diagnostics,  border security, and nuclear nonproliferation.  Novel photonic and optoelectronic applications benefit from new material combinations and structures to be discussed.

  13. Phonon-assisted exciton formation in ZnO/(Zn, Mg)O single quantum wells grown on C-plane oriented substrates

    Energy Technology Data Exchange (ETDEWEB)

    Béaur, L. [Université Montpellier 2, Laboratoire Charles Coulomb, UMR5221, F-34095 Montpellier (France); CNRS, Laboratoire Charles Coulomb, UMR5221, F-34095 Montpellier (France); Bretagnon, T., E-mail: [Université Montpellier 2, Laboratoire Charles Coulomb, UMR5221, F-34095 Montpellier (France); CNRS, Laboratoire Charles Coulomb, UMR5221, F-34095 Montpellier (France); Guillet, T.; Brimont, C. [Université Montpellier 2, Laboratoire Charles Coulomb, UMR5221, F-34095 Montpellier (France); CNRS, Laboratoire Charles Coulomb, UMR5221, F-34095 Montpellier (France); Gallart, M. [IPCMS, UMR 7504 CNRS-Université de Strasbourg, 23, rue du Loess B.P. 43F-67034 Strasbourg (France); Gil, B. [Université Montpellier 2, Laboratoire Charles Coulomb, UMR5221, F-34095 Montpellier (France); CNRS, Laboratoire Charles Coulomb, UMR5221, F-34095 Montpellier (France); Gilliot, P. [IPCMS, UMR 7504 CNRS-Université de Strasbourg, 23, rue du Loess B.P. 43F-67034 Strasbourg (France); Morhain, C. [CRHEA–CNRS, Rue Bernard Grégory, F-06560 Valbonne (France)


    We report on absorption phenomena in ZnO/(Zn, Mg)O quantum wells grown along the c-axis by molecular beam epitaxy. The optical properties of such quantum wells are affected by a huge internal electric field. For wide quantum wells the absorption is driven by Quantum Confined Stark Effect. Phonon-assisted formation of excitons is observed in the case of thin quantum wells. The physical origin of these hot excitons is determined by using both low temperature (T=10 K) photoluminescence excitation spectroscopy and reflectivity measurements. -- Highlights: ► High structural quality ZnO/(Zn, Mg)O quantum wells are growth along the polar c-direction. ► Indirect phonon-assisted formation of excitons in the thin single quantum wells. ► Strong internal electric field present in polar heterostructures prevents the observation of hot excitons.

  14. Characterization of pioglitazone cyclodextrin complexes: Molecular modeling to in vivo evaluation

    Directory of Open Access Journals (Sweden)

    Dinesh M Bramhane


    Full Text Available Aims: The objective of present study was to study the influence of different β-cyclodextrin derivatives and different methods of complexation on aqueous solubility and consequent translation in in vivo performance of Pioglitazone (PE. Material and Methods: Three cyclodextrins: β-cyclodextrin (BCD, hydroxypropyl-β-cyclodextrin (HPBCD and Sulfobutylether-7-β-cyclodextrin (SBEBCD were employed in preparation of 1:1 Pioglitazone complexes by three methods viz. co-grinding, kneading and co-evaporation. Complexation was confirmed by phase solubility, proton NMR, Fourier Transform Infrared spectroscopy, Differential Scanning Calorimetry (DSC and X-Ray diffraction (XRD. Mode of complexation was investigated by molecular dynamic studies. Pharmacodynamic study of blood glucose lowering activity of PE complexes was performed in Alloxan induced diabetic rat model. Results: Aqueous solubility of PE was significantly improved in presence of cyclodextrin. Apparent solubility constants were observed to be 254.33 M–1 for BCD-PE, 737.48 M–1 for HPBCD-PE and 5959.06 M–1 for SBEBCD-PE. The in silico predictions of mode of inclusion were in close agreement with the experimental proton NMR observation. DSC and XRD demonstrated complete amorphization of crystalline PE upon inclusion. All complexes exhibited >95% dissolution within 10 min compared to drug powder that showed <40% at the same time. Marked lowering of blood glucose was recorded for all complexes. Conclusion: Complexation of PE with different BCD significantly influenced its aqueous solubility, improved in vitro dissolution and consequently translated into enhanced pharmacodynamic activity in rats

  15. Roles of binding energy and diffusion length of singlet and triplet excitons in organic heterojunction solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Narayan, Monishka Rita [Centre for Renewable Energy and Low Emission Technology, Charles Darwin University, Darwin, NT 0909 (Australia); Singh, Jai [School of Engineering and IT, Charles Darwin University, Darwin, NT 0909 (Australia)


    The influence of binding energy and diffusion length on the dissociation of excitons in organic solids is studied. The binding energy and excitonic Bohr radius of singlet and triplet excitons are calculated and compared using the dissociation energy of 0.3 eV, which is provided by the lowest unoccupied molecular orbital offset in heterojunction organic solar cells. A relation between the diffusion coefficient and diffusion length of singlet and triplet excitons is derived using the Foerster and Dexter transfer processes and are plotted as a function of the donor-acceptor separation. The diffusion length reduces nearly to a zero if the distance between donor and acceptor is increased to more than 1.5 nm. It is found that the donor-acceptor separation needs to be {<=} 1.5 nm for easy dissociation on singlet excitons leading to better conversion efficiency in heterojunction organic solar cells. (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  16. Excitons in atomically thin 2D semiconductors and their applications

    Directory of Open Access Journals (Sweden)

    Xiao Jun


    Full Text Available The research on emerging layered two-dimensional (2D semiconductors, such as molybdenum disulfide (MoS2, reveals unique optical properties generating significant interest. Experimentally, these materials were observed to host extremely strong light-matter interactions as a result of the enhanced excitonic effect in two dimensions. Thus, understanding and manipulating the excitons are crucial to unlocking the potential of 2D materials for future photonic and optoelectronic devices. In this review, we unravel the physical origin of the strong excitonic effect and unique optical selection rules in 2D semiconductors. In addition, control of these excitons by optical, electrical, as well as mechanical means is examined. Finally, the resultant devices such as excitonic light emitting diodes, lasers, optical modulators, and coupling in an optical cavity are overviewed, demonstrating how excitons can shape future 2D optoelectronics.

  17. Chiral topological excitons in a Chern band insulator (United States)

    Chen, Ke; Shindou, Ryuichi


    A family of semiconductors called Chern band insulators are shown to host exciton bands with nonzero topological Chern integers and chiral exciton edge modes. Using a prototypical two-band Chern insulator model, we calculate a cross-correlation function to obtain the exciton bands and their Chern integers. The lowest exciton band acquires Chern integers such as ±1 and ±2 in the electronic Chern insulator phase. The nontrivial topology can be experimentally observed both by a nonlocal optoelectronic response of exciton edge modes and by a phase shift in the cross-correlation response due to the bulk mode. Our result suggests that magnetically doped HgTe, InAs/GaSb quantum wells, and (Bi,Sb)2Te3 thin films are promising candidates for a platform of topological excitonics.

  18. Exciton Mapping at Subwavelength Scales in Two-Dimensional Materials

    KAUST Repository

    Tizei, Luiz H. G.


    Spatially resolved electron-energy-loss spectroscopy (EELS) is performed at diffuse interfaces between MoS2 and MoSe2 single layers. With a monochromated electron source (20 meV) we successfully probe excitons near the interface by obtaining the low loss spectra at the nanometer scale. The exciton maps clearly show variations even with a 10 nm separation between measurements; consequently, the optical band gap can be measured with nanometer-scale resolution, which is 50 times smaller than the wavelength of the emitted photons. By performing core-loss EELS at the same regions, we observe that variations in the excitonic signature follow the chemical composition. The exciton peaks are observed to be broader at interfaces and heterogeneous regions, possibly due to interface roughness and alloying effects. Moreover, we do not observe shifts of the exciton peak across the interface, possibly because the interface width is not much larger than the exciton Bohr radius.

  19. Multiscale modeling of complex molecular structure and dynamics with MBN Explorer

    CERN Document Server

    Solov’yov, Ilia A; Solov’yov, Andrey V


    This book introduces readers to MesoBioNano (MBN) Explorer – a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface – the MBN Studio – which enables the set-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science, and guides readers through its applications in numerous areas of research in bio- and chemical physics and material science – ranging from the nano- to the meso-scale. MBN Explorer is particularly suited to computing the system’s energy, to optimizing molecular structure, and to exploring the various facets of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potenti...

  20. Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75

    Energy Technology Data Exchange (ETDEWEB)

    Berndsen, Christopher E; Tsubota, Toshiaki; Lindner, Scott E; Lee, Susan; Holton, James M; Kaufman, Paul D; Keck, James L; Denu, John M [UMASS, MED; (UCB); (UW-MED)


    Histone acetylation and nucleosome remodeling regulate DNA damage repair, replication and transcription. Rtt109, a recently discovered histone acetyltransferase (HAT) from Saccharomyces cerevisiae, functions with the histone chaperone Asf1 to acetylate lysine K56 on histone H3 (H3K56), a modification associated with newly synthesized histones. In vitro analysis of Rtt109 revealed that Vps75, a Nap1 family histone chaperone, could also stimulate Rtt109-dependent acetylation of H3K56. However, the molecular function of the Rtt109-Vps75 complex remains elusive. Here we have probed the molecular functions of Vps75 and the Rtt109-Vps75 complex through biochemical, structural and genetic means. We find that Vps75 stimulates the kcat of histone acetylation by {approx}100-fold relative to Rtt109 alone and enhances acetylation of K9 in the H3 histone tail. Consistent with the in vitro evidence, cells lacking Vps75 showed a substantial reduction (60%) in H3K9 acetylation during S phase. X-ray structural, biochemical and genetic analyses of Vps75 indicate a unique, structurally dynamic Nap1-like fold that suggests a potential mechanism of Vps75-dependent activation of Rtt109. Together, these data provide evidence for a multifunctional HAT-chaperone complex that acetylates histone H3 and deposits H3-H4 onto DNA, linking histone modification and nucleosome assembly.

  1. Engineering and manipulating exciton wave packets (United States)

    Zang, Xiaoning; Montangero, Simone; Carr, Lincoln D.; Lusk, Mark T.


    When a semiconductor absorbs light, the resulting electron-hole superposition amounts to a uncontrolled quantum ripple that eventually degenerates into diffusion. If the conformation of these excitonic superpositions could be engineered, though, they would constitute a new means of transporting information and energy. We show that properly designed laser pulses can be used to create such excitonic wave packets. They can be formed with a prescribed speed, direction, and spectral make-up that allows them to be selectively passed, rejected, or even dissociated using superlattices. Their coherence also provides a handle for manipulation using active, external controls. Energy and information can be conveniently processed and subsequently removed at a distant site by reversing the original procedure to produce a stimulated emission. The ability to create, manage, and remove structured excitons comprises the foundation for optoexcitonic circuits with application to a wide range of quantum information, energy, and light-flow technologies. The paradigm is demonstrated using both tight-binding and time-domain density functional theory simulations.

  2. Influence of Countercation Hydration Enthalpies on the Formation of Molecular Complexes: A Thorium-Nitrate Example. (United States)

    Jin, Geng Bang; Lin, Jian; Estes, Shanna L; Skanthakumar, S; Soderholm, L


    The influence of countercations (A n+ ) in directing the composition of monomeric metal-ligand (ML) complexes that precipitate from solution are often overlooked despite the wide usage of A n+ in materials synthesis. Herein, we describe a correlation between the composition of ML complexes and A + hydration enthalpies found for two related series of thorium (Th)-nitrate molecular compounds obtained by evaporating acidic aqueous Th-nitrate solutions in the presence of A + counterions. Analyses of their chemical composition and solid-state structures demonstrate that A + not only affects the overall solid-state packing of the Th-nitrato complexes but also influences the composition of the Th-nitrato monomeric anions themselves. Trends in composition and structure are found to correlate with A + hydration enthalpies, such that the A + with smaller hydration enthalpies associate with less hydrated and more anionic Th-nitrato complexes. This perspective, broader than the general assumption of size and charge as the dominant influence of A n+ , opens a new avenue for the design and synthesis of targeted metal-ligand complexes.

  3. Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II (United States)

    Mulholland, Sam; Turpin, Eleanor R.; Bonev, Boyan B.; Hirst, Jonathan D.


    Lanthionine antibiotics are an important class of naturally-occurring antimicrobial peptides. The best-known, nisin, is a commercial food preservative. However, structural and mechanistic details on nisin-lipid II membrane complexes are currently lacking. Recently, we have developed empirical force-field parameters to model lantibiotics. Docking and molecular dynamics (MD) simulations have been used to study the nisin2:lipid II complex in bacterial membranes, which has been put forward as the building block of nisin/lipid II binary membrane pores. An Ile1Trp mutation of the N-terminus of nisin has been modelled and docked onto lipid II models; the computed binding affinity increased compared to wild-type. Wild-type nisin was also docked onto three different lipid II structures and a stable 2:1 nisin:lipid II complex formed. This complex was inserted into a membrane. Six independent MD simulations revealed key interactions in the complex, specifically the N-terminal engagement of nisin with lipid II at the pyrophosphate and C-terminus of the pentapeptide chain. Nisin2 inserts into the membrane and we propose this as the first step in pore formation, mediated by the nisin N-terminus–lipid II pentapeptide hydrogen bond. The lipid II undecaprenyl chain adopted different conformations in the presence of nisin, which may also have implications for pore formation. PMID:26888784

  4. Influence of Ethanol as a Co-Solvent in Cyclodextrin Inclusion Complexation: A Molecular Dynamics Study. (United States)

    Boonyarattanakalin, Kanokthip; Viernstein, Helmut; Wolschann, Peter; Lawtrakul, Luckhana


    Molecular dynamics (MD) simulations were used to investigate the dynamics and host-guest interactions of the inclusion complexes between a potent anti-HIV agent, UC781, and three different types of cyclodextrins (CDs) including βCD, 2,6-dimethyl-βCD (MβCD), and 2-hydroxypropyl-βCD (HPβCD) in aqueous solution with ethanol (EtOH) as a co-solvent. The MD simulation results revealed that EtOH as the co-solvent and the type of cyclodextrin affected the inclusion complex formation. From this study, UC781/MβCD provided the most stable inclusion complex. The competition for the cavity of βCD between UC781 and EtOH and the ensuing occupation of βCD cavities by EtOH resulted in a weaker interaction between βCD and UC781. In HPβCD, a supramolecular complex of UC781-HPβCD-EtOH was formed. The EtOH could easily fill the residual void space of the interior of unoccupied HPβCD due to the movement of UC781. In MβCD, the strong hydrogen bond interactions between the UC781 amide group and the secondary hydroxyl groups of MβCD significantly stabilized the inclusion complex in the presence of EtOH.

  5. Exciton dephasing in ZnSe quantum wires

    DEFF Research Database (Denmark)

    Wagner, Hans Peter; Langbein, Wolfgang Werner; Hvam, Jørn Märcher


    The homogeneous linewidths of excitons in wet-etched ZnSe quantum wires of lateral sizes down to 23 nm are studied by transient four-wave mixing. The low-density dephasing time is found to increase with decreasing wire width. This is attributed mainly to a reduction of electron-exciton scattering......-one-dimensional system, enhancing the repulsive interaction between excitons due to Pauli blocking....

  6. Study of exciton transfer in dense quantum dot nanocomposites (United States)

    Guzelturk, Burak; Hernandez-Martinez, Pedro Ludwig; Sharma, Vijay Kumar; Coskun, Yasemin; Ibrahimova, Vusala; Tuncel, Donus; Govorov, Alexander O.; Sun, Xiao Wei; Xiong, Qihua; Demir, Hilmi Volkan


    Nanocomposites of colloidal quantum dots (QDs) integrated into conjugated polymers (CPs) are key to hybrid optoelectronics, where engineering the excitonic interactions at the nanoscale is crucial. For such excitonic operation, it was believed that exciton diffusion is essential to realize nonradiative energy transfer from CPs to QDs. In this study, contrary to the previous literature, efficient exciton transfer is demonstrated in the nanocomposites of dense QDs, where exciton transfer can be as efficient as 80% without requiring the assistance of exciton diffusion. This is enabled by uniform dispersion of QDs at high density (up to ~70 wt%) in the nanocomposite while avoiding phase segregation. Theoretical modeling supports the experimental observation of weakly temperature dependent nonradiative energy transfer dynamics. This new finding provides the ability to design hybrid light-emitting diodes that show an order of magnitude enhanced external quantum efficiencies.Nanocomposites of colloidal quantum dots (QDs) integrated into conjugated polymers (CPs) are key to hybrid optoelectronics, where engineering the excitonic interactions at the nanoscale is crucial. For such excitonic operation, it was believed that exciton diffusion is essential to realize nonradiative energy transfer from CPs to QDs. In this study, contrary to the previous literature, efficient exciton transfer is demonstrated in the nanocomposites of dense QDs, where exciton transfer can be as efficient as 80% without requiring the assistance of exciton diffusion. This is enabled by uniform dispersion of QDs at high density (up to ~70 wt%) in the nanocomposite while avoiding phase segregation. Theoretical modeling supports the experimental observation of weakly temperature dependent nonradiative energy transfer dynamics. This new finding provides the ability to design hybrid light-emitting diodes that show an order of magnitude enhanced external quantum efficiencies. Electronic supplementary

  7. Excitons confined in quantum dots spheroidal prolate; Excitones confinados en puntos cuanticos esferoidales prolatos

    Energy Technology Data Exchange (ETDEWEB)

    Corella M, A.; Rosas, R.A.; Marin, J.L.; Riera, R. [Depto. de Fisica, Universidad de Sonora, A.P. 1626, Hermosillo, Sonora (Mexico)


    The variational method is used to solve in approximately way the Schroedinger wave equation associated to a Wannier-Mott exciton confined within a spheroidal quantum dot. The confinement effect on the ground-state energy of the electron-hole pair trapped inside a crystallite with this geometry, and with soft or hard walls, is analyzed. The walls can be modeled as finite or infinite potential barriers with suitable border conditions, which will depend on the considered case. The results of this work are compared with those obtained by other authors through more sophisticated methods. A comparison with experimental data of CdS crystallites embedded in materials of different composition is made, too. For a finite potential barrier, a critical size of the crystallite from which the exciton escapes of the quantum dot, is predicted. This is in opposition with the infinite potential barrier model where the exciton never can leave the region where it is confined. (Author)

  8. Molecular architecture of the αβ T cell receptor-CD3 complex. (United States)

    Birnbaum, Michael E; Berry, Richard; Hsiao, Yu-Shan; Chen, Zhenjun; Shingu-Vazquez, Miguel A; Yu, Xiaoling; Waghray, Deepa; Fischer, Suzanne; McCluskey, James; Rossjohn, Jamie; Walz, Thomas; Garcia, K Christopher


    αβ T-cell receptor (TCR) activation plays a crucial role for T-cell function. However, the TCR itself does not possess signaling domains. Instead, the TCR is noncovalently coupled to a conserved multisubunit signaling apparatus, the CD3 complex, that comprises the CD3εγ, CD3εδ, and CD3ζζ dimers. How antigen ligation by the TCR triggers CD3 activation and what structural role the CD3 extracellular domains (ECDs) play in the assembled TCR-CD3 complex remain unclear. Here, we use two complementary structural approaches to gain insight into the overall organization of the TCR-CD3 complex. Small-angle X-ray scattering of the soluble TCR-CD3εδ complex reveals the CD3εδ ECDs to sit underneath the TCR α-chain. The observed arrangement is consistent with EM images of the entire TCR-CD3 integral membrane complex, in which the CD3εδ and CD3εγ subunits were situated underneath the TCR α-chain and TCR β-chain, respectively. Interestingly, the TCR-CD3 transmembrane complex bound to peptide-MHC is a dimer in which two TCRs project outward from a central core composed of the CD3 ECDs and the TCR and CD3 transmembrane domains. This arrangement suggests a potential ligand-dependent dimerization mechanism for TCR signaling. Collectively, our data advance our understanding of the molecular organization of the TCR-CD3 complex, and provides a conceptual framework for the TCR activation mechanism.

  9. Molecular architecture of the αβ T cell receptor–CD3 complex (United States)

    Birnbaum, Michael E.; Berry, Richard; Hsiao, Yu-Shan; Chen, Zhenjun; Shingu-Vazquez, Miguel A.; Yu, Xiaoling; Waghray, Deepa; Fischer, Suzanne; McCluskey, James; Rossjohn, Jamie; Walz, Thomas; Garcia, K. Christopher


    αβ T-cell receptor (TCR) activation plays a crucial role for T-cell function. However, the TCR itself does not possess signaling domains. Instead, the TCR is noncovalently coupled to a conserved multisubunit signaling apparatus, the CD3 complex, that comprises the CD3εγ, CD3εδ, and CD3ζζ dimers. How antigen ligation by the TCR triggers CD3 activation and what structural role the CD3 extracellular domains (ECDs) play in the assembled TCR–CD3 complex remain unclear. Here, we use two complementary structural approaches to gain insight into the overall organization of the TCR–CD3 complex. Small-angle X-ray scattering of the soluble TCR–CD3εδ complex reveals the CD3εδ ECDs to sit underneath the TCR α-chain. The observed arrangement is consistent with EM images of the entire TCR–CD3 integral membrane complex, in which the CD3εδ and CD3εγ subunits were situated underneath the TCR α-chain and TCR β-chain, respectively. Interestingly, the TCR–CD3 transmembrane complex bound to peptide–MHC is a dimer in which two TCRs project outward from a central core composed of the CD3 ECDs and the TCR and CD3 transmembrane domains. This arrangement suggests a potential ligand-dependent dimerization mechanism for TCR signaling. Collectively, our data advance our understanding of the molecular organization of the TCR–CD3 complex, and provides a conceptual framework for the TCR activation mechanism. PMID:25422432

  10. Molecular complexity in astrophysical environments: From astrochemistry to “astrobiology”?

    Directory of Open Access Journals (Sweden)

    d’Hendecourt L. Le Sergeant


    Full Text Available I present in this paper my own view about the intricate problem between the evolution of molecular complexity as observed from an astrophysicist point of view and its possible relation to the problem of the origin of life as we know it on Earth. Using arguments from observational astrophysics, I propose that life cannot really be based on other elements that the ones organizing our own so that other life forms based on totally different elemental and molecular processes are highly improbable. As a consequence terrestrial-type environments are probably the most favorable ones to life’s “emergence” and subsequent evolution. Discussing molecular (organic complexity, I show where this molecular complexity is located in astrophysical environments, mostly within inter/circumstellar solid state materials known as “grains” which, at least partly, end up in comets and asteroids and finally on planetary surfaces as meteorites. Considerations based on non directed laboratory simulations experiments, recent results regarding chiral asymmetry in potentially prebiotic matter and the possible explanation to the determinism about the choice of the L sign of the enantiomeric excesses in meteoritic amino acids, following a plausible astrophysical scenario, lead to the idea that the origin of life on Earth was indeed the result of a rather deterministic phenomenon, albeit difficult if not impossible to apprehend in its intimate mechanisms via a complete understanding of all the processes involved. Finally, the crucial point in supporting the idea of life’s ubiquity and wide distribution in our Galaxy (or universe? lies in the fact that planetary evolution, another astrophysical argument, is a major and very strong constraint for the development of life above its “minimal definition”. Life, particularly the complex and evolved one, could be indeed very rare in our Galaxy, although the very large number of exoplanets may be a counter-argument to this

  11. Methylene Blue Sensitized Photodechlorination of Isomeric Mono- and Dichloroanilines via Molecular Complex Formation Mechanism

    Directory of Open Access Journals (Sweden)

    U. C. Pande


    Full Text Available The photosensitized dechlorination of isomeric mono- and dichloroanilines has been studied using methylene blue as photosensitizer in alkaline medium. The dechlorination products have been identified and formation of molecular complex between aniline and methylene blue has been observed. The effects of the pH, concentration of the sensitizer, concentration of the substrate, the intensity of the light and the temperature on the rate of the reaction have been studied. The quantum efficiency of the photodechlorination has been evaluated. The mechanism of the photodechlorination has been suggested.

  12. Efficiency Control in Iridium Complex-Based Phosphorescent Light-Emitting Diodes

    Directory of Open Access Journals (Sweden)

    Boucar Diouf


    Full Text Available Key factors to control the efficiency in iridium doped red and green phosphorescent light emitting diodes (PhOLEDs are discussed in this review: exciton confinement, charge trapping, dopant concentration and dopant molecular structure. They are not independent from each other but we attempt to present each of them in a situation where its specific effects are predominant. A good efficiency in PhOLEDs requires the triplet energy of host molecules to be sufficiently high to confine the triplet excitons within the emitting layer (EML. Furthermore, triplet excitons must be retained within the EML and should not drift into the nonradiative levels of the electron or hole transport layer (resp., ETL or HTL; this is achieved by carefully choosing the EML’s adjacent layers. We prove how reducing charge trapping results in higher efficiency in PhOLEDs. We show that there is an ideal concentration for a maximum efficiency of PhOLEDs. Finally, we present the effects of molecular structure on the efficiency of PhOLEDs using red iridium complex dopant with different modifications on the ligand to tune its highest occupied molecular orbital (HOMO and lowest unoccupied molecular orbital (LUMO energies.

  13. A new color pattern of the Bungarus candidus complex (Squamata: Elapidae) from Vietnam based on morphological and molecular data. (United States)

    Nguyen, Sang Ngoc; Nguyen, Vu Dang Hoang; Nguyen, Thang Quoc; Le, Ngan Thanh Thi; Nguyen, Luan Thanh; Vo, Ba Dinh; Vindum, Jens V; Murphy, Robert W; Che, Jing; Zhang, Ya-Ping


    Kraits with black and white bands from Nui Chua National Park, central Vietnam are morphologically similar to the Burmese Krait, Bungarus magnimaculatus, however, analysis of molecular data finds them to be nested within the B. candidus complex.

  14. Molecular Components of the Sporothrix schenckii Complex that Induce Immune Response. (United States)

    Alba-Fierro, Carlos A; Pérez-Torres, Armando; Toriello, Conchita; Romo-Lozano, Yolanda; López-Romero, Everardo; Ruiz-Baca, Estela


    Sporotrichosis is a fungal disease caused by the Sporothrix schenckii complex that includes species such as S. brasiliensis, S. schenckii sensu stricto, S. globosa, S. luriei, S. mexicana, and S. pallida, which exhibit different potentially antigenic molecular components. The immune response of susceptible hosts to control infection and disease caused by these fungi has been little studied. Besides, the fungus-host interaction induces the activation of different types of immune response. This mini-review analyzes and discusses existing reports on the identification and functional characterization of molecules from species of the S. schenckii complex with clinical relevance, and the mechanisms that mediate the type and magnitude of the immune response in experimental models in vivo and in vitro. This knowledge is expected to contribute to the development of protective and therapeutic strategies against sporotrichosis and other mycoses.

  15. Inclusion complexation of sulfapyridine with α- and β-cyclodextrins: Spectral and molecular modeling study (United States)

    Rajendiran, N.; Siva, S.; Saravanan, J.


    The inclusion complexes of sulfapyridine (SFP) with α-CD and β-CD were investigated by absorption, fluorescence, time-resolved fluorescence, FTIR, DSC, XRD, 1H NMR, SEM, TEM and molecular modeling methods. The normal fluorescence takes place from locally excited (LE) state while twisted intramolecular charge transfer (TICT) is responsible for highly Stokes shifted fluorescence. The enhancement of TICT emission in both CDs suggesting that the inclusion process plays the major role in this emission. The spectral shifts revealed that part of pyridine ring of SFP is entrapped in the CDs cavities. TEM images confirmed round shaped nanoparticles with the average size about 20-50 nm were observed in SFP with α-CD and β-CD inclusion complexes. PM3 calculations have suggested that the large stabilization of excited singlet state of SFP with twisted conformation occurring at the amide SN bond between the electron donor group (aniline ring) and the electron acceptor group (pyridine ring).

  16. The Syllis gracilis species complex: A molecular approach to a difficult taxonomic problem (Annelida, Syllidae). (United States)

    Álvarez-Campos, Patricia; Giribet, Gonzalo; Riesgo, Ana


    Syllis gracilis is an emblematic member of the subfamily Syllinae (Syllidae, Annelida), which inhabits shallow, temperate coastal waters and can be found on algae, coral rubble, and sponges. Their distinctive ypsiloid chaetae, usually found in specimens from populations all around the world, led to the consideration of the species as cosmopolitan, even though four other species have similar chaetae: Syllis magellanica, S. picta, S. mayeri and S. ypsiloides. The discovery of deeply divergent lineages in the Mediterranean Sea, that were morphologically similar, questioned the cosmopolitanism of S. gracilis and suggested the possibility of it being a species complex. In order to assess the speciation patterns within the putative S. gracilis complex, we undertook species delimitation and phylogenetic analyses on 61 specimens morphologically ascribed to Syllis gracilis and closely related species using a multilocus molecular dataset (two mitochondrial and two nuclear markers). Our results suggest high levels of genetic differentiation between the S. gracilis populations analyzed, some of which have morphologically distinctive features. Five to eight distinct lineages (depending on the analysis) were identified, all with geographically restricted distributions. Although the presence of ypsiloid chaetae has been traditionally considered the main character to identify S. gracilis, we conclude that this feature is homoplastic. Instead, we propose that characters such as the degree of fusion of blades and shafts in chaetae, the morphology of the posterior chaetae or the animal color pattern should be considered to differentiate lineages within the S. gracilis species complex. Our study does not support the cosmopolitanism of S. gracilis, and instead provides morphological and molecular evidence of the existence of a complex of pseudo-cryptic species. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Dissecting the molecular assembly of theToxoplasma gondiiMyoA motility complex. (United States)

    Powell, Cameron J; Jenkins, Meredith L; Parker, Michelle L; Ramaswamy, Raghavendran; Kelsen, Anne; Warshaw, David M; Ward, Gary E; Burke, John E; Boulanger, Martin J


    Apicomplexan parasites such as Toxoplasma gondii rely on a unique form of locomotion known as gliding motility. Generating the mechanical forces to support motility are divergent class XIV myosins (MyoA) coordinated by accessory proteins known as light chains. Although the importance of the MyoA-light chain complex is well-established, the detailed mechanisms governing its assembly and regulation are relatively unknown. To establish a molecular blueprint of this dynamic complex, we first mapped the adjacent binding sites of light chains MLC1 and ELC1 on the MyoA neck (residues 775-818) using a combination of hydrogen-deuterium exchange mass spectrometry and isothermal titration calorimetry. We then determined the 1.85 Å resolution crystal structure of MLC1 in complex with its cognate MyoA peptide. Structural analysis revealed a bilobed architecture with MLC1 clamping tightly around the helical MyoA peptide, consistent with the stable 10 nm K d measured by isothermal titration calorimetry. We next showed that coordination of calcium by an EF-hand in ELC1 and prebinding of MLC1 to the MyoA neck enhanced the affinity of ELC1 for the MyoA neck 7- and 8-fold, respectively. When combined, these factors enhanced ELC1 binding 49-fold (to a K d of 12 nm). Using the full-length MyoA motor (residues 1-831), we then showed that, in addition to coordinating the neck region, ELC1 appears to engage the MyoA converter subdomain, which couples the motor domain to the neck. These data support an assembly model where staged binding events cooperate to yield high-affinity complexes that are able to maximize force transduction. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. The tomato Prf complex is a molecular trap for bacterial effectors based on Pto transphosphorylation.

    Directory of Open Access Journals (Sweden)

    Vardis Ntoukakis


    Full Text Available The major virulence strategy of phytopathogenic bacteria is to secrete effector proteins into the host cell to target the immune machinery. AvrPto and AvrPtoB are two such effectors from Pseudomonas syringae, which disable an overlapping range of kinases in Arabidopsis and Tomato. Both effectors target surface-localized receptor-kinases to avoid bacterial recognition. In turn, tomato has evolved an intracellular effector-recognition complex composed of the NB-LRR protein Prf and the Pto kinase. Structural analyses have shown that the most important interaction surface for AvrPto and AvrPtoB is the Pto P+1 loop. AvrPto is an inhibitor of Pto kinase activity, but paradoxically, this kinase activity is a prerequisite for defense activation by AvrPto. Here using biochemical approaches we show that disruption of Pto P+1 loop stimulates phosphorylation in trans, which is possible because the Pto/Prf complex is oligomeric. Both P+1 loop disruption and transphosphorylation are necessary for signalling. Thus, effector perturbation of one kinase molecule in the complex activates another. Hence, the Pto/Prf complex is a sophisticated molecular trap for effectors that target protein kinases, an essential aspect of the pathogen's virulence strategy. The data presented here give a clear view of why bacterial virulence and host recognition mechanisms are so often related and how the slowly evolving host is able to keep pace with the faster-evolving pathogen.

  19. Observation of long-lived interlayer excitons in monolayer MoSe2-WSe2 heterostructures

    National Research Council Canada - National Science Library

    Rivera, Pasqual; Schaibley, John R; Jones, Aaron M; Ross, Jason S; Wu, Sanfeng; Aivazian, Grant; Klement, Philip; Seyler, Kyle; Clark, Genevieve; Ghimire, Nirmal J; Yan, Jiaqiang; Mandrus, D G; Yao, Wang; Xu, Xiaodong


    ..., that is, interlayer excitons. Here, we report the observation of interlayer excitons in monolayer MoSe2-WSe2 heterostructures by photoluminescence and photoluminescence excitation spectroscopy...

  20. Formation of plasmon pulses in the cooperative decay of excitons of quantum dots near a metal surface

    Energy Technology Data Exchange (ETDEWEB)

    Shesterikov, A. B.; Gubin, M. Yu. [Vladimir State University (Russian Federation); Gladush, M. G. [Russian Academy of Sciences, Institute of Spectroscopy (Russian Federation); Prokhorov, A. V., E-mail: [Vladimir State University (Russian Federation)


    The formation of pulses of surface electromagnetic waves at a metal–dielectric boundary is considered in the process of cooperative decay of excitons of quantum dots distributed near a metal surface in a dielectric layer. It is shown that the efficiency of exciton energy transfer to excited plasmons can, in principle, be increased by selecting the dielectric material with specified values of the complex permittivity. It is found that in the mean field approximation, the semiclassical model of formation of plasmon pulses in the system under study is reduced to the pendulum equation with the additional term of nonlinear losses.

  1. Molecular identification of Mycobacterium tuberculosis complex isolates from Kermanshah Province, Iran

    Directory of Open Access Journals (Sweden)

    Roghieh Moghaddam


    Full Text Available Tuberculosis is one of the most important zoonotic diseases in the world. Rapid diagnosis of the disease and identification of species is extremely important for proper treatment of the disease as some species of the complex are resistant to the first-line of tuberculosis drugs. The aim of present study was molecular identification of Mycobacterium tuberculosis (MTB complex isolates from Kermanshah Province, Iran, which were submitted to the Tuberculosis Reference Laboratory at Razi Vaccine and Serum Research Institute (Tehran, Iran. To identify the genus Mycobacterium, all isolates were subjected to 16S rRNA polymerase chain reaction (PCR, and PCR-IS6110 was subsequently used to confirm that the isolates belonged to MTB complex. Finally, region of difference (RD typing was used to identify the species in the complex. The results of 16S rRNA and IS6110 PCR analysis showed the presence of 543-bp and 245-bp bands, respectively. Furthermore, 146bp, 172bp, 235bp, and 369bp at RD1, RD4, RD9, and RD12, respectively, were observed during RD typing. Thus, based on the results, all isolates were identified as MTB. It is worth mentioning that most tuberculosis cases are identified on the basis of acid-fast bacilli detection, and antibiotic therapy is immediately initiated subsequently. Moreover, it should be noted that some of these acid-fast positive cases might not be of genus Mycobacterium, and thus, the antibiotics prescribed might threaten the health of the patients. Additionally, if the identified bacilli are not within MTB complex, the drug therapy would differ. However, Mycobacterium bovis, which is a member of MTB complex and is resistant to pyrazinamide, requires exact strain identification. Based on the findings, individual isolates should be identified by RD typing methods, which could clearly discriminate the species from each other.

  2. Molecular identification of Mycobacterium tuberculosis complex isolates from Kermanshah Province, Iran. (United States)

    Moghaddam, Roghieh; Mosavari, Nader; Mahalati, Ardeshir Hesampoor


    Tuberculosis is one of the most important zoonotic diseases in the world. Rapid diagnosis of the disease and identification of species is extremely important for proper treatment of the disease as some species of the complex are resistant to the first-line of tuberculosis drugs. The aim of present study was molecular identification of Mycobacterium tuberculosis (MTB) complex isolates from Kermanshah Province, Iran, which were submitted to the Tuberculosis Reference Laboratory at Razi Vaccine and Serum Research Institute (Tehran, Iran). To identify the genus Mycobacterium, all isolates were subjected to 16S rRNA polymerase chain reaction (PCR), and PCR-IS6110 was subsequently used to confirm that the isolates belonged to MTB complex. Finally, region of difference (RD) typing was used to identify the species in the complex. The results of 16S rRNA and IS6110 PCR analysis showed the presence of 543-bp and 245-bp bands, respectively. Furthermore, 146bp, 172bp, 235bp, and 369bp at RD1, RD4, RD9, and RD12, respectively, were observed during RD typing. Thus, based on the results, all isolates were identified as MTB. It is worth mentioning that most tuberculosis cases are identified on the basis of acid-fast bacilli detection, and antibiotic therapy is immediately initiated subsequently. Moreover, it should be noted that some of these acid-fast positive cases might not be of genus Mycobacterium, and thus, the antibiotics prescribed might threaten the health of the patients. Additionally, if the identified bacilli are not within MTB complex, the drug therapy would differ. However, Mycobacterium bovis, which is a member of MTB complex and is resistant to pyrazinamide, requires exact strain identification. Based on the findings, individual isolates should be identified by RD typing methods, which could clearly discriminate the species from each other. Copyright © 2016.

  3. Surprisingly High Conductivity and Efficient Exciton Blocking in Fullerene/Wide-Energy-Gap Small Molecule Mixtures. (United States)

    Bergemann, Kevin J; Amonoo, Jojo A; Song, Byeongseop; Green, Peter F; Forrest, Stephen R


    We find that mixtures of C60 with the wide energy gap, small molecular weight semiconductor bathophenanthroline (BPhen) exhibit a combination of surprisingly high electron conductivity and efficient exciton blocking when employed as buffer layers in organic photovoltaic cells. Photoluminescence quenching measurements show that a 1:1 BPhen/C60 mixed layer has an exciton blocking efficiency of 84 ± 5% compared to that of 100% for a neat BPhen layer. This high blocking efficiency is accompanied by a 100-fold increase in electron conductivity compared with neat BPhen. Transient photocurrent measurements show that charge transport through a neat BPhen buffer is dispersive, in contrast to nondispersive transport in the compound buffer. Interestingly, although the conductivity is high, there is no clearly defined insulating-to-conducting phase transition with increased insulating BPhen fraction. Thus, we infer that C60 undergoes nanoscale (80%) BPhen fractions.

  4. New features of excitonic emission in metal nanoparticle/semiconductor quantum dot nanosystem (United States)

    Kryuchenko, Yu. V.; Korbutyak, D. V.


    We study theoretically the excitonic emission properties of a hybrid nanosystem composed of a spherical metal nanoparticle (NP) and a spherical quantum dot (QD). We show that electromagnetic field (EMF) emitted by a single QD has only dipole, quadrupole, and octupole components, i.e., QD cannot in principle be regarded as an oscillating point dipole, which emits infinite series of multipoles. This leads to a substantial deviation of the characteristics of QD excitonic emission from the emission characteristics of point dipole (molecular fluorophore) located in a vicinity of metal NP at small interparticle distances. The observed fluorescence spectra of the CdTe QD/Ag NP nanostructure are found to be in good agreement with the calculated ones.

  5. Standardized molecular diagnostic tool for the identification of cryptic species within the Bemisia tabaci complex. (United States)

    Elfekih, Samia; Tay, Wee Tek; Gordon, Karl; Court, Leon N; De Barro, Paul J


    The whitefly Bemisia tabaci complex harbours over 40 cryptic species that have been placed in 11 phylogenetically distinct clades based on the molecular characterization of partial mitochondrial DNA COI (mtCOI) gene region. Four cryptic species are currently within the invasive clade, i.e. MED, MEAM1, MEAM2 and IO. Correct identification of these species is a critical step towards implementing reliable measures for plant biosecurity and border protection; however, no standardized B. tabaci-specific primers are currently available which has caused inconsistencies in the species identification processes. We report three sets of polymerase chain reaction (PCR) primers developed to amplify the mtCOI region which can be used for genotyping MED, MEAM1 and IO species, and tested these primers on 91 MED, 35 MEAM1 and five IO individuals. PCR and sequencing of amplicons identified a total of 21, six and one haplotypes in MED, MEAM1 and IO respectively, of which six haplotypes were new to the B. tabaci database. These primer pairs enabled standardization and robust molecular species identification via mtCOI screening of the targeted invasive cryptic species and will improve quarantine decisions. Use of this diagnostic tool could be extended to other species within the complex. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  6. Resolving detailed molecular structures in complex organic mixtures and modeling their secondary organic aerosol formation (United States)

    Goodman-Rendall, Kevin A. S.; Zhuang, Yang R.; Amirav, Aviv; Chan, Arthur W. H.


    Characterization of unresolved complex mixtures (UCMs) remains an ongoing challenge towards developing detailed and accurate inputs for modeling secondary organic aerosol (SOA) formation. Traditional techniques based on gas chromatography/electron impact-mass spectrometry induce excessive fragmentation, making it difficult to speciate and quantify isomers precisely. The goal of this study is to identify individual organic isomers by gas chromatography/mass spectrometry with supersonic molecular beam (SMB-GC/MS, also known as GC/MS with Cold EI) and to incorporate speciated isomers into an SOA model that accounts for the specific structures elucidated. Two samples containing atmospherically relevant UCMs are analyzed. The relative isomer distributions exhibit remarkably consistent trends across a wide range of carbon numbers. Constitutional isomers of different alkanes are speciated and individually quantified as linear, branched - for the first time by position of branching - multiply branched, or unsaturated - by degree of ring substitution and number of rings. Relative amounts of exact molecular structures are used as input parameters in an SOA box model to study the effects of molecular structures on SOA yields and volatility evolution. Highly substituted cyclic, mono-substituted cyclic, and linear species have the highest SOA yields while branched alkanes formed the least SOA. The rate of functionalization of a representative UCM is found to be in agreement with current volatility basis set (VBS) parameterizations based on detailed knowledge of composition and known oxidation mechanisms, confirming the validity of VBS parameters currently used in air quality models.

  7. Molecular phylogeny and biogeography of air sac catfishes of the Heteropneustes fossilis species complex (Siluriformes: Heteropneustidae). (United States)

    Ratmuangkhwang, Sahat; Musikasinthorn, Prachya; Kumazawa, Yoshinori


    The air sac catfish, Heteropneustes fossilis (Siluriformes: Heteropneustidae), is widely distributed in freshwaters of the Indian subcontinent and mainland southeast Asia. No comprehensive molecular studies that cover the broad distributional areas have been carried out to date. Here, we conducted molecular phylogenetic analyses using both mitochondrial and nuclear gene sequences to suggest that the Heteropneustes fossilis species complex consists of three clades that may potentially be separate species with distinct geographical distribution (southeast Asia, northeastern India, and southwestern India). The first and second clades are more closely related to each other than they are to the third clade. Within the first clade there is a basal divergence of a subclade consisting of individuals from the Upper Irrawaddy River basin of Myanmar, which share some morphological traits with members of the Indian clades. Our molecular and morphological data are congruent with hypotheses that the Early-Middle Miocene disconnection between the paleo-Tsangpo River and the Irrawaddy River caused the vicariant divergence between southeast Asian and northeastern Indian clades, and that the southeast Asian Heteropneustes originated from the Upper Irrawaddy. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Interfacial complex formation in uranyl extraction by tributyl phosphate in dodecane diluent: a molecular dynamics study. (United States)

    Ye, Xianggui; Cui, Shengting; de Almeida, Valmor; Khomami, Bamin


    Atomistic simulations have been carried out in a multicomponent two-phase system (aqueous and organic phases in direct contact) to investigate the interfacial molecular mechanisms leading to uranyl extraction from the aqueous to organic phase. The aqueous phase consists of the dissolved ions UO2(2+) and nitrate NO3-, with or without H3O+, in water to describe acidic or neutral condition; the organic phase consists of tributyl phosphate, the extractant, in dodecane as the diluent. We find that the interface facilitates the formation of various uranyl complexes, with a general formula UO2(2+)(NO3-)n *mTBP*kH2O, with n+m+k=5, suggesting a 5-fold coordination. The coordination for all three molecular entities has the common feature that they all bind to the uranyl at the uranium atom with an oxygen atom in the equatorial plane perpendicular to the molecular axis of the uranyl, forming a 5-fold symmetry plane. Nitric acid has a strong effect in enhancing the formation of extractable species, which is consistent with experimental findings.

  9. Hybrid artificial photosynthetic systems comprising semiconductors as light harvesters and biomimetic complexes as molecular cocatalysts. (United States)

    Wen, Fuyu; Li, Can


    Solar fuel production through artificial photosynthesis may be a key to generating abundant and clean energy, thus addressing the high energy needs of the world's expanding population. As the crucial components of photosynthesis, the artificial photosynthetic system should be composed of a light harvester (e.g., semiconductor or molecular dye), a reduction cocatalyst (e.g., hydrogenase mimic, noble metal), and an oxidation cocatalyst (e.g., photosystem II mimic for oxygen evolution from water oxidation). Solar fuel production catalyzed by an artificial photosynthetic system starts from the absorption of sunlight by the light harvester, where charge separation takes place, followed by a charge transfer to the reduction and oxidation cocatalysts, where redox reaction processes occur. One of the most challenging problems is to develop an artificial photosynthetic solar fuel production system that is both highly efficient and stable. The assembly of cocatalysts on the semiconductor (light harvester) not only can facilitate the charge separation, but also can lower the activation energy or overpotential for the reactions. An efficient light harvester loaded with suitable reduction and oxidation cocatalysts is the key for high efficiency of artificial photosynthetic systems. In this Account, we describe our strategy of hybrid photocatalysts using semiconductors as light harvesters with biomimetic complexes as molecular cocatalysts to construct efficient and stable artificial photosynthetic systems. We chose semiconductor nanoparticles as light harvesters because of their broad spectral absorption and relatively robust properties compared with a natural photosynthesis system. Using biomimetic complexes as cocatalysts can significantly facilitate charge separation via fast charge transfer from the semiconductor to the molecular cocatalysts and also catalyze the chemical reactions of solar fuel production. The hybrid photocatalysts supply us with a platform to study the

  10. The convergence of longitudinal excitons onto the Γ5 transverse exciton in GaN and the thermal activation energy of longitudinal excitons. (United States)

    Elgawadi, Amal; Gainer, Gordon; Krasinski, Jerzy


    The crystal orientation dependence of GaN excitons was investigated via the photoluminescence (PL) technique. The PL emissions at a temperature of 10 K were obtained from two experimental configurations where the emission K vector (the propagation vector) was either parallel (K ∥ c) or perpendicular (K ∥ c) to the crystal c-axis. Longitudinal, transverse and donor-bound excitons were observed in the two configurations. However, the longitudinal excitons converged onto the transverse free exciton Γ5 in the K⊥c emission. This behavior was discussed in terms of electron screening due to the scattering of electrons moving perpendicular to charged dislocation lines. Additionally, the thermal activation energy of the longitudinal excitons was calculated from the temperature dependent PL measurements collected from the K ∥ c emission, and was found to be 5 to 6 times as high as the binding energy of the free excitons. This high energy was interpreted tentatively in view of the creation of polaritons in strong exciton-photon coupling regimes. These findings present fundamental concepts for applications such as vertical cavity surface-emitting lasers (VCSELs) and polariton lasers.

  11. Molecular typing of environmental Cryptococcus neoformans/C. gattii species complex isolates from Manaus, Amazonas, Brazil. (United States)

    Alves, Gleica Soyan Barbosa; Freire, Ana Karla Lima; Bentes, Amaury Dos Santos; Pinheiro, José Felipe de Souza; de Souza, João Vicente Braga; Wanke, Bodo; Matsuura, Takeshi; Jackisch-Matsuura, Ani Beatriz


    Cryptococcus neoformans and Cryptococcus gattii are the main causative agents of cryptococcosis, a systemic fungal disease that affects internal organs and skin, and which is acquired by inhalation of spores or encapsulated yeasts. It is currently known that the C. neoformans/C. gattii species complex has a worldwide distribution, however, some molecular types seem to prevail in certain regions. Few environmental studies of Cryptococcus have been conducted in the Brazilian Amazon. This is the first ecological study of the pathogenic fungi C. neoformans/C. gattii species complex in the urban area of Manaus, Amazonas, Brazil. A total of 506 samples from pigeon droppings (n = 191), captive bird droppings (n = 60) and tree hollows (n = 255) were collected from June 2012 to January 2014 at schools and public buildings, squares, pet shops, households, the zoo and the bus station. Samples were plated on niger seed agar (NSA) medium supplemented with chloramphenicol and incubated at 25°C for 5 days. Dark-brown colonies were isolated and tested for thermotolerance at 37°C, cycloheximide resistance and growth on canavanine-glycine-bromothymol blue agar. Molecular typing was done by PCR-RFLP. Susceptibility to the antifungal drugs amphotericin B, fluconazole, itraconazole and ketoconazole was tested using Etest(®) strips. In total, 13 positive samples were obtained: one tree hollow (C. gattiiVGII), nine pigeon droppings (C. neoformansVNI) and three captive bird droppings (C. neoformansVNI). The environmental cryptococcal isolates found in this study were of the same molecular types as those responsible for infections in Manaus. © 2016 Blackwell Verlag GmbH.

  12. Single-Molecule Investigation of Energy Dynamics in a Coupled Plasmon-Exciton System (United States)

    Imada, Hiroshi; Miwa, Kuniyuki; Imai-Imada, Miyabi; Kawahara, Shota; Kimura, Kensuke; Kim, Yousoo


    We investigate the near-field interaction between an isolated free-base phthalocyanine molecule and a plasmon localized in the gap between an NaCl-covered Ag(111) surface and the tip apex of a scanning tunneling microscope. When the tip is located in the close proximity of the molecule, asymmetric dips emerge in the broad luminescence spectrum of the plasmon generated by the tunneling current. The origin of the dips is explained by energy transfer between the plasmon and molecular excitons and a quantum mechanical interference effect, where molecular vibrations provide additional degrees of freedom in the dynamic process.

  13. Spontaneous Binding of Molecular Oxygen at the Qo-Site of the bc1 Complex Could Stimulate Superoxide Formation

    DEFF Research Database (Denmark)

    Husen, Peter; Solov'yov, Ilia A


    to drive ATP synthesis. This molecular machinery, however, is suspected to be a source of superoxide, which is toxic to the cell, even in minuscular quantities, and believed to be a factor in aging. Through molecular dynamics simulations, we investigate here the migration of molecular oxygen in the bc1...... complex in order to identify possible reaction sites that could lead to superoxide formation. It is found, in particular, that oxygen penetrates spontaneously the Qo binding site of the bc1 complex in the presence of an intermediate semiquinone radical, thus making the Qo-site a strong candidate for being...... a center of superoxide production....

  14. Iterative Calibration: A Novel Approach for Calibrating the Molecular Clock Using Complex Geological Events. (United States)

    Loeza-Quintana, Tzitziki; Adamowicz, Sarah J


    During the past 50 years, the molecular clock has become one of the main tools for providing a time scale for the history of life. In the era of robust molecular evolutionary analysis, clock calibration is still one of the most basic steps needing attention. When fossil records are limited, well-dated geological events are the main resource for calibration. However, biogeographic calibrations have often been used in a simplistic manner, for example assuming simultaneous vicariant divergence of multiple sister lineages. Here, we propose a novel iterative calibration approach to define the most appropriate calibration date by seeking congruence between the dates assigned to multiple allopatric divergences and the geological history. Exploring patterns of molecular divergence in 16 trans-Bering sister clades of echinoderms, we demonstrate that the iterative calibration is predominantly advantageous when using complex geological or climatological events-such as the opening/reclosure of the Bering Strait-providing a powerful tool for clock dating that can be applied to other biogeographic calibration systems and further taxa. Using Bayesian analysis, we observed that evolutionary rate variability in the COI-5P gene is generally distributed in a clock-like fashion for Northern echinoderms. The results reveal a large range of genetic divergences, consistent with multiple pulses of trans-Bering migrations. A resulting rate of 2.8% pairwise Kimura-2-parameter sequence divergence per million years is suggested for the COI-5P gene in Northern echinoderms. Given that molecular rates may vary across latitudes and taxa, this study provides a new context for dating the evolutionary history of Arctic marine life.

  15. A molecular perspective on a complex polymorphic inversion system with cytological evidence of multiply reused breakpoints. (United States)

    Orengo, D J; Puerma, E; Papaceit, M; Segarra, C; Aguadé, M


    Genome sequence comparison across the Drosophila genus revealed that some fixed inversion breakpoints had been multiply reused at this long timescale. Cytological studies of Drosophila inversion polymorphism had previously shown that, also at this shorter timescale, some breakpoints had been multiply reused. The paucity of molecularly characterized polymorphic inversion breakpoints has so far precluded contrasting whether cytologically shared breakpoints of these relatively young inversions are actually reused at the molecular level. The E chromosome of Drosophila subobscura stands out because it presents several inversion complexes. This is the case of the E1+2+9+3 arrangement that originated from the ancestral Est arrangement through the sequential accumulation of four inversions (E1, E2, E9 and E3) sharing some breakpoints. We recently identified the breakpoints of inversions E1 and E2, which allowed establishing reuse at the molecular level of the cytologically shared breakpoint of these inversions. Here, we identified and sequenced the breakpoints of inversions E9 and E3, because they share breakpoints at sections 58D and 64C with those of inversions E1 and E2. This has allowed establishing that E9 and E3 originated through the staggered-break mechanism. Most importantly, sequence comparison has revealed the multiple reuse at the molecular level of the proximal breakpoint (section 58D), which would have been used at least by inversions E2, E9 and E3. In contrast, the distal breakpoint (section 64C) might have been only reused once by inversions E1 and E2, because the distal E3 breakpoint is displaced >70 kb from the other breakpoint limits.

  16. Experimental, molecular docking investigations and bioavailability study on the inclusion complexes of finasteride and cyclodextrins

    Directory of Open Access Journals (Sweden)

    Mady FM


    Full Text Available Fatma M Mady,1,2 Usama Farghaly Aly2 1Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Taibah University, Medina, Saudi Arabia; 2Department of Pharmaceutics, Faculty of Pharmacy, Minia University, Minia, Egypt Abstract: Finasteride (FIN is a Class II candidate of the Biopharmaceutics Classification System (BCS. The lipophilic cavity of cyclodextrins (CyDs enables it to construct a non-covalent inclusion complex with different insoluble drugs. Only β-cyclodextrin (β-CyD and hydroxypropyl-β-CyD (HP-β-CyD have been previously examined with FIN. This study aimed to investigate the consistence of FIN with different kinds of β-CyDs, including dimethyl-β-cyclodextrin (DM-β-CyD, carboxymethyl-β-cyclodextrin (CM-β-CyD, HP-β-CyD, sulfobutyl ether-β-cyclodextrin (SBE-β-CyD, and β-CyD, by the coprecipitation method. The resultant inclusion systems were characterized by differential scanning calorimetry, infrared spectroscopy, X-ray diffractometry, and dissolution studies. Moreover, molecular docking for the selected inclusion systems was carried out to explore the suitable arrangements of FIN in the cavity of β-CyD or its derivatives. The results suggested that the DM-β-CyD inclusion system gave the higher complexation efficiency for improvement in solubility of FIN and hence enhancement of its bioavailability. Pharmacokinetic parameters displayed a higher absorption rate and higher area under the curve of the FIN/DM-β-CyD inclusion complex when compared with the drug alone, which indicates an improvement in the absorption and bioavailability of FIN in the DM-β-CyD inclusion system. Keywords: finasteride, cyclodextrins, molecular docking, pharmacokinetics, bioavailability

  17. Self-trapped exciton configurations in Beryllium Oxide (United States)

    Botov, M. A.; Kuznetsov, A. Yu; Sobolev, A. B.


    The modern radiation technology, nuclear engineering, non-linear optics are associated with radiation-resistant optical material study. Evolution of electronic excitations in these materials is a complex multichannel process which currently has no integrated model. A special role belongs to the low-symmetry single crystals, such as beryllium oxide (BeO). We present theoretical results that advance our understanding of exciton-based channel of electronic excitations relaxation. The four possible self-trapped exciton (STE) configurations in beryllia single crystal have been investigated by using a quantum mechanical approach (Hartree-Fock and B3LYP HF-DFT hybrid functional, as implemented in the CRYSTAL09 code). B3LYP DFT functional with 30% of exact exchange was used (B3LYP30). All calculations were performed using periodic boundary conditions and full SC geometry relaxation. The lattice distortion and charge density distribution for considered defect configurations were obtained. STE-A1 luminescence energy was found to be 6.0 eV for HF and 6.5 eV for B3LYP30; STE-A2 luminescence energy was found to be 9.2 eV for HF and 7.8 eV for B3LYP30. STE-B1 luminescence energy was found to be 5.5 eV for HF, 6.2 eV for B3LYP30; STE-B2 luminescence energy was found to be 4.7 eV for HF.


    NARCIS (Netherlands)


    The synthesis and molecular structures of two iron(III) phenolate complexes [(L(1))FeCl] (1) and [(L(2))(2)Fe][BPh(4)] (2) are described, where L(1)H(2) is 2,3-dimethyl-2,3-bis(3-tert-butylsalicylideneamino) butane and L(2)H is 2-(2-pyridyl)-1-salicylideneaminoethane. The complexes have been

  19. Molecular Phylogeny and Zoogeography of the Capoeta damascina Species Complex (Pisces: Teleostei: Cyprinidae.

    Directory of Open Access Journals (Sweden)

    Nisreen Alwan

    Full Text Available Capoeta damascina was earlier considered by many authors as one of the most common freshwater fish species found throughout the Levant, Mesopotamia, Turkey, and Iran. However, owing to a high variation in morphological characters among and within its various populations, 17 nominal species were described, several of which were regarded as valid by subsequent revising authors. Capoeta damascina proved to be a complex of closely related species, which had been poorly studied. The current study aims at defining C. damascina and the C. damascina species complex. It investigates phylogenetic relationships among the various members of the C. damascina complex, based on mitochondrial and nuclear DNA sequences. Phylogenetic relationships were projected against paleogeographical events to interpret the geographic distribution of the taxa under consideration in relation to the area's geological history. Samples were obtained from throughout the geographic range and were subjected to genetic analyses, using two molecular markers targeting the mitochondrial cytochrome oxidase I (n = 103 and the two adjacent divergence regions (D1-D2 of the nuclear 28S rRNA genes (n = 65. Six closely related species were recognized within the C. damascina complex, constituting two main lineages: A western lineage represented by C. caelestis, C. damascina, and C. umbla and an eastern lineage represented by C. buhsei, C. coadi, and C. saadii. The results indicate that speciation of these taxa is rather a recent event. Dispersal occurred during the Pleistocene, resulting in present-day distribution patterns. A coherent picture of the phylogenetic relationships and evolutionary history of the C. damascina species complex is drawn, explaining the current patterns of distribution as a result of paleogeographic events and ecological adaptations.

  20. Directing energy transport in organic photovoltaic cells using interfacial exciton gates. (United States)

    Menke, S Matthew; Mullenbach, Tyler K; Holmes, Russell J


    Exciton transport in organic semiconductors is a critical, mediating process in many optoelectronic devices. Often, the diffusive and subdiffusive nature of excitons in these systems can limit device performance, motivating the development of strategies to direct exciton transport. In this work, directed exciton transport is achieved with the incorporation of exciton permeable interfaces. These interfaces introduce a symmetry-breaking imbalance in exciton energy transfer, leading to directed motion. Despite their obvious utility for enhanced exciton harvesting in organic photovoltaic cells (OPVs), the emergent properties of these interfaces are as yet uncharacterized. Here, directed exciton transport is conclusively demonstrated in both dilute donor and energy-cascade OPVs where judicious optimization of the interface allows exciton transport to the donor-acceptor heterojunction to occur considerably faster than when relying on simple diffusion. Generalized systems incorporating multiple exciton permeable interfaces are also explored, demonstrating the ability to further harness this phenomenon and expeditiously direct exciton motion, overcoming the diffusive limit.

  1. Anisotropy of exciton migration in poly(p-phenylene vinylene)

    NARCIS (Netherlands)

    Markov, D. E.; Blom, P. W. M.

    The dynamics of the exciton transport in poly(p-phenylene vinylene) (PPV) blended with a low concentration of fullerene molecules is monitored by time-resolved photoluminescence measurements. The diffusion driven motion of excitons toward these scavengers is modeled using a theory based on a random

  2. Temperature dependence of exciton diffusion in conjugated polymers

    NARCIS (Netherlands)

    Mikhnenko, O.V.; Cordella, F.; Sieval, A.B.; Hummelen, J.C.; Blom, P.W.M.; Loi, M.A.


    The temperature dependence of the exciton dynamics in a conjugated polymer is studied using time-resolved spectroscopy. Photoluminescence decays were measured in heterostructured samples containing a sharp polymer-fullerene interface, which acts as an exciton quenching wall. Using a ID diffusion

  3. Bose Condensation of Interwell Excitons in Double Quantum Wells

    DEFF Research Database (Denmark)

    Larionov, A. V.; Timofeev, V. B.; Ni, P. A.


    in the domain. With a rise in temperature, this line disappears from the spectrum (Tc 3.4 K). The observed phenomenon is attributed to Bose–Einstein condensation in a quasi-two-dimensional system of interwell excitons. In the temperature range studied (1.5–3.4 K), the critical exciton density and temperature...

  4. Optical properties of localized excitons in semiconductor nanostructures

    DEFF Research Database (Denmark)

    Leosson, Kristjan; Hvam, Jørn Märcher; Langbein, Wolfgang Werner


    Denne afhandling beskriver optiske undersøgelser af lokaliserede excitoner i III-V halvleder nanostrukturer. Det drejer sig især om tredimensional lokalisering af excitoner i to typer af selvorganiserede systemer, nemlig kvantebrønde med fluktuerende lagtykkelse og såkaldte selv-dannede kvantepun...

  5. Interlayer excitons in a bulk van der Waals semiconductor

    DEFF Research Database (Denmark)

    Arora, Ashish; Drueppel, Matthias; Schmidt, Robert


    , dissipationless current flow, and the light-induced exciton spin Hall effect. Here we report on the discovery of interlayer excitons in a bulk van der Waals semiconductor. They form due to strong localization and spin-valley coupling of charge carriers. By combining high-field magneto-reflectance experiments...

  6. Exciton ionization in multilayer transition-metal dichalcogenides

    DEFF Research Database (Denmark)

    Pedersen, Thomas Garm; Latini, Simone; Thygesen, Kristian Sommer


    Photodetectors and solar cells based on materials with strongly bound excitons rely crucially on field-assisted exciton ionization. We study the ionization process in multilayer transition-metal dichalcogenides (TMDs) within the Mott-Wannier model incorporating fully the pronounced anisotropy...

  7. Coherent excitonic nonlinearity versus inhomogeneous broadening in single quantum wells

    DEFF Research Database (Denmark)

    Langbein, Wolfgang Werner; Borri, Paola; Hvam, Jørn Märcher


    The coherent response of excitons in semiconductor nanostructures, as measured in four wave mixing (FWM) experiments, depends strongly on the inhomogeneous broadening of the exciton transition. We investigate GaAs-AlGaAs single quantum wells (SQW) of 4 nm to 25 nm well width. Two main mechanisms ...

  8. Magnetic excitons in singlet-ground-state ferromagnets

    DEFF Research Database (Denmark)

    Birgeneau, R.J.; Als-Nielsen, Jens Aage; Bucher, E.


    The authors report measurements of the dispersion of singlet-triplet magnetic excitons as a function of temperature in the singlet-ground-state ferromagnets fcc Pr and Pr3Tl. Well-defined excitons are observed in both the ferromagnetic and paramagnetic regions, but with energies which are nearly...

  9. Storing excitons in transition-metal dichalcogenides using dark states (United States)

    Gunlycke, Daniel; Tseng, Frank; Simsek, Ergun

    Monolayer transition-metal dichalcogenides exhibit strongly bound excitons confined to two dimensions. One challenge in exploiting these excitons is that they have a finite life time and collapse through electron-hole recombination. We propose that the exciton life time could be extended by transitioning the exciton population into dark states. The symmetry of these dark states require the electron and hole to be spatially separated, which not only causes these states to be optically inactive but also inhibits electron-hole recombination. Based on an atomistic model we call the Triangular Lattice Exciton (3ALE) model, we derive transition matrix elements and approximate selection rules showing that excitons could be transitioned into and out of dark states using a pulsed infrared laser. For illustration, we also present exciton population scenarios based on different recombination decay constants. Longer exciton lifetimes could make these materials candidates for applications in energy management and quantum information processing. This work was supported by the Office of Naval Research, directly and through the Naval Research Laboratory.

  10. Engineering excitonic dynamics and environmental stability of post-transition metal chalcogenides by pyridine functionalization technique (United States)

    Meng, Xiuqing; Pant, Anupum; Cai, Hui; Kang, Jun; Sahin, Hasan; Chen, Bin; Wu, Kedi; Yang, Sijie; Suslu, Aslihan; Peeters, F. M.; Tongay, Sefaattin


    Owing to their strong photon emission, low excitonic binding energies, and nearly-ideal band offset values for water splitting reactions, direct gap quasi-2D gallium chalcogenides are potential candidates for applications in energy harvesting, optoelectronics, and photonics. Unlike other 2D materials systems, chemical functionalization of gallium chalcogenides is still at its seminal stages. Here, we propose vapor phase pyridine intercalation technique to manipulate optical properties of gallium chalcogenides. After functionalization, the excitonic dynamics of quasi-2D GaSe change significantly as evidenced by an increase in integrated PL intensity and emergence of a new emission feature that is below the band edge. Based on our DFT calculations, we attribute these to formation of bound exciton complexes at the trap sites introduced by chemical reaction between pyridine and GaSe. On the contrary, pyridine functionalization does not impact the optical properties of GaTe, instead treats GaTe surface to prevent oxidization of tellurium atoms. Overall, results suggest novel ways to control properties of gallium chalcogenides on demand and unleash their full potential for a range of applications in photonics and optoelectronics.Owing to their strong photon emission, low excitonic binding energies, and nearly-ideal band offset values for water splitting reactions, direct gap quasi-2D gallium chalcogenides are potential candidates for applications in energy harvesting, optoelectronics, and photonics. Unlike other 2D materials systems, chemical functionalization of gallium chalcogenides is still at its seminal stages. Here, we propose vapor phase pyridine intercalation technique to manipulate optical properties of gallium chalcogenides. After functionalization, the excitonic dynamics of quasi-2D GaSe change significantly as evidenced by an increase in integrated PL intensity and emergence of a new emission feature that is below the band edge. Based on our DFT calculations

  11. Unusual molecular-ionic complex of tetrabutylammonium 5,5'-dibromo-2,2'-biphenolate (United States)

    Wojciechowski, G.; Katrusiak, A.; Brzezinski, B.


    Very unusual coexistence of neutral and ionic forms of identical molecules have been found in the molecular ionic crystal of one neutral 5,5'-dibromo-2,2'-biphenol molecule, its two anions and two tetrabutylammonium cations [C 12H 8O 2Br 2(C 12H 7O 2Br 2-) 2(C 16H 36N +) 2, 1:2:2 complex]. This exceptional structure is stabilised by intramolecular and intermolecular O-H⋯O hydrogen bonds. The FTIR spectrum of the complex in the solid shows intense bands of the hydrogen-bonded motif as well as the continuous absorption indicating fluctuation of the proton in the OH +⋯O - intramolecular hydrogen bond. In chloroform and acetonitrile solutions the structure of the complex is completely different from the solid: fast fluctuations of the protons in circular hydrogen-bonded arrangement is proposed and these hydrogen bonds show large proton polarisability indicated by intense continuous absorption in the FTIR spectrum below 2000 cm -1.

  12. Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera). (United States)

    Gómez, Africa; Serra, Manuel; Carvalho, Gary R; Lunt, David H


    Continental lake-dwelling zooplanktonic organisms have long been considered cosmopolitan species with little geographic variation in spite of the isolation of their habitats. Evidence of morphological cohesiveness and high dispersal capabilities support this interpretation. However, this view has been challenged recently as many such species have been shown either to comprise cryptic species complexes or to exhibit marked population genetic differentiation and strong phylogeographic structuring at a regional scale. Here we investigate the molecular phylogeny of the cosmopolitan passively dispersing rotifer Brachionus plicatilis (Rotifera: Monogononta) species complex using nucleotide sequence variation from both nuclear (ribosomal internal transcribed spacer 1, ITS1) and mitochondrial (cytochrome c oxidase subunit I, COI) genes. Analysis of rotifer resting eggs from 27 salt lakes in the Iberian Peninsula plus lakes from four continents revealed nine genetically divergent lineages. The high level of sequence divergence, absence of hybridization, and extensive sympatry observed support the specific status of these lineages. Sequence divergence estimates indicate that the B. plicatilis complex began diversifying many millions of years ago, yet has showed relatively high levels of morphological stasis. We discuss these results in relation to the ecology and genetics of aquatic invertebrates possessing dispersive resting propagules and address the apparent contradiction between zooplanktonic population structure and their morphological stasis.

  13. Mouse Acetylcholinesterase Unliganded and in Complex with Huperzine A: A Comparison of Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Tara, Sylvia; Straatsma, TP; Mccammon, Andy


    A 1 ns molecular dynamics simulation of unliganded mouse acetylcholinesterase (AChE) is compared to a previous simulation of mouse AChE complexed with Huperzine A (HupA). Several common features are observed. In both simulations, the active site gorge fluctuates in size during the 1 ns trajectory, and is completely pinched off several times. Many of the residues in the gorge that formed hydrogen bonds with HupA in the simulation of the complex, now form hydrogen bonds with other protein residues and water molecules in the gorge. The opening of a "backdoor" entrance to the active site that was found in the simulation of the complex is also observed in the unliganded simulation. Differences between the two simulations include overall lower structural RMS deviations for residues in the gorge in the unliganded simulation, a smaller diameter of the gorge in the absence of HupA, and the disappearance of a side channel that was frequently present in the liganded simulation. The differences between the two simulations can be attributed, in part, to the interaction of AChE with HupA.

  14. Parameterization of the prosthetic redox centers of the bacterial cytochrome bc(1) complex for atomistic molecular dynamics simulations

    DEFF Research Database (Denmark)

    Kaszuba, K.; Postila, P. A.; Cramariuc, O.


    studied in large-scale classical molecular dynamics (MD) simulations. In part, this is due to lack of suitable force field parameters, centered atomic point charges in particular, for the complex's prosthetic redox centers. Accurate redox center charges are needed to depict realistically the inter-molecular......Cytochrome (cyt) bc(1) is a multi-subunit membrane protein complex that is a vital component of the respiratory and photosynthetic electron transfer chains both in bacteria and eukaryotes. Although the complex's dimer structure has been solved using X-ray crystallography, it has not yet been...

  15. Bistable Topological Insulator with Exciton-Polaritons (United States)

    Kartashov, Yaroslav V.; Skryabin, Dmitry V.


    The functionality of many nonlinear and quantum optical devices relies on the effect of optical bistability. Using microcavity exciton-polaritons in a honeycomb arrangement of microcavity pillars, we report the resonance response and bistability of topological edge states. A balance between the pump, loss, and nonlinearity ensures a broad range of dynamical stability and controls the distribution of power between counterpropagating states on the opposite edges of the honeycomb lattice stripe. Tuning energy and polarization of the pump photons, while keeping their momentum constant, we demonstrate control of the propagation direction of the dominant edge state. Our results facilitate the development of practical applications of topological photonics.

  16. Exploring the energy landscape of antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition. (United States)

    Thielges, Megan C; Zimmermann, Jörg; Yu, Wayne; Oda, Masayuki; Romesberg, Floyd E


    The production of antibodies that selectively bind virtually any foreign compound is the hallmark of the immune system. While much is understood about how sequence diversity contributes to this remarkable feat of molecular recognition, little is known about how sequence diversity impacts antibody dynamics, which is also expected to contribute to molecular recognition. Toward this goal, we examined a panel of antibodies elicited to the chromophoric antigen fluorescein. On the basis of isothermal titration calorimetry, we selected six antibodies that bind fluorescein with diverse binding entropies, suggestive of varying contributions of dynamics to molecular recognition. Sequencing revealed that two pairs of antibodies employ homologous heavy chains that were derived from common germline genes, while the other two heavy chains and all six of the light chains were derived from different germline genes and are not homologous. Interestingly, more than half of all the somatic mutations acquired during affinity maturation among the six antibodies are located in positions unlikely to contact fluorescein directly. To quantify and compare the dynamics of the antibody-fluorescein complexes, three-pulse photon echo peak shift and transient grating spectroscopy were employed. All of the antibodies exhibited motions on three distinct time scales, ultrafast motions on the <100 fs time scale, diffusive motions on the picosecond time scale, and motions that occur on time scales longer than nanoseconds and thus appear static. However, the exact frequency of the picosecond time scale motion and the relative contribution of the different motions vary significantly among the antibody-chromophore complexes, revealing a high level of dynamic diversity. Using a hierarchical model, we relate the data to features of the antibodies' energy landscapes as well as their flexibility in terms of elasticity and plasticity. In all, the data provide a consistent picture of antibody flexibility

  17. Anomalies in the equilibrium and nonequilibrium properties of correlated ions in complex molecular environments (United States)

    Mahakrishnan, Sathiya; Chakraborty, Subrata; Vijay, Amrendra


    Emergent statistical attributes, and therefore the equations of state, of an assembly of interacting charge carriers embedded within a complex molecular environment frequently exhibit a variety of anomalies, particularly in the high-density (equivalently, the concentration) regime, which are not well understood, because they do not fall under the low-concentration phenomenologies of Debye-Hückel-Onsager and Poisson-Nernst-Planck, including their variants. To go beyond, we here use physical concepts and mathematical tools from quantum scattering theory, transport theory with the Stosszahlansatz of Boltzmann, and classical electrodynamics (Lorentz gauge) and obtain analytical expressions both for the average and the frequency-wave vector-dependent longitudinal and transverse current densities, diffusion coefficient, and the charge density, and therefore the analytical expressions for (a) the chemical potential, activity coefficient, and the equivalent conductivity for strong electrolytes and (b) the current-voltage characteristics for ion-transport processes in complex molecular environments. Using a method analogous to the notion of Debye length and thence the electrical double layer, we here identify a pair of characteristic length scales (longitudinal and the transverse), which, being wave vector and frequency dependent, manifestly exhibit nontrivial fluctuations in space-time. As a unifying theme, we advance a quantity (inverse length dimension), gscat(a ), which embodies all dynamical interactions, through various quantum scattering lengths, relevant to molecular species a, and the analytical behavior which helps us to rationalize the properties of strong electrolytes, including anomalies, in all concentration regimes. As an example, the behavior of gscat(a ) in the high-concentration regime explains the anomalous increase of the Debye length with concentration, as seen in a recent experiment on electrolyte solutions. We also put forth an extension of the

  18. Structure determination of fexofenadine-α-cyclodextrin complex by quantitative 2D ROESY analysis and molecular mechanics studies. (United States)

    Ali, Syed Mashhood; Khan, Shania; Crowyn, Gregory


    Complexation of fexofenadine with α-cyclodextrin in aqueous medium was studied. The stoichiometry of the resulting inclusion complex was determined by (1) H NMR titration data. 2D ROESY data provided the evidence of formation of the complex by entry of the phenyl ring into the α-cyclodextrin cavity probably from wider opening. Determination of relative peak intensities of intermolecular cross-peaks for the most stable complexes obtained by molecular mechanics (MM2) studies and from 2D ROESY spectral data confirmed the presence of only one complex in solution that has been fully characterized. Copyright © 2012 John Wiley & Sons, Ltd.

  19. Single-photon source based on Rydberg exciton blockade (United States)

    Khazali, Mohammadsadegh; Heshami, Khabat; Simon, Christoph


    Bound states of electron–hole pairs in semiconductors demonstrate a hydrogen-like behavior in their high-lying excited states that are also known as Rydberg exciton states. The strong interaction between excitons in levels with high principal quantum numbers prevents the creation of more than one exciton in a small crystal; resulting in the Rydberg blockade effect. Here, we propose a new kind of solid-state single-photon source based on the recently observed Rydberg blockade effect for excitons in cuprous oxide. Our quantitative estimates based on single and double excitation probability dynamics indicate that GHz rates and values of the second-order correlation function {g}2(0) below the percent level can be simultaneously achievable. These results should pave the way to explore applications of Rydberg excitons in photonic quantum information processing.

  20. Vibronic effects and destruction of exciton coherence in optical spectra of J-aggregates: A variational polaron transformation approach

    Energy Technology Data Exchange (ETDEWEB)

    Bloemsma, E.A.; Silvis, M.H.; Stradomska, A.; Knoester, J., E-mail:


    Using a symmetry adapted polaron transformation of the Holstein Hamiltonian, we study the interplay of electronic excitation-vibration couplings, resonance excitation transfer interactions, and temperature in the linear absorption spectra of molecular J-aggregates. Semi-analytical expressions for the spectra are derived and compared with results obtained from direct numerical diagonalization of the Hamiltonian in the two-particle basis set representation. At zero temperature, we show that our polaron transformation reproduces both the collective (exciton) and single-molecule (vibrational) optical response associated with the appropriate standard perturbation limits. Specifically, for the molecular dimer excellent agreement with the spectra from the two-particle approach for the entire range of model parameters is obtained. This is in marked contrast to commonly used polaron transformations. Upon increasing the temperature, the spectra show a transition from the collective to the individual molecular features, which results from the thermal destruction of the exciton coherence.

  1. Oxygen Passivation Mediated Tunability of Trion and Excitons in MoS2

    KAUST Repository

    Gogoi, Pranjal Kumar


    Using wide spectral range in situ spectroscopic ellipsometry with systematic ultrahigh vacuum annealing and in situ exposure to oxygen, we report the complex dielectric function of MoS2 isolating the environmental effects and revealing the crucial role of unpassivated and passivated sulphur vacancies. The spectral weights of the A (1.92 eV) and B (2.02 eV) exciton peaks in the dielectric function reduce significantly upon annealing, accompanied by spectral weight transfer in a broad energy range. Interestingly, the original spectral weights are recovered upon controlled oxygen exposure. This tunability of the excitonic effects is likely due to passivation and reemergence of the gap states in the band structure during oxygen adsorption and desorption, respectively, as indicated by ab initio density functional theory calculation results. This Letter unravels and emphasizes the important role of adsorbed oxygen in the optical spectra and many-body interactions of MoS2.

  2. Light-induced nonadiabatic dynamics in molecular assemblies and nanostructures (United States)

    Mitric, Roland

    The combination of mixed quantum-classical dynamics with efficient electronic structure methods was developed in order to simulate the light-induced processes in complex molecules, multichromophoric aggregates and metallic nanostructures. We will demonstrate how the combination of nonadiabatic dynamics with experimental pump-probe techniques such as time-resolved photoelectron imaging (TRPEI) allows to fully resolve the mechanism of excited state relaxation through conical intersections in several prototype organic- and biomolecules. Specifically, the role of the solvent in the excited state relaxation in microsolvated and fully solvated systems will be addressed. Currently there is growing evidence that nonadiabatic relaxation processes also play a fundamental role in determining the efficiency of excitonic transfer or charge injection in multichromophoric assemblies. Since such systems are currently out of the reach of the state-of-the-art quantum chemistry a development of even more efficient quantum chemical approaches is necessary in order to describe the excited state dynamics in such assemblies. For this purpose we have recently developed long-range corrected time-dependent density functional tight binding (LC-TDDFTB) nonadiabatic dynamics and combined it with the QM/MM approach in order to simulate exciton relaxation in complex systems. The applications of the method to the investigation of the optical properties and dynamics in multichromophoric assemblies including stacked pi-conjugated organic chromophores, model molecular crystals as well as self-organized dye aggregates will be presented. Finally, we will address exciton transport dynamics coupled with the light propagation in hybrid exciton-plasmon nanostructures, which represent promising materials fort the development of novel light-harvesting systems.

  3. A molecular timescale of eukaryote evolution and the rise of complex multicellular life

    Directory of Open Access Journals (Sweden)

    Venturi Maria L


    Full Text Available Abstract Background The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. Results Our phylogenetic analyses revealed that (i animals are more closely related to fungi than to plants, (ii red algae are closer to plants than to animals or fungi, (iii choanoflagellates are closer to animals than to fungi or plants, (iv diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v diplomonads are basal to other eukaryotes (including alveolates and euglenozoans. Divergence times were estimated from global and local clock methods using 20–188 proteins per node, with data treated separately (multigene and concatenated (supergene. Different time estimation methods yielded similar results (within 5%: vertebrate-arthropod (964 million years ago, Ma, Cnidaria-Bilateria (1,298 Ma, Porifera-Eumetozoa (1,351 Ma, Pyrenomycetes-Plectomycetes (551 Ma, Candida-Saccharomyces (723 Ma, Hemiascomycetes-filamentous Ascomycota (982 Ma, Basidiomycota-Ascomycota (968 Ma, Mucorales-Basidiomycota (947 Ma, Fungi-Animalia (1,513 Ma, mosses-vascular plants (707 Ma, Chlorophyta-Tracheophyta (968 Ma, Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma, Plantae-Animalia (1,609 Ma, Alveolata-plants+animals+fungi (1,973 Ma, Euglenozoa-plants+animals+fungi (1,961 Ma, and Giardia-plants+animals+fungi (2,309 Ma. By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to ~10

  4. A molecular timescale of eukaryote evolution and the rise of complex multicellular life (United States)

    Hedges, S. Blair; Blair, Jaime E.; Venturi, Maria L.; Shoe, Jason L.


    BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20-188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to

  5. Cloud fluid compression and softening in spiral arms and the formation of giant molecular cloud complexes (United States)

    Cowie, L. L.


    With regard to the galactodynamics of the cloudy interstellar medium, the paper considers the response of such a gas to a forcing potential in the tight-winding density wave theory. The cloud fluid is treated in the hydrodynamic limit with an equation of state which softens at high densities. It is shown that in the inner regions of the galaxy, cooling of the cloud fluid in the arms can result in gravitational instability and the formation of large bound complexes of clouds which are identified with the giant molecular clouds (GMCs). Masses, dimensions, distributions, and scale heights of the GMCs are predicted by the theory. It is suggested that the interstellar gas density in the disk is regulated by the gravitational instability mechanism in the arms which siphons material into star formation. Implications for the evolution of individual GMCs and for galactic morphology are discussed.

  6. The Microwave Spectrum and Molecular Structure of the Hydrogen-Bonded Aniline-Methanol Complex. (United States)

    Haeckel; Stahl


    The rotational spectrum of aniline-methanol was investigated in the frequency region 3-19 GHz using a pulsed molecular beam Fourier transform microwave spectrometer. Sixty-three measured a- and b-type transitions show a fine structure due to internal rotation of the methyl group. The resulting A and E lines are additionally split into hyperfine components arising from quadrupole coupling of the (14)N nucleus. The torsional motion of the methyl group is hindered by an effective barrier V(3) of nearly 215 cm(-1), which is almost one-half of the methanol barrier height. The structure of the complex was calculated assuming a common symmetry plane for the monomers. These form a linear N vertical ellipsis H-O hydrogen bond. Its distance was found to be 3.03 Å, which is identical with that of aniline-water. Copyright 1999 Academic Press.

  7. Largely Enhanced Saturable Absorption of a Complex of Plasmonic and Molecular-Like Au Nanocrystals (United States)

    Ding, Si-Jing; Nan, Fan; Yang, Da-Jie; Liu, Xiao-Li; Wang, Ya-Lan; Zhou, Li; Hao, Zhong-Hua; Wang, Qu-Quan


    A saturable absorber is a nonlinear functional material widely used in laser and photonic nanodevices. Metallic nanostructures have prominent saturable absorption (SA) at the plasmon resonance frequency owing to largely enhanced ground state absorption. However, the SA of plasmonic metal nanostructures is hampered by excited-state absorption processes at very high excitation power, which usually leads to a changeover from SA to reversed SA (SA→RSA). Here, we demonstrate tunable nonlinear absorption behaviours of a nanocomplex of plasmonic and molecular-like Au nanocrystals. The SA→RSA process is efficiently suppressed, and the stepwise SA→SA process is fulfilled owing to energy transfer in the nanocomplex. Our observations offer a strategy for preparation of the saturable absorber complex and have prospective applications in liquid lasers as well as one-photon nonlinear nanodevices. PMID:25875139

  8. The molecular evolution of four anti-malarial immune genes in the Anopheles gambiae species complex

    Directory of Open Access Journals (Sweden)

    Simard Frederic


    Full Text Available Abstract Background If the insect innate immune system is to be used as a potential blocking step in transmission of malaria, then it will require targeting one or a few genes with highest relevance and ease of manipulation. The problem is to identify and manipulate those of most importance to malaria infection without the risk of decreasing the mosquito's ability to stave off infections by microbes in general. Molecular evolution methodologies and concepts can help identify such genes. Within the setting of a comparative molecular population genetic and phylogenetic framework, involving six species of the Anopheles gambiae complex, we investigated whether a set of four pre-selected immunity genes (gambicin, NOS, Rel2 and FBN9 might have evolved under selection pressure imposed by the malaria parasite. Results We document varying levels of polymorphism within and divergence between the species, in all four genes. Introgression and the sharing of ancestral polymorphisms, two processes that have been documented in the past, were verified in this study in all four studied genes. These processes appear to affect each gene in different ways and to different degrees. However, there is no evidence of positive selection acting on these genes. Conclusion Considering the results presented here in concert with previous studies, genes that interact directly with the Plasmodium parasite, and play little or no role in defense against other microbes, are probably the most likely candidates for a specific adaptive response against P. falciparum. Furthermore, since it is hard to establish direct evidence linking the adaptation of any candidate gene to P. falciparum infection, a comparative framework allowing at least an indirect link should be provided. Such a framework could be achieved, if a similar approach like the one involved here, was applied to all other anopheline complexes that transmit P. falciparum malaria.

  9. The roles of template complexation and ligand binding conditions on recognition in bupivacaine molecularly imprinted polymers. (United States)

    Karlsson, Jesper G; Karlsson, Björn; Andersson, Lars I; Nicholls, Ian A


    A model for the molecular basis for ligand recognition in bupivacaine imprinted methacrylic acid-ethylene glycol dimethacrylate co-polymers has been developed based upon a series of (1)H-NMR studies in conjunction with HPLC and radioligand binding analyses. (1)H-NMR studies indicated that functional monomer-template complexes survive the polymerisation process, at least up until the stage of gelation. Polymers were synthesised and characterised by surface area analysis (BET), FT-IR and SEM. A combination of zonal and frontal chromatographic studies in aqueous and non-polar media indicate that selectivity arises from a combination of hydrophobic and electrostatic interactions. However, in the concentration regime employed for LC-based studies, ligand recognition in aqueous media was shown to be predominantly non-specific and hydrophobic in character. Radioligand binding studies, in lower ligand binding concentration regimes, permitted closer examination of the higher affinity binding sites. It was shown that the presence of a polar modifier in a non-polar solvent, or an organic modifier in water, produced enhanced selectivity. Variable temperature studies showed that the temperature of binding influences selectivity as well as the apparent number of sites available and that this effect is different in organic and aqueous environments. This indicates that the system studied is more complex in character than is generally appreciated. A comparison of the techniques employed here indicates that although chromatographic studies provide a valuable first-round screen for polymer-ligand selectivities, the level of detail obtainable using radioligand binding studies (lower concentrations and true equilibrium binding) makes them superior for detailed evaluations of molecularly imprinted polymers.

  10. Molecular dynamics simulations of the cardiac troponin complex performed with FRET distances as restraints. (United States)

    Jayasundar, Jayant James; Xing, Jun; Robinson, John M; Cheung, Herbert C; Dong, Wen-Ji


    Cardiac troponin (cTn) is the Ca(2+)-sensitive molecular switch that controls cardiac muscle activation and relaxation. However, the molecular detail of the switching mechanism and how the Ca(2+) signal received at cardiac troponin C (cTnC) is communicated to cardiac troponin I (cTnI) are still elusive. To unravel the structural details of troponin switching, we performed ensemble Förster resonance energy transfer (FRET) measurements and molecular dynamic (MD) simulations of the cardiac troponin core domain complex. The distance distributions of forty five inter-residue pairs were obtained under Ca(2+)-free and saturating Ca(2+) conditions from time-resolved FRET measurements. These distances were incorporated as restraints during the MD simulations of the cardiac troponin core domain. Compared to the Ca(2+)-saturated structure, the absence of regulatory Ca(2+) perturbed the cTnC N-domain hydrophobic pocket which assumed a closed conformation. This event partially unfolded the cTnI regulatory region/switch. The absence of Ca(2+), induced flexibility to the D/E linker and the cTnI inhibitory region, and rotated the cTnC N-domain with respect to rest of the troponin core domain. In the presence of saturating Ca(2+) the above said phenomenon were absent. We postulate that the secondary structure perturbations experienced by the cTnI regulatory region held within the cTnC N-domain hydrophobic pocket, coupled with the rotation of the cTnC N-domain would control the cTnI mobile domain interaction with actin. Concomitantly the rotation of the cTnC N-domain and perturbation of the D/E linker rigidity would control the cTnI inhibitory region interaction with actin to effect muscle relaxation.

  11. Molecular dynamics simulations of the cardiac troponin complex performed with FRET distances as restraints.

    Directory of Open Access Journals (Sweden)

    Jayant James Jayasundar

    Full Text Available Cardiac troponin (cTn is the Ca(2+-sensitive molecular switch that controls cardiac muscle activation and relaxation. However, the molecular detail of the switching mechanism and how the Ca(2+ signal received at cardiac troponin C (cTnC is communicated to cardiac troponin I (cTnI are still elusive. To unravel the structural details of troponin switching, we performed ensemble Förster resonance energy transfer (FRET measurements and molecular dynamic (MD simulations of the cardiac troponin core domain complex. The distance distributions of forty five inter-residue pairs were obtained under Ca(2+-free and saturating Ca(2+ conditions from time-resolved FRET measurements. These distances were incorporated as restraints during the MD simulations of the cardiac troponin core domain. Compared to the Ca(2+-saturated structure, the absence of regulatory Ca(2+ perturbed the cTnC N-domain hydrophobic pocket which assumed a closed conformation. This event partially unfolded the cTnI regulatory region/switch. The absence of Ca(2+, induced flexibility to the D/E linker and the cTnI inhibitory region, and rotated the cTnC N-domain with respect to rest of the troponin core domain. In the presence of saturating Ca(2+ the above said phenomenon were absent. We postulate that the secondary structure perturbations experienced by the cTnI regulatory region held within the cTnC N-domain hydrophobic pocket, coupled with the rotation of the cTnC N-domain would control the cTnI mobile domain interaction with actin. Concomitantly the rotation of the cTnC N-domain and perturbation of the D/E linker rigidity would control the cTnI inhibitory region interaction with actin to effect muscle relaxation.

  12. Ions interacting with complex molecular systems: The effect of a surrounding environment (United States)

    Zettergren, Henning


    This paper highlight results from studies of keV-ion impact on complex molecules and molecular clusters, which have been carried out at the ARIBE facility in Caen (France) during the last decade. Studies of fullerenes, Polycyclic Aromatic Hydrocarbons (PAHs), and biomolecules are reviewed with focus on the effect of a surrounding environment when ions interact with weakly bound clusters of theses species. One common result is that charge and energy are rapidly shared between the individual molecules in the clusters, in contrast to e.g. weakly bound atomic clusters where the charge stay localized to a few atoms from which the electrons are removed during the collisions. Another important finding is that ion collisions may induce reactions within clusters such as e.g. proton transfer and different types of molecular growth processes. In the latter case, these processes may be driven by prompt non-statistical atom knockouts in billiard-ball like atom-atom collisions favouring highly reactive fragments. In contrast, statistical fragmentation in general yields different and less reactive fragments.

  13. Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity (United States)

    Simon, Joseph R.; Carroll, Nick J.; Rubinstein, Michael; Chilkoti, Ashutosh; López, Gabriel P.


    Dynamic protein-rich intracellular structures that contain phase-separated intrinsically disordered proteins (IDPs) composed of sequences of low complexity (SLC) have been shown to serve a variety of important cellular functions, which include signalling, compartmentalization and stabilization. However, our understanding of these structures and our ability to synthesize models of them have been limited. We present design rules for IDPs possessing SLCs that phase separate into diverse assemblies within droplet microenvironments. Using theoretical analyses, we interpret the phase behaviour of archetypal IDP sequences and demonstrate the rational design of a vast library of multicomponent protein-rich structures that ranges from uniform nano-, meso- and microscale puncta (distinct protein droplets) to multilayered orthogonally phase-separated granular structures. The ability to predict and program IDP-rich assemblies in this fashion offers new insights into (1) genetic-to-molecular-to-macroscale relationships that encode hierarchical IDP assemblies, (2) design rules of such assemblies in cell biology and (3) molecular-level engineering of self-assembled recombinant IDP-rich materials.

  14. Rotational Spectroscopy of the NH{sub 3}–H{sub 2} Molecular Complex

    Energy Technology Data Exchange (ETDEWEB)

    Surin, L. A.; Schlemmer, S. [I. Physikalisches Institut, University of Cologne, Zülpicher Str. 77, D-50937 Cologne (Germany); Tarabukin, I. V. [Institute of Spectroscopy of Russian Academy of Sciences, Fizicheskaya Str. 5, 108840 Troitsk, Moscow, Russia (Russian Federation); Breier, A. A.; Giesen, T. F. [Institute of Physics, University of Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel (Germany); McCarthy, M. C. [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA 02138 (United States); Avoird, A. van der, E-mail:, E-mail: [Theoretical Chemistry, Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands)


    We report the first high resolution spectroscopic study of the NH{sub 3}–H{sub 2} van der Waals molecular complex. Three different experimental techniques, a molecular beam Fourier transform microwave spectrometer, a millimeter-wave intracavity jet OROTRON spectrometer, and a submillimeter-wave jet spectrometer with multipass cell, were used to detect pure rotational transitions of NH{sub 3}–H{sub 2} in the wide frequency range from 39 to 230 GHz. Two nuclear spin species, ( o )-NH{sub 3}–( o )-H{sub 2} and ( p )-NH{sub 3}–( o )-H{sub 2}, have been assigned as carriers of the observed lines on the basis of accompanying rovibrational calculations performed using the ab initio intermolecular potential energy surface (PES) of Maret et al. The experimental spectra were compared with the theoretical bound state results, thus providing a critical test of the quality of the NH{sub 3}–H{sub 2} PES, which is a key issue for reliable computations of the collisional excitation and de-excitation of ammonia in the dense interstellar medium.

  15. Epigenetics and Shared Molecular Processes in the Regeneration of Complex Structures

    Directory of Open Access Journals (Sweden)

    Labib Rouhana


    Full Text Available The ability to regenerate complex structures is broadly represented in both plant and animal kingdoms. Although regenerative abilities vary significantly amongst metazoans, cumulative studies have identified cellular events that are broadly observed during regenerative events. For example, structural damage is recognized and wound healing initiated upon injury, which is followed by programmed cell death in the vicinity of damaged tissue and a burst in proliferation of progenitor cells. Sustained proliferation and localization of progenitor cells to site of injury give rise to an assembly of differentiating cells known as the regeneration blastema, which fosters the development of new tissue. Finally, preexisting tissue rearranges and integrates with newly differentiated cells to restore proportionality and function. While heterogeneity exists in the basic processes displayed during regenerative events in different species—most notably the cellular source contributing to formation of new tissue—activation of conserved molecular pathways is imperative for proper regulation of cells during regeneration. Perhaps the most fundamental of such molecular processes entails chromatin rearrangements, which prime large changes in gene expression required for differentiation and/or dedifferentiation of progenitor cells. This review provides an overview of known contributions to regenerative processes by noncoding RNAs and chromatin-modifying enzymes involved in epigenetic regulation.

  16. PbSe Nanocrystal Excitonic Solar Cells

    KAUST Repository

    Choi, Joshua J.


    We report the design, fabrication, and characterization of colloidal PbSe nanocrystal (NC)-based photovoltaic test structures that exhibit an excitonic solar cell mechanism. Charge extraction from the NC active layer is driven by a photoinduced chemical potential energy gradient at the nanostructured heterojunction. By minimizing perturbation to PbSe NC energy levels and thereby gaining insight into the "intrinsic" photovoltaic properties and charge transfer mechanism of PbSe NC, we show a direct correlation between interfacial energy level offsets and photovoltaic device performance. Size dependent PbSe NC energy levels were determined by cyclic voltammetry and optical spectroscopy and correlated to photovoltaic measurements. Photovoltaic test structures were fabricated from PbSe NC films sandwiched between layers of ZnO nanoparticles and PEDOT:PSS as electron and hole transporting elements, respectively. The device current-voltage characteristics suggest a charge separation mechanism that Is distinct from previously reported Schottky devices and consistent with signatures of excitonic solar cells. Remarkably, despite the limitation of planar junction structure, and without film thickness optimization, the best performing device shows a 1-sun power conversion efficiency of 3.4%, ranking among the highest performing NC-based solar cells reported to date. © 2009 American Chemical Society.

  17. Characterization and Physiological Function of Class I Low-Molecular-Mass, Heat-Shock Protein Complex in Soybean. (United States)

    Jinn, T. L.; Chen, Y. M.; Lin, C. Y.


    Examination of an ammonium sulfate-enriched fraction (70-100% saturation) of heat-shock proteins (HSPs) by nondenaturing polyacrylamide gel electrophoresis revealed the presence of a high molecular mass complex (280 kD) in soybean (Glycine max) seedlings. This complex cross-reacted with antibodies raised against soybean class I low-molecular-mass (LMW) HSPs. Dissociation of the complex by denaturing polyacrylamide gel electrophoresis showed the complex to contain at least 15 polypeptides of the 15-to 18-kD class I LMW HSPs that could be detected by staining, radiolabeling, and western blotting. A similar LMW-HSP complex was observed in mung bean (Vigna radiata L.; 295 kD), in pea (Pisum sativum L.; 270 kD), and in rice (Oryza sativa L.; 310 kD). The complex was stable under high salt conditions (250 mM KCI), and the integrity was not affected by 1% Nonidet P-40 and 3 [mu]g/ML RNase treatment. The size of the isolated HSP complex in vitro was conserved to 55[deg]C; however, starting at 37.5[deg]C, it changed to higher molecular forms in the presence of soluble proteins. The isolated HSP complex was able to protect up to 75% of the soluble proteins from heat denaturation in vitro.

  18. Donor-acceptor complex formation in evaporated small molecular organic photovoltaic cells

    Energy Technology Data Exchange (ETDEWEB)

    Susarova, Diana K.; Troshin, Pavel A.; Lyubovskaya, Rimma N.; Razumov, Vladimir F. [Institute of Problems of Chemical Physics of Russian Academy of Sciences, Semenov Prospect 1, Chernogolovka, Moscow 142432 (Russian Federation); Hoeglinger, Doris; Koeppe, Robert; Serdar Sariciftci, N. [Linz Institute for Organic Solar Cells (LIOS), Johannes Kepler University Linz, Altenbergerstrasse 69, A-4040 Linz (Austria); Babenko, Sergey D. [Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences (Branch), Semenov Prospect 1/10, Chernogolovka, Moscow 142432 (Russian Federation)


    Novel perylene diimide Py-PDI and naphthalene diimide Py-NDI possessing chelating pyridyl groups have been synthesized. The materials are comparatively investigated as electron acceptors in small molecular photovoltaic cells comprising zinc phthalocyanine ZnPc as an electron donor component. It was shown that these compounds form self-assembled coordination complexes with ZnPc in solution and co-evaporated solid blends. Py-PDI and Py-NDI used as electron acceptor materials in photovoltaic cells with donor ZnPc significantly outperform the reference materials, i.e. perylene and naphthalene diimides that possess no chelating pyridyl groups. Superior photovoltaic performance of Py-PDI and Py-NDI is explained by a complex formation between these compounds and ZnPc. Such interactions of donor and acceptor materials strongly improve photoinduced charge carrier generation. This gives great advantages not just for the construction of organic solar cells but also for organic photodetectors. The devices fabricated in this study are also useful as fast and highly sensitive photodetectors with response times of less than 10 microseconds as well as a strong photoconductive behavior under forward bias. (author)

  19. Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes. (United States)

    Risthaus, Tobias; Grimme, Stefan


    A new test set (S12L) containing 12 supramolecular noncovalently bound complexes is presented and used to evaluate seven different methods to account for dispersion in DFT (DFT-D3, DFT-D2, DFT-NL, XDM, dDsC, TS-vdW, M06-L) at different basis set levels against experimental, back-corrected reference energies. This allows conclusions about the performance of each method in an explorative research setting on "real-life" problems. Most DFT methods show satisfactory performance but, due to the largeness of the complexes, almost always require an explicit correction for the nonadditive Axilrod-Teller-Muto three-body dispersion interaction to get accurate results. The necessity of using a method capable of accounting for dispersion is clearly demonstrated in that the two-body dispersion contributions are on the order of 20-150% of the total interaction energy. MP2 and some variants thereof are shown to be insufficient for this while a few tested D3-corrected semiempirical MO methods perform reasonably well. Overall, we suggest the use of this benchmark set as a "sanity check" against overfitting to too small molecular cases.

  20. Mechanisms of nuclear pore complex assembly - two different ways of building one molecular machine. (United States)

    Otsuka, Shotaro; Ellenberg, Jan


    The nuclear pore complex (NPC) mediates all macromolecular transport across the nuclear envelope. In higher eukaryotes that have an open mitosis, NPCs assemble at two points in the cell cycle: during nuclear assembly in late mitosis and during nuclear growth in interphase. How the NPC, the largest nonpolymeric protein complex in eukaryotic cells, self-assembles inside cells remained unclear. Recent studies have started to uncover the assembly process, and evidence has been accumulating that postmitotic and interphase NPC assembly use fundamentally different mechanisms; the duration, structural intermediates, and regulation by molecular players are different and different types of membrane deformation are involved. In this Review, we summarize the current understanding of these two modes of NPC assembly and discuss the structural and regulatory steps that might drive the assembly processes. We furthermore integrate understanding of NPC assembly with the mechanisms for rapid nuclear growth in embryos and, finally, speculate on the evolutionary origin of the NPC implied by the presence of two distinct assembly mechanisms. © 2017 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

  1. Molecular recognition between DNA and a copper-based anticancer complex. (United States)

    Galindo-Murillo, Rodrigo; Ruíz-Azuara, Lena; Moreno-Esparza, Rafael; Cortés-Guzmán, Fernando


    The aim of this work is to describe the specific recognition site between DNA and an anticancer copper complex by means of computational methods. Molecular dynamics were used to find the preferred site of binding between selected DNA chains and [Cu(2,2'-bipyridine)(acetylacetonate)(H(2)O)](+) (Cas). Full DFT optimizations of selected geometries extracted from simulations, followed by a topological analysis of electron density allowed us to define the specific interactions inside the recognition site. Cas links deoxyribose-phosphate by a coordination bond between metal and the phosphate group. There are several C-H···π, O···π(C) and O···π(N) interactions between the sugar group and the aromatic ligand of Cas. The results indicate that the adduct Cas-deoxyribose-phosphate may be an initial step toward the hydrolysis of DNA chains. Overall, this study provides insights into the initial step of the action mechanism of copper complexes as apoptosis-inducing agents and provides guidelines for the design of this kind of drugs.

  2. Molecular phylogeny of Glossodoris (Ehrenberg, 1831) nudibranchs and related genera reveals cryptic and pseudocryptic species complexes

    KAUST Repository

    Matsuda, Shayle B.


    Chromodorid nudibranchs (Chromodorididae) are brightly coloured sea slugs that live in some of the most biodiverse and threatened coral reefs on the planet. However, the evolutionary relationships within this family have not been well understood, especially in the genus Glossodoris. Members of Glossodoris have experienced large-scale taxonomic instability over the last century and have been the subject of repeated taxonomic changes, in part due to morphological characters being the sole traditional taxonomic sources of data. Changing concepts of traditional generic boundaries based on morphology also have contributed to this instability. Despite recent advances in molecular systematics, many aspects of chromodorid taxonomy remain poorly understood, particularly at the traditional species and generic levels. In this study, 77 individuals comprising 32 previously defined species were used to build the most robust phylogenetic tree of Glossodoris and related genera using mitochondrial genes cytochrome c oxidase subunit I and 16S, and the nuclear gene 28S. Bayesian inference, maximum likelihood, and maximum parsimony analyses verify the most recent hypothesized evolutionary relationships within Glossodoris. Additionally, a pseudocryptic and cryptic species complex within Glossodoris cincta and a pseudocryptic complex within Glossodoris pallida emerged, and three new species of Doriprismatica are identified.

  3. Synthesis, anticancer activity and molecular docking study of Schiff base complexes containing thiazole moiety

    Directory of Open Access Journals (Sweden)

    Mokhles M. Abd-Elzaher


    Full Text Available A Schiff base ligand 1 was prepared from condensation of salicyaldehyde with 2-amino-4-phenyl-5-methyl thiazole. The ligand forms complexes with CoII, NiII, CuII, and ZnII in good yield. The synthesized compounds were characterized by elemental analysis, magnetic susceptibility, molar conductance, infrared spectra, 1H and 13C NMR, mass, electronic absorption and ESR spectroscopy. The anticancer activity of the synthesized compounds was studied against different human tumor cell lines: breast cancer MCF-7, liver cancer HepG2, lung carcinoma A549 and colorectal cancer HCT116 in comparison with the activity of doxorubicin as a reference drug. The study showed that ZnII complex showed potent inhibition against human TRK in the four cell lines (HepG2, MCF7, A549, HCT116 by the ratio 80, 70, 61 and 64% respectively as compared to the inhibition in the untreated cells. Moreover, the molecular docking into TRK (PDB: 1t46 was done for the optimization of the aforementioned compounds as potential TRK inhibitors.

  4. Synthesis and Self-Assembly of Chiral Cylindrical Molecular Complexes: Functional Heterogeneous Liquid-Solid Materials Formed by Helicene Oligomers

    Directory of Open Access Journals (Sweden)

    Nozomi Saito


    Full Text Available Chiral cylindrical molecular complexes of homo- and hetero-double-helices derived from helicene oligomers self-assemble in solution, providing functional heterogeneous liquid-solid materials. Gels and liotropic liquid crystals are formed by fibril self-assembly in solution; molecular monolayers and fibril films are formed by self-assembly on solid surfaces; gels containing gold nanoparticles emit light; silica nanoparticles aggregate and adsorb double-helices. Notable dynamics appears during self-assembly, including multistep self-assembly, solid surface catalyzed double-helix formation, sigmoidal and stairwise kinetics, molecular recognition of nanoparticles, discontinuous self-assembly, materials clocking, chiral symmetry breaking and homogeneous-heterogeneous transitions. These phenomena are derived from strong intercomplex interactions of chiral cylindrical molecular complexes.

  5. Molecular phylogenetics and historical biogeography of the west-palearctic common toads (Bufo bufo species complex). (United States)

    Garcia-Porta, J; Litvinchuk, S N; Crochet, P A; Romano, A; Geniez, P H; Lo-Valvo, M; Lymberakis, P; Carranza, S


    In most pan-Eurasiatic species complexes, two phenomena have been traditionally considered key processes of their cladogenesis and biogeography. First, it is hypothesized that the origin and development of the Central Asian Deserts generated a biogeographic barrier that fragmented past continuous distributions in Eastern and Western domains. Second, Pleistocene glaciations have been proposed as the main process driving the regional diversification within each of these domains. The European common toad and its closest relatives provide an interesting opportunity to examine the relative contributions of these paleogeographic and paleoclimatic events to the phylogeny and biogeography of a widespread Eurasiatic group. We investigate this issue by applying a multiproxy approach combining information from molecular phylogenies, a multiple correspondence analysis of allozyme data and species distribution models. Our study includes 304 specimens from 164 populations, covering most of the distributional range of the Bufo bufo species complex in the Western Palearctic. The phylogenies (ML and Bayesian analyses) were based on a total of 1988 bp of mitochondrial DNA encompassing three genes (tRNAval, 16S and ND1). A dataset with 173 species of the family Bufonidae was assembled to estimate the separation of the two pan-Eurasiatic species complexes of Bufo and to date the main biogeographic events within the Bufo bufo species complex. The allozyme study included sixteen protein systems, corresponding to 21 presumptive loci. Finally, the distribution models were based on maximum entropy. Our distribution models show that Eastern and Western species complexes are greatly isolated by the Central Asian Deserts, and our dating estimates place this divergence during the Middle Miocene, a moment in which different sources of evidence document a major upturn of the aridification rate of Central Asia. This climate-driven process likely separated the Eastern and Western species. At the

  6. Very stable high molecular mass multiprotein complex with DNase and amylase activities in human milk. (United States)

    Soboleva, Svetlana E; Dmitrenok, Pavel S; Verkhovod, Timofey D; Buneva, Valentina N; Sedykh, Sergey E; Nevinsky, Georgy A


    For breastfed infants, human milk is more than a source of nutrients; it furnishes a wide array of proteins, peptides, antibodies, and other components promoting neonatal growth and protecting infants from viral and bacterial infection. It has been proposed that most biological processes are performed by protein complexes. Therefore, identification and characterization of human milk components including protein complexes is important for understanding the function of milk. Using gel filtration, we have purified a stable high molecular mass (~1000 kDa) multiprotein complex (SPC) from 15 preparations of human milk. Light scattering and gel filtration showed that the SPC was stable in the presence of high concentrations of NaCl and MgCl2 but dissociated efficiently under the conditions that destroy immunocomplexes (2 M MgCl2 , 0.5 M NaCl, and 10 mM DTT). Such a stable complex is unlikely to be a casual associate of different proteins. The relative content of the individual SPCs varied from 6% to 25% of the total milk protein. According to electrophoretic and mass spectrometry analysis, all 15 SPCs contained lactoferrin (LF) and α-lactalbumin as major proteins, whereas human milk albumin and β-casein were present in moderate or minor amounts; a different content of IgGs and sIgAs was observed. All SPCs efficiently hydrolyzed Plasmid supercoiled DNA and maltoheptaose. Some freshly prepared SPC preparations contained not only intact LF but also small amounts of its fragments, which appeared in all SPCs during their prolonged storage; the fragments, similar to intact LF, possessed DNase and amylase activities. LF is found in human epithelial secretions, barrier body fluids, and in the secondary granules of leukocytes. LF is a protein of the acute phase response and nonspecific defense against different types of microbial and viral infections. Therefore, LF complexes with other proteins may be important for its functions not only in human milk. Copyright © 2014

  7. Biochemical and molecular characterization of senescence-related cysteine protease-cystatin complex from spinach leaf. (United States)

    Tajima, Takayuki; Yamaguchi, Akemi; Matsushima, Shuhei; Satoh, Masashi; Hayasaka, Satoshi; Yoshimatsu, Katsuhiko; Shioi, Yuzo


    Cysteine proteases (CPs) with N-succinyl-Leu-Tyr-4-methylcoumaryl-7-amide (Suc-LY-MCA) cleavage activity were investigated in green and senescent leaves of spinach. The enzyme activity was separated into two major and several faint minor peaks by hydrophobic chromatography. These peaks were conventionally designated as CP1, CP2 and CP3, according to their order of elution. From the analyses of molecular mass, subunit structure, amino acid sequences and cDNA cloning, CP2 was a monomer complex (SoCP-CPI) (51 kDa) composed of a 41-kDa core protein, SoCP (Spinacia oleracea cysteine protease), and 14-kDa cystatin, a cysteine protease inhibitor (CPI), while CP3 was a trimer complex (SoCP-CPI)(3) (151 kDa) of the same subunits as SoCP-CPI and showed a wider range of specificity toward natural substrates than SoCP-CPI. Trimer (SoCP-CPI)(3) was irreversibly formed from monomers through association. The results of reverse transcription-polymerase chain reaction (RT-PCR) revealed that mRNAs of CPI and SoCP are hardly expressed in green leaves, but they are coordinately expressed in senescent leaves, suggesting that these proteases involve in senescence. Purified recombinant CPI had strong inhibitory activity against trimer SoCP, (SoCP)(3) , which had a cystatin deleted with K(i) value of 1.33 × 10(-9) M. After treatment of the enzyme with a succinate buffer (pH 5) at the most active pH of the enzyme, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and activity analyses showed that cystatin was released from both monomer SoCP-CPI and trimer (SoCP-CPI)(3) complexes with a concomitant activation. Thus, the removal of a cystatin is necessary to activate the enzyme activity.

  8. Biological Activity and Molecular Structures of Bis(benzimidazole and Trithiocyanurate Complexes

    Directory of Open Access Journals (Sweden)

    Pavel Kopel


    Full Text Available 1-(1H-Benzimidazol-2-yl-N-(1H-benzimidazol-2-ylmethylmethanamine (abb and 2-(1H-benzimidazol-2-ylmethylsulfanylmethyl-1H-benzimidazole (tbb have been prepared and characterized by elemental analysis. These bis(benzimidazoles have been further used in combination with trithiocyanuric acid for the preparation of complexes. The crystal and molecular structures of two of them have been solved. Each nickel atom in the structure of trinuclear complex [Ni3(abb3(H2O3(μ-ttc](ClO43·3H2O·EtOH (1, where ttcH3 = trithiocyanuric acid, is coordinated with three N atoms of abb, the N,S donor set of ttc anion and an oxygen of a water molecule. The crystal of [(tbbH2(ttcH22(ttcH3(H2O] (2 is composed of a protonated bis(benzimidazole, two ttcH2 anions, ttcH3 and water. The structure is stabilized by a network of hydrogen bonds. These compounds were primarily synthesized for their potential antimicrobial activity and hence their possible use in the treatment of infections caused by bacteria or yeasts (fungi. The antimicrobial and antifungal activity of the prepared compounds have been evaluated on a wide spectrum of bacterial and yeast strains and clinical specimens isolated from patients with infectious wounds and the best antimicrobial properties were observed in strains after the use of ligand abb and complex 1, when at least 80% growth inhibition was achieved.

  9. Visualizing molecular juggling within a B[subscript 12]-dependent methyltransferase complex

    Energy Technology Data Exchange (ETDEWEB)

    Kung, Yan; Ando, Nozomi; Doukov, Tzanko I.; Blasiak, Leah C.; Bender, Güne; #351; ; Seravalli, Javier; Ragsdale, Stephen W.; Drennan, Catherine L. (MIT); (Michigan); (UNL)


    Derivatives of vitamin B{sub 12} are used in methyl group transfer in biological processes as diverse as methionine synthesis in humans and CO{sub 2} fixation in acetogenic bacteria. This seemingly straightforward reaction requires large, multimodular enzyme complexes that adopt multiple conformations to alternately activate, protect and perform catalysis on the reactive B{sub 12} cofactor. Crystal structures determined thus far have provided structural information for only fragments of these complexes, inspiring speculation about the overall protein assembly and conformational movements inherent to activity. Here we present X-ray crystal structures of a complete 220 kDa complex that contains all enzymes responsible for B{sub 12}-dependent methyl transfer, namely the corrinoid iron-sulphur protein and its methyltransferase from the model acetogen Moorella thermoacetica. These structures provide the first three-dimensional depiction of all protein modules required for the activation, protection and catalytic steps of B{sub 12}-dependent methyl transfer. In addition, the structures capture B{sub 12} at multiple locations between its 'resting' and catalytic positions, allowing visualization of the dramatic protein rearrangements that enable methyl transfer and identification of the trajectory for B{sub 12} movement within the large enzyme scaffold. The structures are also presented alongside in crystallo spectroscopic data, which confirm enzymatic activity within crystals and demonstrate the largest known conformational movements of proteins in a crystalline state. Taken together, this work provides a model for the molecular juggling that accompanies turnover and helps explain why such an elaborate protein framework is required for such a simple, yet biologically essential reaction.

  10. Experimental and molecular modeling studies on the DNA-binding of diazacyclam-based acrocyclic copper complex. (United States)

    Shahabadi, Nahid; Hakimi, Mohammad; Morovati, Teimoor; Falsafi, Monireh; Fili, Soraya Moradi


    The interaction of a new macrocyclic copper complex, [CuL(NO 3 ) 2 ] in which L is 1,3,6,10,12,15-hexaaza tricyclo[ 6,10 ] eicosane was investigated in vitro under simulated physiological conditions by multi-spectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated the complex interacted with ct-DNA in a groove binding mode while the binding constant of UV-vis and the number of binding sites were 1.0±0.2×10 4 Lmol -1 and 1.01, respectively. The fluorometric studies showed that the reaction between the complex with ct-DNA is exothermic (ΔH=14.85kJmol -1 ; ΔS=109.54Jmol -1 K -1 ). Circular dichroism spectroscopy (CD) was employed to measure the conformational change of DNA in the presence of [CuL(NO 3 ) 2 ] complex. Furthermore, the complex induces detectable changes in the viscosity of DNA. The molecular modeling results illustrated that the complex strongly binds to groove of DNA. Experimental and molecular modeling results showed that Cu(II) complex bound to DNA by a groove binding mode. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Molecular dynamics simulations show altered secondary structure of clawless in binary complex with DNA providing insights into aristaless-clawless-DNA ternary complex formation. (United States)

    Kachhap, Sangita; Priyadarshini, Pragya; Singh, Balvinder


    Aristaless (Al) and clawless (Cll) homeodomains that are involved in leg development in Drosophila melanogaster are known to bind cooperatively to 5'-(T/C)TAATTAA(T/A)(T/A)G-3' DNA sequence, but the mechanism of their binding to DNA is unknown. Molecular dynamics (MD) studies have been carried out on binary, ternary, and reconstructed protein-DNA complexes involving Al, Cll, and DNA along with binding free energy analysis of these complexes. Analysis of MD trajectories of Cll-3A01, binary complex reveals that C-terminal end of helixIII of Cll, unwind in the absence of Al and remains so in reconstructed ternary complex, Cll-3A01-Al. In addition, this change in secondary structure of Cll does not allow it to form protein-protein interactions with Al in the ternary reconstructed complex. However, secondary structure of Cll and its interactions are maintained in other reconstructed ternary complex, Al-3A01-Cll where Cll binds to Al-3A01, binary complex to form ternary complex. These interactions as observed during MD simulations compare well with those observed in ternary crystal structure. Thus, this study highlights the role of helixIII of Cll and protein-protein interactions while proposing likely mechanism of recognition in ternary complex, Al-Cll-DNA.

  12. MesoBioNano Explorer-A Universal Program for Multiscale Computer Simulations of Complex Molecular Structure and Dynamics

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander V.; Nikolaev, Pavel V.


    We present a multipurpose computer code MesoBioNano Explorer (MBN Explorer). The package allows to model molecular systems of varied level of complexity. In particular, MBN Explorer is suited to compute system's energy, to optimize molecular structure as well as to consider the molecular and random...... it significantly different from the existing codes, is its universality and applicability to the description of a broad range of problems involving different molecular systems. Most of the existing codes are developed for particular classes of molecular systems and do not permit multiscale approach while MBN...... Explorer goes beyond these drawbacks. On demand, MBN Explorer allows to group particles in the system into rigid fragments, thereby significantly reducing the number of dynamical degrees of freedom. Despite the universality, the computational efficiency of MBN Explorer is comparable (and in some cases even...

  13. Photogenerated Exciton Dissociation in Highly Coupled Lead Salt Nanocrystal Assemblies

    KAUST Repository

    Choi, Joshua J.


    Internanocrystal coupling induced excitons dissociation in lead salt nanocrystal assemblies is investigated. By combining transient photoluminescence spectroscopy, grazing incidence small-angle X-ray scattering, and time-resolved electric force microscopy, we show that excitons can dissociate, without the aid of an external bias or chemical potential gradient, via tunneling through a potential barrier when the coupling energy is comparable to the exciton binding energy. Our results have important implications for the design of nanocrystal-based optoelectronic devices. © 2010 American Chemical Society.

  14. Excitonic AND Logic Gates on DNA Brick Nanobreadboards (United States)


    A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, we have demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore density achievable via this brick-based approach provide a viable path toward developing information processing and storage systems. PMID:25839049

  15. Ordered Dissipative Structures in Exciton Systems in Semiconductor Quantum Wells

    Directory of Open Access Journals (Sweden)

    Andrey A. Chernyuk


    Full Text Available A phenomenological theory of exciton condensation in conditions of inhomogeneous excitation is proposed. The theory is applied to the study of the development of an exciton luminescence ring and the ring fragmentation at macroscopical distances from the central excitation spot in coupled quantum wells. The transition between the fragmented and the continuous ring is considered. With assumption of a defect in the structure, a possibility of a localized island of the condensed phase in a fixed position is shown. Exciton density distribution is also analyzed in the case of two spatially separated spots of the laser excitation.

  16. Influence of the sign of the coupling on the temperature dependence of optical properties of one-dimensional exciton models

    Energy Technology Data Exchange (ETDEWEB)

    Cruzeiro, L [CCMAR and FCT, Universidade of Algarve, Campus de Gambelas, 8005-139 Faro (Portugal)


    A new physical cause for a temperature-dependent double peak in exciton systems is put forward within a thermal equilibrium approach for the calculation of optical properties of exciton systems. Indeed, it is found that one-dimensional exciton systems with only one molecule per unit cell can have an absorption spectrum characterized by a double peak provided that the coupling between excitations in different molecules is positive. The two peaks, whose relative intensities vary with temperature, are located around the exciton band edges, being separated by an energy of approximately 4V, where V is the average coupling between nearest neighbours. For small amounts of diagonal and off-diagonal disorder, the contributions from the intermediate states in the band are also visible as intermediate structure between the two peaks, this being enhanced for systems with periodic boundary conditions. At a qualitative level, these results correlate well with experimental observations in the molecular aggregates of the thiacarbocyanine dye THIATS and in the organic crystals of acetanilide and N-methylacetamide.

  17. Hot exciton cooling and multiple exciton generation in PbSe quantum dots. (United States)

    Kumar, Manoj; Vezzoli, Stefano; Wang, Zilong; Chaudhary, Varun; Ramanujan, Raju V; Gurzadyan, Gagik G; Bruno, Annalisa; Soci, Cesare


    Multiple exciton generation (MEG) is a promising process to improve the power conversion efficiency of solar cells. PbSe quantum dots (QDs) have shown reasonably high MEG quantum yield (QY), although the photon energy threshold for this process is still under debate. One of the reasons for this inconsistency is the complicated competition of MEG and hot exciton cooling, especially at higher excited states. Here, we investigate MEG QY and the origin of the photon energy threshold for MEG in PbSe QDs of three different sizes by studying the transient absorption (TA) spectra, both at the band gap (near infrared, NIR) and far from the band gap energy (visible range). The comparison of visible TA spectra and dynamics for different pump wavelengths, below, around and above the MEG threshold, provides evidence of the role of the Σ transition in slowing down the exciton cooling process that can help MEG to take over the phonon relaxation process. The universality of this behavior is confirmed by studying QDs of three different sizes. Moreover, our results suggest that MEG QY can be determined by pump-probe experiments probed above the band gap.

  18. Molecular markers for the identification and global tracking of whitefly vector-Begomovirus complexes. (United States)

    Brown, J K


    basis in the most highly conserved viral ORFs, CP (V1) and a portion of replication-associated protein (REP) (L1/C1), and a key non-coding sequence that contain sufficient variability and/or virus-specific sequences, and are consequently of potential epidemiological relevance. Because B. tabaci occurs as a cryptic species, or species complex, that exhibits biotic polymorphism, yet morphological invariance, traditional morphologically based identification is impossible. An overriding complication to establishing molecular markers for identifying whitefly vector variants is that whitefly sequences in general, have not been available. However, recent work has shown that a partial mitochondria cytochrome oxidase I (mt COI) sequence separates vector variants with a basis in geographical origin, suggesting it is useful for further exploring variability and the phylogenetic history of whiteflies on a large scale. Here, the utility of whitefly mt COI nucleotides (nt) sequences is illustrated for inferring relationships between B. tabaci collected from major world regions. Used collectively, these approaches permit investigations of the patterns of distribution and dissemination of begomovirus-whitefly vector complexes for the first time. Ultimately, more immediate recognition of exotic viruses and whitefly vectors and early detection of upsurges in vector populations and of emerging viruses will be possible.

  19. Three-dimensional Aquila Rift: magnetized H I arch anchored by molecular complex (United States)

    Sofue, Yoshiaki; Nakanishi, Hiroyuki


    Three-dimensional structure of the Aquila Rift of magnetized neutral gas is investigated by analysing H I and CO line data. The projected distance on the Galactic plane of the H I arch of the Aquila Rift is r⊥ ˜ 250 pc from the Sun. The H I arch emerges at l ˜ 30°, reaches to altitudes as high as ˜500 pc above the plane at l ˜ 350°, and returns to the disc at l ˜ 270°. The extent of arch at positive latitudes is ˜1 kpc and the width is ˜100 pc. The eastern root is associated with the giant molecular cloud complex, which is the main body of the optically defined Aquila Rift. The H I and molecular masses of the Rift are estimated to be M_{H I}˜ 1.4{×} 10^5 M_{⊙} and M_H_2˜ 3{×} 10^5 M_{⊙}. Gravitational energies to lift the gases to their heights are E_{grav: H I}˜ 1.4{×} 10^{51} erg and E_{grav: H_2}˜ 0.3{×} 10^{51} erg, respectively. Magnetic field is aligned along the H I arch of the Rift, and the strength is measured to be B ˜ 10 μG using Faraday rotation measures of extragalactic radio sources. The magnetic energy is estimated to be Emag ˜ 1.2 × 1051 erg. A possible mechanism of formation of the Aquila Rift is proposed in terms of interstellar magnetic inflation by a sinusoidal Parker instability of wavelength of ˜2.5 kpc and amplitude ˜500 pc.

  20. Constructing Molecular Complexity and Diversity: Total Synthesis of Natural Products of Biological and Medicinal Importance (United States)

    Nicolaou, K. C.; Hale, Christopher R. H.; Nilewski, Christian; Ioannidou, Heraklidia A.


    The advent of organic synthesis and the understanding of the molecule as they occurred in the nineteenth century and were refined in the twentieth century constitute two of the most profound scientific developments of all time. These discoveries set in motion a revolution that shaped the landscape of the molecular sciences and changed the world. Organic synthesis played a major role in this revolution through its ability to construct the molecules of the living world and others like them whose primary element is carbon. Although the early beginnings of organic synthesis came about serendipitously, organic chemists quickly recognized its potential and moved decisively to advance and exploit it in myriad ways for the benefit of mankind. Indeed, from the early days of the synthesis of urea and the construction of the first carbon-carbon bond, the art of organic synthesis improved to impressively high levels of sophistication. Through its practice, today chemists can synthesize organic molecules—natural and designed—of all types of structural motifs and for all intents and purposes. The endeavor of constructing natural products—the organic molecules of nature—is justly called both a creative art and an exact science. Often called simply total synthesis, the replication of nature’s molecules in the laboratory reflects and symbolizes the state of the art of synthesis in general. In the last few decades a surge in total synthesis endeavors around the world led to a remarkable collection of achievements that covers a wide ranging landscape of molecular complexity and diversity. In this article, we present highlights of some of our contributions in the field of total synthesis of natural products of biological and medicinal importance. For perspective, we also provide a listing of selected examples of additional natural products synthesized in other laboratories around the world over the last few years. PMID:22743704

  1. Highly efficient excitonic emission of CBD grown ZnO micropods (Presentation Recording) (United States)

    Aad, Roy; Gokarna, Anisha; Nomenyo, Komla; Miska, Patrice; Geng, Wei; Couteau, Christophe; Lérondel, Gilles


    Due to its wide direct band gap and large exciton binding energy allowing for efficient excitonic emission at room temperature, ZnO has attracted attention as a luminescent material in various applications such as UV-light emitting diodes, chemical sensors and solar cells. While low-cost growth techniques, such as chemical bath deposition (CBD), of ZnO thin films and nanostructures have been already reported; nevertheless, ZnO thin films and nanostructures grown by costly techniques, such as metalorganic vapour phase epitaxy, still present the most interesting properties in terms of crystallinity and internal quantum efficiency. In this work, we report on highly efficient and highly crystalline ZnO micropods grown by CBD at a low temperature (ZnO micropods revealed a highly crystalline ZnO structure and a strong UV excitonic emission with internal quantum efficiency (IQE) of 10% at room temperature. Thermal annealing at 900°C of the as-grown ZnO micropods leads to further enhancement in their structural and optical properties. Low-temperature PL measurements on annealed ZnO micropods showed the presence of phonon replicas, which was not the case for as-grown samples. The appearance of phonon replicas provides a strong proof of the improved crystal quality of annealed ZnO micropods. Most importantly, low-temperature PL reveals an improved IQE of 15% in the excitonic emission of ZnO micropods. The ZnO micropods IQE reported here are comparable to IQEs reported on ZnO structures obtained by costly and more complex growth techniques. These results are of great interest demonstrating that high quality ZnO microstructures can be obtained at low temperatures using a low-cost CBD growth technique.

  2. Electrical Control of Excitons in Semiconductor Nanostructures

    DEFF Research Database (Denmark)

    Kirsanské, Gabija

    The scope of this thesis covers investigation of the exciton Mott transition in coupled quantum wells, fabrication of photonic-crystal structures with embedded self-assembled quantum dots, and tuning of their properties by means of an external electric field. In the first part of the thesis...... the focus is on quantum dots in photonic nanostructures. The fabrication process of reproducible high-quality photonic-crystal structures on electrically gated GaAs samples is presented. This process is employed to investigate light localization in short photonic-crystal waveguides with a dispersion...... relation facilitating a slow-light effect. The effect of the variations in the local density of optical states on electrically tuned quantum dots embedded in photonic structures is investigated. An electric field is employed to induce strain in suspended GaAs structures, where a bidirectional spectral...

  3. A low complexity rapid molecular method for detection of Clostridium difficile in stool.

    Directory of Open Access Journals (Sweden)

    Cathal J McElgunn

    Full Text Available Here we describe a method for the detection of Clostridium difficile from stool using a novel low-complexity and rapid extraction process called Heat Elution (HE. The HE method is two-step and takes just 10 minutes, no specialist instruments are required and there is minimal hands-on time. A test method using HE was developed in conjunction with Loop-mediated Isothermal Amplification (LAMP combined with the real-time bioluminescent reporter system known as BART targeting the toxin B gene (tcdB. The HE-LAMP-BART method was evaluated in a pilot study on clinical fecal samples (tcdB(+, n = 111; tcdB(-, n= 107. The HE-LAMP-BART method showed 95.5% sensitivity and 100% specificity against a gold standard reference method using cytotoxigenic culture and also a silica-based robotic extraction followed by tcdB PCR to control for storage. From sample to result, the HE-LAMP-BART method typically took 50 minutes, whereas the PCR method took >2.5 hours. In a further study (tcdB(+, n = 47; tcdB(-, n= 28 HE-LAMP-BART was compared to an alternative commercially available LAMP-based method, Illumigene (Meridian Bioscience, OH, and yielded 87.2% sensitivity and 100% specificity for the HE-LAMP-BART method compared to 76.6% and 100%, respectively, for Illumigene against the reference method. A subset of 27 samples (tcdB(+, n = 25; tcdB(-, n= 2 were further compared between HE-LAMP-BART, Illumigene, GeneXpert (Cepheid, Sunnyvale, CA and RIDA®QUICK C. difficile Toxin A/B lateral flow rapid test (R-Biopharm, Darmstadt, Germany resulting in sensitivities of HE-LAMP-BART 92%, Illumigene 72% GeneXpert 96% and RIDAQuick 76% against the reference method. The HE-LAMP-BART method offers the advantages of molecular based approaches without the cost and complexity usually associated with molecular tests. Further, the rapid time-to-result and simple protocol means the method can be applied away from the centralized laboratory settings.

  4. Synthesis, crystal and molecular structures, UV–Vis spectroscopy and electrochemical properties of two iron(III) phenolate complexes

    NARCIS (Netherlands)

    Lubben, Marcel; Meetsma, Auke; Bolhuis, Fré van; Feringa, Bernard


    The synthesis and molecular structures of two iron(III) phenolate complexes [(L1)FeCl] (1) and [(L2)2Fe][BPh4] (2) are described, where L1H2 is 2,3-dimethyl-2,3-bis(3-tert-butylsalicylideneamino)butane and L2H is 2-(2-pyridyl)-1-salicylideneaminoethane. The complexes have been characterized by

  5. An unusual highly emissive water-soluble iridium lissamine-alanine complex and its use in a molecular logic gate. (United States)

    Oliveira, Elisabete; Santos, Sérgio M; Núñez, Cristina; Capelo, José Luis; Lodeiro, Carlos


    The interaction of iridium(iii) with a new lissamine rhodamine B sulfonyl derivative, bearing alanine as a building block, (1) with an orange emission in water results in a green highly emissive Ir@1 complex at room temperature. The new Ir@1 complex can sense the toxic Hg(2+) metal ion and cysteine. Based on such properties, a new sophisticated molecular logic gate with three inputs was designed.

  6. Coordination compounds for molecular electronics: Synthesis, characterization and electronic transport properties of copper rotaxanes and molecular complexes


    Ponce González, Julia


    Esta tesis se centra en el estudio de compuestos de coordinación de interés en el campo de la electrónica molecular. Este campo tiene como objetivo la utilización de unidades moleculares como componentes activos en circuitos electrónicos. Los dispositivos unimoleculares presentan cualidades únicas, inherentes a la nanoescala, que no poseen equivalencia en los componentes convencionales, actualmente basados en el silicio. Además, la síntesis de moléculas dispone de un altísimo grado de control...

  7. Molecular characterization and identification of members of the Anopheles subpictus complex in Sri Lanka. (United States)

    Surendran, Sinnathamby N; Sarma, Devojit K; Jude, Pavilupillai J; Kemppainen, Petri; Kanthakumaran, Nadarajah; Gajapathy, Kanapathy; Peiris, Lalanthika B S; Ramasamy, Ranjan; Walton, Catherine


    Anopheles subpictus sensu lato is a major malaria vector in South and Southeast Asia. Based initially on polytene chromosome inversion polymorphism, and subsequently on morphological characterization, four sibling species A-D were reported from India. The present study uses molecular methods to further characterize and identify sibling species in Sri Lanka. Mosquitoes from Sri Lanka were morphologically identified to species and sequenced for the ribosomal internal transcribed spacer-2 (ITS2) and the mitochondrial cytochrome c oxidase subunit-I (COI) genes. These sequences, together with others from GenBank, were used to construct phylogenetic trees and parsimony haplotype networks and to test for genetic population structure. Both ITS2 and COI sequences revealed two divergent clades indicating that the Subpictus complex in Sri Lanka is composed of two genetically distinct species that correspond to species A and species B from India. Phylogenetic analysis showed that species A and species B do not form a monophyletic clade but instead share genetic similarity with Anopheles vagus and Anopheles sundaicus s.l., respectively. An allele specific identification method based on ITS2 variation was developed for the reliable identification of species A and B in Sri Lanka. Further multidisciplinary studies are needed to establish the species status of all chromosomal forms in the Subpictus complex. This study emphasizes the difficulties in using morphological characters for species identification in An. subpictus s.l. in Sri Lanka and demonstrates the utility of an allele specific identification method that can be used to characterize the differential bio-ecological traits of species A and B in Sri Lanka.

  8. Automated builder and database of protein/membrane complexes for molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Sunhwan Jo

    Full Text Available Molecular dynamics simulations of membrane proteins have provided deeper insights into their functions and interactions with surrounding environments at the atomic level. However, compared to solvation of globular proteins, building a realistic protein/membrane complex is still challenging and requires considerable experience with simulation software. Membrane Builder in the CHARMM-GUI website ( helps users to build such a complex system using a web browser with a graphical user interface. Through a generalized and automated building process including system size determination as well as generation of lipid bilayer, pore water, bulk water, and ions, a realistic membrane system with virtually any kinds and shapes of membrane proteins can be generated in 5 minutes to 2 hours depending on the system size. Default values that were elaborated and tested extensively are given in each step to provide reasonable options and starting points for both non-expert and expert users. The efficacy of Membrane Builder is illustrated by its applications to 12 transmembrane and 3 interfacial membrane proteins, whose fully equilibrated systems with three different types of lipid molecules (DMPC, DPPC, and POPC and two types of system shapes (rectangular and hexagonal are freely available on the CHARMM-GUI website. One of the most significant advantages of using the web environment is that, if a problem is found, users can go back and re-generate the whole system again before quitting the browser. Therefore, Membrane Builder provides the intuitive and easy way to build and simulate the biologically important membrane system.

  9. Optical Dynamics of Exciton and Polaron Formation in Molecular Aggregates

    NARCIS (Netherlands)

    de Boer, S.; Wiersma, Douwe A.


    Results of femtosecond accumulated photon echo, picosecond pump-probe and fluorescence lifetime measurements are reported on aggregates of the dyes pseudoisocyanine (PIC) and substituted thiapyrylium (TPY), embedded in a polycarbonate matrix. It is concluded that in the PIC aggregate, delocalized

  10. Molecular and Nanoscale Engineering of High Efficiency Excitonic Solar Cells

    Energy Technology Data Exchange (ETDEWEB)

    Jenekhe, Samson A. [Univ. of Washington, Seattle, WA (United States); Ginger, David S. [Univ. of Washington, Seattle, WA (United States); Cao, Guozhong [Univ. of Washington, Seattle, WA (United States)


    We combined the synthesis of new polymers and organic-inorganic hybrid materials with new experimental characterization tools to investigate bulk heterojunction (BHJ) polymer solar cells and hybrid organic-inorganic solar cells during the 2007-2010 period (phase I) of this project. We showed that the bulk morphology of polymer/fullerene blend solar cells could be controlled by using either self-assembled polymer semiconductor nanowires or diblock poly(3-alkylthiophenes) as the light-absorbing and hole transport component. We developed new characterization tools in-house, including photoinduced absorption (PIA) spectroscopy, time-resolved electrostatic force microscopy (TR-EFM) and conductive and photoconductive atomic force microscopy (c-AFM and pc-AFM), and used them to investigate charge transfer and recombination dynamics in polymer/fullerene BHJ solar cells, hybrid polymer-nanocrystal (PbSe) devices, and dye-sensitized solar cells (DSSCs); we thus showed in detail how the bulk photovoltaic properties are connected to the nanoscale structure of the BHJ polymer solar cells. We created various oxide semiconductor (ZnO, TiO2) nanostructures by solution processing routes, including hierarchical aggregates and nanorods/nanotubes, and showed that the nanostructured photoanodes resulted in substantially enhanced light-harvesting and charge transport, leading to enhanced power conversion efficiency of dye-sensitized solar cells.

  11. Toward molecular mechanism of xenon anesthesia: a link to studies of xenon complexes with small aromatic molecules. (United States)

    Andrijchenko, Natalya N; Ermilov, Alexander Yu; Khriachtchev, Leonid; Räsänen, Markku; Nemukhin, Alexander V


    The present study illustrates the steps toward understanding molecular mechanism of xenon anesthesia by focusing on a link to the structures and spectra of intermolecular complexes of xenon with small aromatic molecules. A primary cause of xenon anesthesia is attributed to inhibition of N-methyl-D-aspartate (NMDA) receptors by an unknown mechanism. Following the results of quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) calculations we report plausible xenon action sites in the ligand binding domain of the NMDA receptor, which are due to interaction of xenon atoms with aromatic amino-acid residues. We rely in these calculations on computational protocols adjusted in combined experimental and theoretical studies of intermolecular complexes of xenon with phenol. Successful reproduction of vibrational shifts in molecular species upon complexation with xenon measured in low-temperature matrices allowed us to select a proper functional form in density functional theory (DFT) approach for use in QM subsystems, as well as to calibrate force field parameters for MD simulations. The results of molecular modeling show that xenon atoms can compete with agonists for a place in the corresponding protein cavity, thus indicating their active role in anesthetic action.

  12. Plasmon-Exciton Resonant Energy Transfer: Across Scales Hybrid Systems

    Directory of Open Access Journals (Sweden)

    Mohamed El Kabbash


    Full Text Available The presence of an excitonic element in close proximity of a plasmonic nanostructure, under certain conditions, may lead to a nonradiative resonant energy transfer known as Exciton Plasmon Resonant Energy Transfer (EPRET process. The exciton-plasmon coupling and dynamics have been intensely studied in the last decade; still many relevant aspects need more in-depth studies. Understanding such phenomenon is not only important from fundamental viewpoint, but also essential to unlock many promising applications. In this review we investigate the plasmon-exciton resonant energy transfer in different hybrid systems at the nano- and mesoscales, in order to gain further understanding of such processes across scales and pave the way towards active plasmonic devices.

  13. Excitons in ultrathin organic-inorganic perovskite crystals (United States)

    Yaffe, Omer; Chernikov, Alexey; Norman, Zachariah M.; Zhong, Yu; Velauthapillai, Ajanthkrishna; van der Zande, Arend; Owen, Jonathan S.; Heinz, Tony F.


    We demonstrate the formation of large sheets of layered organic-inorganic perovskite (OIPC) crystals, as thin as a single unit cell, prepared by mechanical exfoliation. The resulting two-dimensional OIPC nanosheets of 2.4 nm thickness are direct semiconductors with an optical band gap of 2.4 eV. They exhibit unusually strong light-matter interaction with an optical absorption as high as 25% at the main excitonic resonance, as well as bright photoluminescence. We extract an exciton binding energy of 490 meV from measurement of the series of excited exciton states. The properties of the excitons are shown to be strongly influenced by the changes in the dielectric surroundings. The environmental sensitivity of these ultrathin OIPC sheets is further reflected in the strong suppression of a thermally driven phase transition present in the bulk crystals.

  14. Spin-excitons in heavy-fermion semimetals

    Energy Technology Data Exchange (ETDEWEB)

    Riseborough, Peter S., E-mail: [Temple University, Philadelphia (United States); Magalhaes, S.G. [Univ. Federal, Fluminense, Niteroi, Rio de Janeiro (Brazil)


    Spin-excitons are sharp and dispersive magnetic fluctuations in paramagnetic semiconductors where the dispersion relation lies within the semiconducting gap. Spin-excitons are found in the vicinity of magnetic quantum critical points in semiconductors, much the same as antiparamagnons are precursor fluctuations for quantum critical points in metals. Here we show that this concept of spin-exciton excitations can be extended to heavy-fermion semimetals and provides a natural explanation of the magnetic modes found by inelastic neutron scattering experiments on paramagnetic CeFe{sub 2}Al{sub 10}. - Highlights: • We discuss the theory of spin excitons in heavy-fermion semiconductors as precritical fluctuations. • We show that relatively sharp magnetic in-gap excitations can also occur in semiconductors. • The magnetic excitations are only sharp for a restricted range of center of mass momenta. • They may merge with the quasi-elastic peak associated with incommensurate nesting of electron and hole pockets.

  15. Excitonic giant-dipole potentials in cuprous oxide (United States)

    Kurz, Markus; Grünwald, Peter; Scheel, Stefan


    In this paper we predict the existence of a novel species of Wannier excitons when exposed to crossed electric and magnetic fields. In particular, we present a theory of giant-dipole excitons in Cu2O in crossed fields. Within our theoretical approach we perform a pseudoseparation of the center-of-mass motion for the field-dressed excitonic species, thereby obtaining an effective single-particle Hamiltonian for the relative motion. For arbitrary gauge fields we exactly separate the gauge-dependent kinetic-energy terms from the effective single-particle interaction potential. Depending on the applied field strengths and the specific field orientation, the potential for the relative motion of electron and hole exhibits an outer well at spatial separations up to several micrometers and depths up to 380 μ eV , leading to possible permanent excitonic electric dipole moments of around 3 ×106 D.

  16. How bilayer excitons can greatly enhance thermoelectric efficiency (United States)

    Wu, Kai; Rademaker, Louk; Zaanen, Jan


    Presently, a major nanotechnological challenge is to design thermoelectric devices that have a high figure of merit. To that end, we propose to use bilayer excitons in two-dimensional nanostructures. Bilayer exciton systems are shown to have an improved thermopower and an enhanced electric counterflow and thermal conductivity, with respect to regular semiconductor-based thermoelectrics. We suggest an experimental realization of a bilayer exciton thermocouple. Based on current experimental parameters, a bilayer exciton heterostructures of p- and n-doped Bi2Te3 can enhance the figure of merit an order of magnitude compared to bulk Bi2Te3. Another material suggestion is to make a bilayer out of electron-doped SrTiO3 and hole-doped Ca3Co4O9.

  17. Characterization of macromolecular complexes in red wine: Composition, molecular mass distribution and particle size. (United States)

    Bindon, Keren A; Carew, Anna L; Mierczynska-Vasilev, Agnieszka; Kassara, Stella; Kerslake, Fiona; Smith, Paul A


    Precipitates were prepared from two compositionally different Pinot noir wines with addition of excess ethanol, and contained primarily polysaccharide, tannin and protein. The ethanol-soluble material was further fractionated into polymeric (tannin) and monomeric phenolics. Tannin associated with precipitates was of a higher molecular mass than that remaining in ethanolic solution. Wine fractions were reconstituted at the ratios of the original wine and analyzed using nanoparticle tracking analysis. The average particle size of the tannin fraction was 75-89 nm, and increased when combined with the precipitate (≅ 200 nm). Addition of the monomeric fraction to the tannin-precipitate complex increased both the incidence and concentration of smaller particles, reducing the average particle size. The formation of aggregates occurred in all fractions and only minor differences in particle size distribution were found between wines. Differences in particle concentration between wines appear to be due to differences in the total concentration of macromolecules rather than compositional differences. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Assessment of rDNA IGS as a molecular marker in the Simulium damnosum complex. (United States)

    Morales-Hojas, R; Post, R J; Cheke, R A; Wilson, M D


    For five cytospecies of the Simulium damnosum Theobald complex of blackflies (Diptera: Simuliidae) from West Africa, both ends of the intergenic spacer region (IGS) of the rDNA have been sequenced with the aim of developing specific molecular markers. No specific differences in these two regions were detected between Simulium sanctipauli V. & D., Simulium sirbanum V. & D., Simulium soubrense V. & D., Simulium squamosum Enderlein and Simulium yahense V. & D., except in the number of A subrepeats at the 5' end of the IGS (two in S. squamosum and four or five in the others) and in position 310 of the 3' end (a C in S. squamosum and a G in the others). However, genetic distances within and between species overlapped. These DNA sequences had no strong phylogenetic signal, and the trees obtained were mostly unresolved. Although most sequences from S. squamosum clustered together, a few of them were more similar to those in other cytospecies. These results could be explained either by hybridization with genetic introgression or by ancestral polymorphism and recent speciation.

  19. Species Identification of Mycobacterium avium Complex Isolates by a Variety of Molecular Techniques (United States)

    Beggs, Marjorie L.; Stevanova, Rossina; Eisenach, Kathleen D.


    Organisms in the Mycobacterium avium complex (MAC; M. avium, M. intracellulare, and “nonspecific or X” MAC) are emerging pathogens among individual organisms of which significant genetic variability is displayed. The objective of the present study was to evaluate various molecular methods for the rapid and definitive identification of MAC species. Isolates were obtained from both human immunodeficiency virus (HIV)-positive patients and HIV-negative patients with and without known predisposing conditions. The isolates were initially hybridized with nucleic acid probes complementary to the rRNA of the respective mycobacterial species (AccuProbe Culture Confirmation kits for M. avium, M. intracellulare, and MAC species; Gen-Probe). Isolates were also examined by PCR and in some cases by Southern blot hybridization for the insertion element IS1245. Two other techniques included a PCR assay that amplifies the mig gene, a putative virulence factor for MAC, and hsp65 gene amplification and sequencing. This study led to the following observations. Eighty-five percent of the isolates from HIV-positive patients were M. avium and 86% of the isolates from HIV-negative patients were M. intracellulare. Fifteen of the M. avium isolates did not contain IS1245 and 7% of the M. intracellulare isolates were found to carry IS1245. All of the M. avium strains were mig positive, and all of the M. intracellulare strains were mig negative. PMID:10655336

  20. Understanding Autoimmune Diabetes through the Prism of the Tri-Molecular Complex

    Directory of Open Access Journals (Sweden)

    Matthew L. Bettini


    Full Text Available The strongest susceptibility allele for Type 1 Diabetes (T1D is human leukocyte antigen (HLA, which supports a central role for T cells as the drivers of autoimmunity. However, the precise mechanisms that allow thymic escape and peripheral activation of beta cell antigen-specific T cells are still largely unknown. Studies performed with the non-obese diabetic (NOD mouse have challenged several immunological dogmas, and have made the NOD mouse a key experimental system to study the steps of immunodysregulation that lead to autoimmune diabetes. The structural similarities between the NOD I-Ag7 and HLA-DQ8 have revealed the stability of the T cell receptor (TCR/HLA/peptide tri-molecular complex as an important parameter in the development of autoimmune T cells, as well as afforded insights into the key antigens targeted in T1D. In this review, we will provide a summary of the current understanding with regard to autoimmune T cell development, the significance of the antigens targeted in T1D, and the relationship between TCR affinity and immune regulation.

  1. Molecular characterization of the Trichomonas gallinae morphologic complex in the United States. (United States)

    Gerhold, Richard W; Yabsley, Michael J; Smith, Autumn J; Ostergaard, Elissa; Mannan, William; Cann, Jeff D; Fischer, John R


    Forty-two Trichomonas gallinae isolates were molecularly characterized to determine whether isolates differed in genetic sequence of multiple gene targets depending on host species or geographical location. The 5.8S ribosomal RNA (rRNA) and flanking internal transcribed spacer (ITS) gene regions were amplified by polymerase chain reaction, and the sequences were analyzed phylogenetically. The results of the sequence analysis strongly suggest at least 2 species may exist within the T. gallinae morphologic complex. Based on ITS sequences, one group demonstrated high nucleotide identity to the 3 T. gallinae sequences available in GenBank, whereas the second group was more closely related to T. vaginalis (98%) than to T. gallinae (92%). Two common ground-dove (Columbina passerina) isolates shared a 95% identity with T. vaginalis and a 92% identity with T. gallinae and T. tenax. Sequence analysis of both the 18S rRNA and alpha-tubulin genes from a subset of the isolates supports the 5.8S-ITS sequence results. All of the T. vaginalis-like isolates originated from Arizona, California, or Texas, whereas T. gallinae isolates were found in all sampled states. Both T. vaginalis-like and T. gallinae isolates were involved in trichomoniasis outbreaks in California and Arizona.

  2. Detection of complex molecular samples by low-cost surface enhanced raman spectroscopy (SERS) substrate (United States)

    Hou, Hsuan-Chao; Banadaki, Yaser Mohammadi; Sharifi, Safura


    Raman scattering is a well-known technique for detecting and identifying complex molecular samples. The weak Raman signals are enormously enhanced in the presence of a nano-patterned metallic surface next to the specimen. This paper reports new techniques to obtain the nanostructures required for Surface Enhanced Raman Scattering (SERS) without costly and sophisticated fabrication steps, which are nanoimprint lithography (NIL), electrochemical deposition, electron beam induced deposition, and focus ion beam (FIB). 20 nm Au thicknesses of sputtered Au were deposited on etched household aluminum foil (base substrate) for vitro application. The Raman signal were caused by the Aluminum pre-etched times. In preliminary results, enhancement factors of 106 times were observed from SERS substrate for in vitro measurements. Moreover, the ability to perform in vivo measurements was demonstrated after removing the base aluminum foil substrate. This application allows Raman signals to be obtained from the surface or interior of opaque specimens. The nano-patterned gold may also be coupled in a probe to a remote spectrometer via an articulated arm. This opens up Raman spectroscopy for use in a clinical environment.

  3. New Insights into Molecular Mechanisms of Immune Complex-induced Injury in Lung

    Directory of Open Access Journals (Sweden)

    Peter A. Ward


    Full Text Available While the phlogistic activities of IgM or IgG immune complexes (IC have been well established as complement-activating agents and seem likely to play important roles in humans with vasculitis, certain types of glomerulonephritis as well as in a variety of autoimmune diseases, the predominant clinical strategies have involved the use of immunosuppressive or antiinflammatory drugs. Over the past decade, new insights into molecular events developing during IC models in rodents have identified new phlogistic products that may be candidates for therapeutic blockade. Extracellular histones, located in the web-like structures of neutrophil extracellular traps (NETs, are released from complement-activated polymorphonuclear neutrophils (PMNs downstream of IC deposition. Extracellular histones appear to be a new class of highly tissue-damaging products derived from complement-activated PMNs. Histones have also been discovered in cell-free broncho-alveolar lavage fluids (BALFs from humans with acute respiratory distress syndrome (ARDS. Recent studies emphasize that, in the setting of ARDS-like reactions in rodents, extracellular histones are released and are exceedingly proinflammatory, tissue damaging and prothrombotic. Such studies suggest that in humans with ARDS, extracellular histones may represent therapeutic targets for blockade.

  4. A niosomal bilayer of sorbitan monostearate in complex with flavones: a molecular dynamics simulation study. (United States)

    Myung, Yoochan; Yeom, Seongyeol; Han, Sanghwa


    Bilayers prepared from sorbitan fatty acid esters (Span) have been frequently used for delivery of drugs including flavonoids. We applied molecular dynamics simulation to characterize the structure of a sorbitan monostearate (Span 60) bilayer in complex with three representative flavones, a subclass of flavonoids. At a low concentration, unsubstituted flavone, the most hydrophobic member, was able to flip over and cross the bilayer with a large diffusion coefficient. At a high concentration, it was accumulated at the bilayer center resulting in a phase separation. The leaflets of the bilayer were pushed in the opposite directions increasing the membrane thickness. Order parameter of the stearate chain of Span 60 was not affected significantly by unsubstituted flavone. In contrast, chrysin with hydroxylated ring A was lined up with the acyl chains of Span 60 with its hydroxyl group facing the membrane surface. Neither flipping nor transbilayer movement were allowed. Diffusion coefficient was only 15-25% of that of unsubstituted flavone and order parameter decreased with the concentration of chrysin. Luteolin, the most hydroxylated member, interacted mainly with the headgroup of Span 60 and assumed many different orientations without crossing the bilayer. Unlike chrysin and unsubstituted flavone the bilayer integrity was disrupted at 50 mol% luteolin. These behaviors and structures of flavones in a Span 60 bilayer can be accounted for by their hydrophobicity and sites of hydroxylation.

  5. Mapping of Drug-like Chemical Universe with Reduced Complexity Molecular Frameworks. (United States)

    Kontijevskis, Aleksejs


    The emergence of the DNA-encoded chemical libraries (DEL) field in the past decade has attracted the attention of the pharmaceutical industry as a powerful mechanism for the discovery of novel drug-like hits for various biological targets. Nuevolution Chemetics technology enables DNA-encoded synthesis of billions of chemically diverse drug-like small molecule compounds, and the efficient screening and optimization of these, facilitating effective identification of drug candidates at an unprecedented speed and scale. Although many approaches have been developed by the cheminformatics community for the analysis and visualization of drug-like chemical space, most of them are restricted to the analysis of a maximum of a few millions of compounds and cannot handle collections of 108-1012 compounds typical for DELs. To address this big chemical data challenge, we developed the Reduced Complexity Molecular Frameworks (RCMF) methodology as an abstract and very general way of representing chemical structures. By further introducing RCMF descriptors, we constructed a global framework map of drug-like chemical space and demonstrated how chemical space occupied by multi-million-member drug-like Chemetics DNA-encoded libraries and virtual combinatorial libraries with >1012 members could be analyzed and mapped without a need for library enumeration. We further validate the approach by performing RCMF-based searches in a drug-like chemical universe and mapping Chemetics library selection outputs for LSD1 targets on a global framework chemical space map.

  6. Molecular Identification and Echinocandin Susceptibility of Candida parapsilosis Complex Bloodstream Isolates in Italy, 2007-2014.

    Directory of Open Access Journals (Sweden)

    Grazia Lovero

    Full Text Available The Candida parapsilosis group encompasses three species: C. parapsilosis, C. orthopsilosis, and C. metapsilosis. Here, we describe the incidence and echinocandin susceptibility profile of bloodstream isolates of these three species collected from patients admitted to an Italian university hospital from 2007 to 2014. Molecular identification of cryptic species of the C. parapsilosis complex was performed using polymerase chain reaction amplification of the gene encoding secondary alcohol dehydrogenase, followed by digestion with the restriction enzyme BanI. Minimum inhibitory concentrations were determined using the broth microdilution method according to European Committee for Antimicrobial Susceptibility Testing (EUCAST EDef 7.2 and Clinical Laboratory Standards Institute (CLSI M27-A3 guidelines, and the results were compared with those obtained using the E-test and Sensititre methods. Of the 163 C. parapsilosis complex isolates, 136 (83.4% were identified as C. parapsilosis, and 27 (16.6% as C. orthopsilosis. The species-specific incidences were 2.9/10,000 admissions for C. parapsilosis and 0.6/10,000 admissions for C. orthopsilosis. No resistance to echinocandins was detected with any of the methods. The percent essential agreement (EA between the EUCAST and E-test/Sensititre methods for anidulafungin, caspofungin, and micafungin susceptibility was, respectively, as follows: C. parapsilosis, 95.6/97.8, 98.5/88.2, and 93.4/96.3; C. orthopsilosis, 92.6/92.6, 96.3/77.8, and 63.0/66.7. The EA between the CLSI and E-test/Sensititre methods was, respectively, as follows: C. parapsilosis, 99.3/100, 98.5/89.0, and 96.3/98.5; C. orthopsilosis, 96.3/92.6, 100/81.5, and 92.6/88.9. Only minor discrepancies, ranging from 16.9% (C. parapsilosis to 11.1% (C. orthopsilosis, were observed between the CLSI and E-test/Sensititre methods. In conclusion, this epidemiologic study shows a typical C. parapsilosis complex species distribution, no echinocandin

  7. Structural Elucidation of Dendritic Host-Guest Complexes by X-ray Crystallography and Molecular Dynamics Simulations

    NARCIS (Netherlands)

    Chang, T.; Pieterse, K.; Broeren, M.A.C.; Kooijman, H.|info:eu-repo/dai/nl/091208610; Spek, A.L.|info:eu-repo/dai/nl/156517566; Hilbers, M.F.; Meijer, E.W.


    The multiple monovalent binding of adamantyl-urea poly(propyleneimine) dendrimers with carboxylic acid-urea guests was investigated using molecular dynamics simulations and Xray crystallography to better understand the structure and behavior of the dynamic multivalent complex in solution. The

  8. Reversible binding of molecular oxygen to catecholate and amidophenolate complexes of SbV: electronic and steric factors. (United States)

    Fukin, Georgy K; Baranov, Evgenii V; Poddel'sky, Andrey I; Cherkasov, Vladimir K; Abakumov, Gleb A


    Edge of reactivity: The reactions of reversible binding of molecular oxygen to catecholate and amidophenolate complexes of Sb(V) are investigated by analyzing the position of electronic (E(HOMO)) and steric (G-parameter) factors. The optimal electronic and steric parameters for such type reactions are found. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. The effect of PEG molecular weights on the thermal stability and dissolution behaviors of griseofulvin-PEG crystalline inclusion complexes. (United States)

    Yang, Xiaotong; Zhong, Zhi; Huang, Yanbin


    Co-crystals formed between small molecular drugs and hydrophilic co-formers have shown great potential to optimize the dissolution profiles of drug substances. So far most of the co-formers used are small molecules. However, linear polymers are also able to form drug-polymer crystalline inclusion complexes (ICs). In contrast to the small molecular co-formers, molecular weight of the polymer co-formers can be easily changed without disrupting the IC crystal structure, and hence represents an interesting approach to tune the IC properties. In this study, we investigated the effect of PEG molecular weights on the thermal stability and dissolution behavior of Gris-PEG ICs. It was found that the thermal stability of Gris-PEG IC crystals first increased with PEG molecular weight, and then reached a plateau value, while an optimized PEG molecular weight existed for the dissolution profile. The experimental results were explained by the formation of two types of crystal defects during the IC growth in PEG melt: the void defects and the grain boundary defects. This is the first study on the pharmaceutical profiles of drug-polymer crystalline inclusion complexes. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Exciton spectrum in multi-shell hexagonal semiconductor nanotube

    Directory of Open Access Journals (Sweden)

    O.M. Makhanets


    Full Text Available The theory of exciton spectrum in multi-shell hexagonal semiconductor nanotube is developed within the effective masses and rectangular potentials approximations using the method of effective potential. It is shown that the exciton binding energy for all states non-monotonously depends on the inner wire diameter, approaching several minimal and maximal magnitudes. The obtained theoretical results explain well the experimental positions of luminescence peaks for GaAs/Al0.4Ga0.6As nanotubes.

  11. Optical absorption of charged excitons in semiconducting carbon nanotubes

    DEFF Research Database (Denmark)

    Rønnow, Troels Frimodt; Pedersen, Thomas Garm; Cornean, Horia


    In this article we examine the absorption coefficient of charged excitons in carbon nanotubes. We investigate the temperature and damping dependence of the absorption spectra. We show that the trion peak in the spectrum is asymmetric for temperatures greater than approximately 1 K whereas...... the absorption peak arising from excitons is symmetric. We expect the positive and negative trion absorption line shapes to be identical, independently of the chiral index (n,m)....

  12. One dimensional models of excitons in carbon nanotubes

    DEFF Research Database (Denmark)

    Cornean, Horia Decebal; Duclos, P.; Pedersen, Thomas Garm

    Excitons in carbon nanotubes may be modeled by two oppositely charged particles living on the surface of a cylinder. We derive three one dimensional effective Hamiltonians which become exact as the radius of the cylinder vanishes. Two of them are solvable.......Excitons in carbon nanotubes may be modeled by two oppositely charged particles living on the surface of a cylinder. We derive three one dimensional effective Hamiltonians which become exact as the radius of the cylinder vanishes. Two of them are solvable....

  13. Exciton-plasmon coupling interactions: from principle to applications

    Directory of Open Access Journals (Sweden)

    Cao En


    Full Text Available The interaction of exciton-plasmon coupling and the conversion of exciton-plasmon-photon have been widely investigated experimentally and theoretically. In this review, we introduce the exciton-plasmon interaction from basic principle to applications. There are two kinds of exciton-plasmon coupling, which demonstrate different optical properties. The strong exciton-plasmon coupling results in two new mixed states of light and matter separated energetically by a Rabi splitting that exhibits a characteristic anticrossing behavior of the exciton-LSP energy tuning. Compared to strong coupling, such as surface-enhanced Raman scattering, surface plasmon (SP-enhanced absorption, enhanced fluorescence, or fluorescence quenching, there is no perturbation between wave functions; the interaction here is called the weak coupling. SP resonance (SPR arises from the collective oscillation induced by the electromagnetic field of light and can be used for investigating the interaction between light and matter beyond the diffraction limit. The study on the interaction between SPR and exaction has drawn wide attention since its discovery not only due to its contribution in deepening and broadening the understanding of SPR but also its contribution to its application in light-emitting diodes, solar cells, low threshold laser, biomedical detection, quantum information processing, and so on.

  14. Bose condensation of interwell excitons in double quantum wells

    CERN Document Server

    Larionov, A V; Ni, P A; Dubonos, S V; Hvam, I; Soerensen, K


    The luminescence of the interwell excitons in the GaAs/AlGaAs double quantum wells, containing large-scale fluctuations of the random potential in the heteroboundary planes, is studied. The properties of the excitons, wherein the excited electron and hole are spatially separated between the neighboring quantum wells by the density and temperature variation within the domain limits of the scale below one micron, are investigated. The interwell excitons by low pumping (below 50 mW) are strongly localized due to the small-scale fluctuations of the random potential. The localized excitons line grows by increase in the resonance excitation capacity through the threshold method. With the temperature growth this line disappears in the spectrum (T sub c <= 3.4 K). The above phenomenon is related to the Bose-Einstein condensation in the quasi-two-dimensional system of the interwell excitons. The critical values of the exciton density and temperature in the studied temperature range (1.5-3.4 K) grow according to the...

  15. Excitonic photoluminescence and photoresponse of ZnS nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Jun, E-mail: [Department of Physics, Jiangsu University of Science and Technology, Zhenjiang 212003 (China); Song, Xing [School of Material Science and Engineering, Jiangsu University, Zhenjiang 212003 (China); Zheng, Hongge [Department of Physics, Jiangsu University of Science and Technology, Zhenjiang 212003 (China); Wu, Chunxia, E-mail: [School of Material Science and Engineering, Jiangsu University, Zhenjiang 212003 (China)


    Single crystal ZnS nanowires are fabricated by vapor phase transport method on sapphire substrate in the presence of Au catalyst. The morphology, composition, and crystal structure are characterized by field emission scanning electron microscopy (FESEM), X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM). XRD and HRTEM reveal that the ZnS nanowires have perfect single crystal wurtzite structure. The temperature-dependent photoluminescence spectra show that the ZnS nanowires present pure near-bandgap ultraviolet exciton recombination emission at 347 nm. The exciton-related optical properties, including exciton activation energy, temperature-dependent exciton energy and Varshni coefficients describing exciton energy variation, are systematically discussed. In addition, an individual ZnS nanowire-based ultraviolet photodetector is fabricated, which shows good photoresponse ability and fast response rate. The result shows that the ZnS nanowires are particularly suitable for UV photodetectors. - Highlights: • Single crystal ultrathin ZnS nanowires with diameter of 20–100 nm were fabricated by vapor phase transport method. • Exciton-related optical properties were fitted by temperature-dependent photoluminescence spectra. • Single ZnS nanowire ultraviolet photodetector with good photoswitch ability and high photocurrent was demonstrated.

  16. Exciton-plasmon coupling interactions: from principle to applications (United States)

    Cao, En; Lin, Weihua; Sun, Mengtao; Liang, Wenjie; Song, Yuzhi


    The interaction of exciton-plasmon coupling and the conversion of exciton-plasmon-photon have been widely investigated experimentally and theoretically. In this review, we introduce the exciton-plasmon interaction from basic principle to applications. There are two kinds of exciton-plasmon coupling, which demonstrate different optical properties. The strong exciton-plasmon coupling results in two new mixed states of light and matter separated energetically by a Rabi splitting that exhibits a characteristic anticrossing behavior of the exciton-LSP energy tuning. Compared to strong coupling, such as surface-enhanced Raman scattering, surface plasmon (SP)-enhanced absorption, enhanced fluorescence, or fluorescence quenching, there is no perturbation between wave functions; the interaction here is called the weak coupling. SP resonance (SPR) arises from the collective oscillation induced by the electromagnetic field of light and can be used for investigating the interaction between light and matter beyond the diffraction limit. The study on the interaction between SPR and exaction has drawn wide attention since its discovery not only due to its contribution in deepening and broadening the understanding of SPR but also its contribution to its application in light-emitting diodes, solar cells, low threshold laser, biomedical detection, quantum information processing, and so on.

  17. Quantum Hall drag of exciton condensate in graphene (United States)

    Liu, Xiaomeng; Watanabe, Kenji; Taniguchi, Takashi; Halperin, Bertrand I.; Kim, Philip


    An exciton condensate is a Bose-Einstein condensate of electron and hole pairs bound by the Coulomb interaction. In an electronic double layer (EDL) subject to strong magnetic fields, filled Landau states in one layer bind with empty states of the other layer to form an exciton condensate. Here we report exciton condensation in a bilayer graphene EDL separated by hexagonal boron nitride. Driving current in one graphene layer generates a near-quantized Hall voltage in the other layer, resulting in coherent exciton transport. Owing to the strong Coulomb coupling across the atomically thin dielectric, quantum Hall drag in graphene appears at a temperature ten times higher than previously observed in a GaAs EDL. The wide-range tunability of densities and displacement fields enables exploration of a rich phase diagram of Bose-Einstein condensates across Landau levels with different filling factors and internal quantum degrees of freedom. The observed robust exciton condensation opens up opportunities to investigate various many-body exciton phases.

  18. Exciton-plasmon coupling in monolayer molybdenum disulfide (United States)

    Ziegler, Jed; Newaz, A. K. M.; Bolotin, Kirill; Haglund, Richard


    Two-dimensional materials such as monolayer molybdenum disulfide (MoS2) represent a unique platform for investigating the dynamics of exciton-plasmon coupling. We report on the generation and modulation of coherent and incoherent coupled states between excitons in monolayer MoS2 and plasmons in an array of gold nanoparticle deposited onto the surface of MoS2. We study the behavior of these coherent states, termed plexcitons using a combination of photoluminescence, extinction and ultrafast spectroscopies. The close proximity of the two characteristic exciton bands of MoS2 presents multiple coherent coupling configurations, including A-or-B exciton-plasmon, and A-and-B exciton-plasmon interactions. These configurations of plexciton formation that are shown to modulate both the extinction and photoluminescence spectra of the hybrid system. This includes broadband photoluminescence and Fano-type resonances. This behavior is distinct from the spectral response of the MoS2 and plasmonic components of the system. Incoherent exciton-plasmon coupling, achieved by detuning from the plasmon extinction peaks, enhances the interaction of MoS2 with light by focusing the plasmon energy. Depending on which coupling configuration is chosen, our results show that the MoS2/plasmon hybrid systems can act as high efficiency light harvesters, broadband emitters and as tunable visible and NIR photodetectors. Support by Defense Threat Reduction Agency (HDTRA1-1-10-1-0047) and NSF DMR-1056859

  19. Exciton Band Structure in Two-Dimensional Materials. (United States)

    Cudazzo, Pierluigi; Sponza, Lorenzo; Giorgetti, Christine; Reining, Lucia; Sottile, Francesco; Gatti, Matteo


    Low-dimensional materials differ from their bulk counterparts in many respects. In particular, the screening of the Coulomb interaction is strongly reduced, which can have important consequences such as the significant increase of exciton binding energies. In bulk materials the binding energy is used as an indicator in optical spectra to distinguish different kinds of excitons, but this is not possible in low-dimensional materials, where the binding energy is large and comparable in size for excitons of very different localization. Here we demonstrate that the exciton band structure, which can be accessed experimentally, instead provides a powerful way to identify the exciton character. By comparing the ab initio solution of the many-body Bethe-Salpeter equation for graphane and single-layer hexagonal boron nitride, we draw a general picture of the exciton dispersion in two-dimensional materials, highlighting the different role played by the exchange electron-hole interaction and by the electronic band structure. Our interpretation is substantiated by a prediction for phosphorene.

  20. Direct real-time molecular scale visualisation of the degradation of condensed DNA complexes exposed to DNase I. (United States)

    Abdelhady, Hosam G; Allen, Stephanie; Davies, Martyn C; Roberts, Clive J; Tendler, Saul J B; Williams, Philip M


    The need to protect DNA from in vivo degradation is one of the basic tenets of therapeutic gene delivery and a standard test for any proposed delivery vector. The currently employed in vitro tests, however, presently provide no direct link between the molecular structure of the vector complexes and their success in this role, thus hindering the rational design of successful gene delivery agents. Here we apply atomic force microscopy (AFM) in liquid to visualise at the molecular scale and in real time, the effect of DNase I on generation 4 polyamidoamine dendrimers (G4) complexed with DNA. These complexes are revealed to be dynamic in nature showing a degree of mobility, in some cases revealing the addition and loss of dendrimers to individual complexes. The formation of the G4-DNA complexes is observed to provide a degree of protection to the DNA. This protection is related to the structural morphology of the formed complex, which is itself shown to be dependent on the dendrimer loading and the time allowed for complex formation.

  1. Acousto-exciton interaction in a gas of 2D indirect dipolar excitons in the presence of disorder

    Energy Technology Data Exchange (ETDEWEB)

    Kovalev, V. M.; Chaplik, A. V., E-mail: [Russian Academy of Sciences, Rzhanov Institute of Semiconductor Physics, Siberian Branch (Russian Federation)


    A theory for the linear and quadratic responses of a 2D gas of indirect dipolar excitons to an external surface acoustic wave perturbation in the presence of a static random potential is considered. The theory is constructed both for high temperatures, definitely greater than the exciton gas condensation temperature, and at zero temperature by taking into account the Bose–Einstein condensation effects. The particle Green functions, the density–density correlation function, and the quadratic response function are calculated by the “cross” diagram technique. The results obtained are used to calculate the absorption of Rayleigh surface waves and the acoustic exciton gas drag by a Rayleigh wave. The damping of Bogoliubov excitations in an exciton condensate due to theirs scattering by a random potential has also been determined.

  2. Binding of molecular oxygen by an artificial heme analogue: investigation on the formation of an Fe–tetracarbene superoxo complex

    KAUST Repository

    Anneser, Markus R.


    The dioxygen reactivity of a cyclic iron(II) tetra–NHC-complex (NHC: N-heterocyclic carbene) is investigated. Divergent oxidation behavior is observed depending on the choice of the solvent (acetonitrile or acetone). In the first case, exposure to molecular oxygen leads to an oxygen free Fe(III) whereas in the latter case an oxide bridged Fe(III) dimer is formed. In acetone, an Fe(III)-superoxide can be trapped, isolated and characterized as intermediate at low temperatures. An Fe(III)–O–Fe(III) dimer is formed from the Fe(III) superoxide in acetone upon warming and the molecular structure has been revealed by single crystal X-ray diffraction. It is shown that the oxidation of the Fe(II) complex in both solvents is a reversible process. For the regeneration of the initial Fe(II) complex both organic and inorganic reducing agents can be used.

  3. [Molecular aspects of the impact of the Speroton complex on the male fertility in idiopathic infertility]. (United States)

    Galimov, Sh N; Akhmetov, R M; Galimova, E F; Bairamgulov, F M; Bikkulova, L R


    To characterize the effect of the Speroton complex on the free radical homeostasis in the ejaculate of males of infertile couples and the likelihood of pregnancy in partners. The study group comprised 30 men aged between 26 and 43 years (mean 33 +/- 4.8 years) with idiopathic infertility. All patients received Speroton one sachet once daily during meals for 3 months. The comparison group consisted of 29 men of fertile age having 1 to 3 healthy children. In infertile men, standard semen parameters including the ejaculate volume, sperm concentration, total count and proportion of abnormal forms were within the normal range. Markers of oxidative damage to ejaculate macromolecules were determined using standard diagnostic testing systems. The patients with idiopathic infertility were found to have statistically significant changes in the degree of chemical modification of ejaculate biopolymers. The level of lipid hydroperoxides in infertile men was significantly higher than in fertile participants. Taking Speroton resulted in the decrease of lipid hydroperoxides to the level that did not differ from that in the control group. Using Speroton was also accompanied by a decrease in the level of the oxidative damage DNA biomarker 8-oxodGu and a tendency toward normalization of the carbonyl modification of the ejaculate proteins. Five married couples in the treatment group reported achieving pregnancy. Taking Speroton was associated with the normalization of the balance of pro- and antioxidant processes in the ejaculate, as indicated by a decrease in the oxidative destruction of sperm biopolymers. The revealed molecular mechanism of the drug action is the basis for restoring the fertilizing ability and increasing the likelihood of pregnancy. The treatment effectiveness was 16.7%. Speroton is a promising drug that improves the functional sperm characteristics and contributes to achieving pregnancy in couples with a male infertility factor.

  4. Auricularia auricular polysaccharide-low molecular weight chitosan polyelectrolyte complex nanoparticles: Preparation and characterization

    Directory of Open Access Journals (Sweden)

    Wei Xiong


    Full Text Available Novel polyelectrolyte complex nanoparticles (AAP/LCS NPs were prepared in this study and these were produced by mixing negatively charged auricularia auricular polysaccharide (AAP with positively charged low molecular weight chitosan (LCS in an aqueous medium. The AAP was extracted and purified from auricularia auricular, and then characterized by micrOTOF-Q mass spectrometry, UV/Vis spectrophotometry, moisture analyzer and SEM. The yield, moisture, and total sugar content of the AAP were 4.5%, 6.2% and 90.12% (w/w, respectively. The AAP sample was water-soluble and exhibited white flocculence. The characteristics of AAP/LCS NPs, such as the particle size, zeta potential, morphology, FT-IR spectra, DSC were investigated. The results obtained revealed that the AAP/LCS NPs had a spherical shape with a diameter of 223 nm and a smooth surface, and the results of the FT-IR spectra and DSC investigations indicated that there was an electrostatic interaction between the two polyelectrolyte polymers. Bovine serum albumin (BSA, pI = 4.8 and bovine hemoglobin (BHb, pI = 6.8 were used as model drugs to investigate the loading and release features of the AAP/LCS NPs. The results obtained showed that the AAP/LCS NPs had a higher entrapment efficiency (92.6% for BHb than for BSA (81.5%. The cumulative release of BSA and BHb from AAP/LCS NPs after 24 h in vitro was 95.4% and 91.9%, respectively. The in vitro release demonstrated that AAP/LCS NPs provided a sustained release matrix suitable for the delivery of protein drugs. These studies demonstrate that AAP/LCS NPs have a very promising potential as a delivery system for protein drugs.

  5. Molecular Characterization and Functional Analysis of Annulate Lamellae Pore Complexes in Nuclear Transport in Mammalian Cells.

    Directory of Open Access Journals (Sweden)

    Sarita Raghunayakula

    Full Text Available Annulate lamellae are cytoplasmic organelles containing stacked sheets of membranes embedded with pore complexes. These cytoplasmic pore complexes at annulate lamellae are morphologically similar to nuclear pore complexes at the nuclear envelope. Although annulate lamellae has been observed in nearly all types of cells, their biological functions are still largely unknown. Here we show that SUMO1-modification of the Ran GTPase-activating protein RanGAP1 not only target RanGAP1 to its known sites at nuclear pore complexes but also to annulate lamellae pore complexes through interactions with the Ran-binding protein RanBP2 and the SUMO-conjugating enzyme Ubc9 in mammalian cells. Furthermore, upregulation of annulate lamellae, which decreases the number of nuclear pore complexes and concurrently increases that of annulate lamellae pore complexes, causes a redistribution of nuclear transport receptors including importin α/β and the exportin CRM1 from nuclear pore complexes to annulate lamellae pore complexes and also reduces the rates of nuclear import and export. Moreover, our results reveal that importin α/β-mediated import complexes initially accumulate at annulate lamellae pore complexes upon the activation of nuclear import and subsequently disassociate for nuclear import through nuclear pore complexes in cells with upregulation of annulate lamellae. Lastly, CRM1-mediated export complexes are concentrated at both nuclear pore complexes and annulate lamellae pore complexes when the disassembly of these export complexes is inhibited by transient expression of a Ran GTPase mutant arrested in its GTP-bound form, suggesting that RanGAP1/RanBP2-activated RanGTP hydrolysis at these pore complexes is required for the dissociation of the export complexes. Hence, our findings provide a foundation for further investigation of how upregulation of annulate lamellae decreases the rates of nuclear transport and also for elucidation of the biological

  6. Statistical study of stacked/coupled site-controlled pyramidal quantum dots and their excitonic properties (United States)

    Moroni, S. T.; Chung, T. H.; Juska, G.; Gocalinska, A.; Pelucchi, E.


    We report on stacked multiple quantum dots (QDs) formed inside inverted pyramidal recesses, which allow for the precise positioning of the QDs themselves. Specifically, we fabricated double QDs with varying inter-dot distances and ensembles with more than two nominally highly symmetric QDs. For each, the effect of the interaction between QDs is studied by characterizing a large number of QDs through photoluminescence spectroscopy. A clear red-shift of the emission energy is observed together with a change in the orientation of its polarization, suggesting an increasing interaction between the QDs. Finally, we show how stacked QDs can help influencing the charging of the excitonic complexes.

  7. Spintronic characteristics of self-assembled neurotransmitter acetylcholine molecular complexes enable quantum information processing in neural networks and brain (United States)

    Tamulis, Arvydas; Majauskaite, Kristina; Kairys, Visvaldas; Zborowski, Krzysztof; Adhikari, Kapil; Krisciukaitis, Sarunas


    Implementation of liquid state quantum information processing based on spatially localized electronic spin in the neurotransmitter stable acetylcholine (ACh) neutral molecular radical is discussed. Using DFT quantum calculations we proved that this molecule possesses stable localized electron spin, which may represent a qubit in quantum information processing. The necessary operating conditions for ACh molecule are formulated in self-assembled dimer and more complex systems. The main quantum mechanical research result of this paper is that the neurotransmitter ACh systems, which were proposed, include the use of quantum molecular spintronics arrays to control the neurotransmission in neural networks.

  8. Relativistic corrections for non-Born-Oppenheimer molecular wave functions expanded in terms of complex explicitly correlated Gaussian functions (United States)

    Bubin, Sergiy; Stanke, Monika; Adamowicz, Ludwik


    In our previous work S. Bubin et al., Chem. Phys. Lett. 647, 122 (2016), 10.1016/j.cplett.2016.01.056, it was established that complex explicitly correlated one-center all-particle Gaussian functions (CECGs) provide effective basis functions for very accurate nonrelativistic molecular non-Born-Oppenheimer calculations. In this work, we advance the molecular CECGs approach further by deriving and implementing algorithms for calculating the leading relativistic corrections within this approach. The algorithms are tested in the calculations of the corrections for all 23 bound pure vibrational states of the HD+ ion.

  9. Palladium(II) and platinum(II) complexes containing benzimidazole ligands: Molecular structures, vibrational frequencies and cytotoxicity (United States)

    Abdel Ghani, Nour T.; Mansour, Ahmed M.


    (1H-benzimidazol-2-ylmethyl)-(4-methoxyl-phenyl)-amine (L 1), (1H-benzimidazol-2-ylmethyl)-(4-methyl-phenyl)-amine (L 2) and their Pd(II) and Pt(II) complexes have been synthesized as potential anticancer compounds and their structures were elucidated using a variety of physico-chemical techniques. Theoretical calculations invoking geometry optimization, vibrational assignments, 1H NMR, charge distribution and molecular orbital description HOMO and LUMO were done using density functional theory. Natural bond orbital analysis (NBO) method was performed to provide details about the type of hybridization and the nature of bonding in the studied complexes. Strong coordination bonds (LP(1)N11 → σ *(M sbnd Cl22)) and (LP(1)N21 → σ *(M sbnd Cl23)) (M = Pd or Pt) result from donation of electron density from a lone pair orbital on the nitrogen atoms to the acceptor metal molecular orbitals. The experimental results and the calculated molecular parameters revealed square-planar geometries around the metallic centre through the pyridine-type nitrogen of the benzimidazole ring and secondary amino group and two chlorine atoms. The activation thermodynamic parameters were calculated using non-isothermal methods. The synthesized ligands, in comparison to their metal complexes were screened for their antibacterial activity. In addition, the studied complexes showed activity against three cell lines of different origin, breast cancer (MCF-7), Colon Carcinoma (HCT) and human heptacellular carcinoma (Hep-G2) comparable to cis-platin.

  10. Impact of charge-transfer excitons in regioregular polythiophene on the charge separation at polythiophene-fullerene heterojunctions (United States)

    Polkehn, M.; Tamura, H.; Burghardt, I.


    This study addresses the mechanism of ultrafast charge separation in regioregular oligothiophene-fullerene assemblies representative of poly-3-hexylthiophene (P3HT)-[6,6]-phenyl-C61 butyric acid methyl ester (PCBM) heterojunctions, with special emphasis on the inclusion of charge transfer excitons in the oligothiophene phase. The formation of polaronic inter-chain charge separated species in highly ordered oligothiophene has been demonstrated in recent experiments and could have a significant impact on the net charge transfer to the fullerene acceptor. The present approach combines a first-principles parametrized multi-site Hamiltonian, based on time-dependent density functional theory calculations, with accurate quantum dynamics simulations using the multi-layer multi-configuration time-dependent Hartree method. Quantum dynamical studies are carried out for up to 182 electronic states and 112 phonon modes. The present analysis follows up on our previous study of (Huix-Rotllant et al 2015 J. Phys. Chem. Lett. 6 1702) and significantly expands the scope of this analysis by including the dynamical role of charge transfer excitons. Our investigation highlights the pronounced mixing of photogenerated Frenkel excitons with charge transfer excitons in the oligothiophene domain, and the opening of new transfer channels due the creation of such charge-separated species. As a result, it turns out that the interfacial donor/acceptor charge transfer state can be largely circumvented due to the presence of charge transfer excitons. However, the latter states in turn act as a trap, such that the free carrier yield observed on ultrafast time scales is tangibly reduced. The present analysis underscores the complexity of the transfer pathways at P3HT-PCBM type junctions.

  11. Excitonically Coupled States in Crystalline Coordination Networks. (United States)

    Haldar, Ritesh; Mazel, Antoine; Joseph, Reetu; Adams, Michael; Howard, Ian A; Richards, Bryce S; Tsotsalas, Manuel; Redel, Engelbert; Diring, Stéphane; Odobel, Fabrice; Wöll, Christof


    When chromophores are brought into close proximity, noncovalent interactions (π-π/CH-π) can lead to the formation of excitonically coupled states, which bestow new photophysical properties upon the aggregates. Because the properties of the new states not only depend on the strength of intermolecular interactions, but also on the relative orientation, supramolecular assemblies, where these parameters can be varied in a deliberate fashion, provide novel possibilities for the control of photophysical properties. This work reports that core-substituted naphthalene diimides (cNDIs) can be incorporated into surface-mounted metal- organic structures/frameworks (SURMOFs) to yield optical properties strikingly different from conventional aggregates of such molecules, for example, formed in solution or by crystallization. Organic linkers are used, based on cNDIs, well-known organic chromophores with numerous applications in different optoelectronic devices, to fabricate MOF thin films on transparent substrates. A thorough characterization of the properties of these highly ordered chromophoric assemblies reveals the presence of non-emissive excited states in the crystalline material. Structural modulations provide further insights into the nature of the coupling that gives rise to an excited-state energy level in the periodic structure. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Dark High Density Dipolar Liquid of Excitons. (United States)

    Cohen, Kobi; Shilo, Yehiel; West, Ken; Pfeiffer, Loren; Rapaport, Ronen


    The possible phases and the nanoscale particle correlations of two-dimensional interacting dipolar particles is a long-sought problem in many-body physics. Here we observe a spontaneous condensation of trapped two-dimensional dipolar excitons with internal spin degrees of freedom from an interacting gas into a high density, closely packed liquid state made mostly of dark dipoles. Another phase transition, into a bright, highly repulsive plasma, is observed at even higher excitation powers. The dark liquid state is formed below a critical temperature Tc ≈ 4.8 K, and it is manifested by a clear spontaneous spatial condensation to a smaller and denser cloud, suggesting an attractive part to the interaction which goes beyond the purely repulsive dipole-dipole forces. Contributions from quantum mechanical fluctuations are expected to be significant in this strongly correlated, long living dark liquid. This is a new example of a two-dimensional atomic-like interacting dipolar liquid, but where the coupling of light to its internal spin degrees of freedom plays a crucial role in the dynamical formation and the nature of resulting condensed dark ground state.

  13. Synthesis, interactions, molecular structure, biological properties and molecular docking studies on Mn, Co, Zn complexes containing acetylacetone and pyridine ligands with DNA duplex. (United States)

    Thamilarasan, V; Sengottuvelan, N; Stalin, N; Srinivasan, P; Chakkaravarthi, G


    Three metal complexes (1-3) of the type [Mn(acac)2(py)·H2O] (1), [Co(acac)2(py)·H2O] (2) and [Zn(acac)2(py)·H2O] (3), [Where acac=acetylacetone, py=pyridine] were synthesized and characterized by spectral (UV-vis, FT-IR, ESI-mass) analysis. The structure of complex 2 has been determined by single crystal X-ray diffraction studies and the configuration of ligand-coordinated to metal(II) ion was well described as distorted octahedral coordination geometry. The interaction of the complexes with CT-DNA has been explored by absorption, fluorescence, circular dichromism spectroscopy, viscosity measurements and molecular docking studies. The intrinsic binding constant Kb of complexes 1-3 with CT-DNA obtained from UV-vis absorption spectral studies were 2.1×10(4), 2.1×10(5) and 1.98×10(4)M(-1), respectively, which revealed that the complexes could interact with CT-DNA through groove binding. The results indicated that the complexes (1-3) were able to bind to DNA with different binding affinity, in the order: 2>1>3. The interaction of the compounds with bovine serum albumins were also investigated using fluorescence methods and the gel electrophoresis assay demonstrates weak cleavage ability of the pBR322 plasmid DNA in the presence of the metal complexes (1-3) with various activators. Further, the in vitro cytotoxic effect of the complexes were examined on cancerous cell line, with human breast cancer cells MCF-7. Copyright © 2016. Published by Elsevier B.V.

  14. Probing the Interlayer Exciton Physics in a MoS2/MoSe2/MoS2 van der Waals Heterostructure (United States)

    Baranowski, M.; Surrente, A.; Klopotowski, L.; Urban, J. M.; Zhang, N.; Maude, D. K.; Wiwatowski, K.; Mackowski, S.; Kung, Y. C.; Dumcenco, D.; Kis, A.; Plochocka, P.


    Stacking atomic monolayers of semiconducting transition metal dichalcogenides (TMDs) has emerged as an effective way to engineer their properties. In principle, the staggered band alignment of TMD heterostructures should result in the formation of inter-layer excitons with long lifetimes and robust valley polarization. However, these features have been observed simultaneously only in MoSe$_2$/WSe$_2$ heterostructures. Here we report on the observation of long lived inter-layer exciton emission in a MoS$_2$/MoSe$_2$/MoS$_2$ trilayer van der Waals heterostructure. The inter-layer nature of the observed transition is confirmed by photoluminescence spectroscopy, as well as by analyzing the temporal, excitation power and temperature dependence of the inter-layer emission peak. The observed complex photoluminescence dynamics suggests the presence of quasi-degenerate momentum-direct and momentum-indirect bandgaps. We show that circularly polarized optical pumping results in long lived valley polarization of inter-layer exciton. Intriguingly, the inter-layer exciton photoluminescence has helicity opposite to the excitation. Our results show that through a careful choice of the TMDs forming the van der Waals heterostructure it is possible to control the circular polarization of the inter-layer exciton emission.

  15. Probing the Interlayer Exciton Physics in a MoS2/MoSe2/MoS2van der Waals Heterostructure. (United States)

    Baranowski, M; Surrente, A; Klopotowski, L; Urban, J M; Zhang, N; Maude, D K; Wiwatowski, K; Mackowski, S; Kung, Y C; Dumcenco, D; Kis, A; Plochocka, P


    Stacking atomic monolayers of semiconducting transition metal dichalcogenides (TMDs) has emerged as an effective way to engineer their properties. In principle, the staggered band alignment of TMD heterostructures should result in the formation of interlayer excitons with long lifetimes and robust valley polarization. However, these features have been observed simultaneously only in MoSe 2 /WSe 2 heterostructures. Here we report on the observation of long-lived interlayer exciton emission in a MoS 2 /MoSe 2 /MoS 2 trilayer van der Waals heterostructure. The interlayer nature of the observed transition is confirmed by photoluminescence spectroscopy, as well as by analyzing the temporal, excitation power, and temperature dependence of the interlayer emission peak. The observed complex photoluminescence dynamics suggests the presence of quasi-degenerate momentum-direct and momentum-indirect bandgaps. We show that circularly polarized optical pumping results in long-lived valley polarization of interlayer exciton. Intriguingly, the interlayer exciton photoluminescence has helicity opposite to the excitation. Our results show that through a careful choice of the TMDs forming the van der Waals heterostructure it is possible to control the circular polarization of the interlayer exciton emission.

  16. Inclusion complexes of β-cyclodextrin with tricyclic drugs: an X-ray diffraction, NMR and molecular dynamics study

    Directory of Open Access Journals (Sweden)

    Franca Castiglione


    Full Text Available Tricyclic fused-ring cyclobenzaprine (1 and amitriptyline (2 form 1:1 inclusion complexes with β-cyclodextrin (β-CD in the solid state and in water solution. Rotating frame NOE experiments (ROESY showed the same geometry of inclusion for both 1/β-CD and 2/β-CD complexes, with the aromatic ring system entering the cavity from the large rim of the cyclodextrin and the alkylammonium chain protruding out of the cavity and facing the secondary OH rim. These features matched those found in the molecular dynamics (MD simulations in solution and in the solid state from single-crystal X-ray diffraction of 1/β-CD and 2/β-CD complexes. The latter complex was found in a single conformation in the solid state, whilst the MD simulations in explicit water reproduced the conformational transitions observed experimentally for the free molecule.

  17. Spectroscopic, electrochemical, docking and molecular dynamics studies on the interaction of three oxovanadium (IV) Schiff base complexes with bovine serum albumin and their cytotoxicity against cancer. (United States)

    Amiri, Majid; Ajloo, Davood; Fazli, Mostafa; Mokhtarieh, Amir; Grivani, Gholamhossein; Saboury, A A


    This study was designed to investigate the interaction of three oxovanadium (IV) Schiff base complexes with bovine serum albumin (BSA) by means of various spectroscopic and electrochemical methods along with molecular docking study and molecular dynamics (MD) simulations. Binding constants were estimated by fluorescence and UV-Vis spectroscopy. The results indicated a good affinity of the complexes for BSA in which furyl derivative had more activity. Molecular docking study showed that these complexes have the similar binding modes and located within subdomain IB in site III of BSA. The supporting of molecular docking and molecular dynamics results by experimental data, confirms the validity of the interactions data obtained by these methods. Biological activity against cancer cell showed that furyl derivative has higher activity than other complexes. Pharmaceutical analysis also showed that, these complexes potentially can be used as cancer daisies.

  18. Theory of Anisotropic Circular Dichroism of Excitonically Coupled Systems: Application to the Baseplate of Green Sulfur Bacteria. (United States)

    Lindorfer, Dominik; Renger, Thomas


    A simple exciton theory for the description of anisotropic circular dichroism (ACD) spectra of multichromophoric systems is presented that is expected to be of general use for the analysis of structure-function relationships of molecular aggregates such as photosynthetic light-harvesting antennae. The theory is applied to the baseplate of green sulfur bacteria. It is demonstrated that only the combined analysis of ACD and circular dichroism (CD) spectra for the present baseplate bacteriochlorophyll (BChl) a dimer allows for an unambiguous determination of the parameters of the exciton Hamiltonian from experimental data. The analysis of experimental absorption and linear dichroism spectra suggests that either the NMR structure has to be refined or in addition to the dimers seen in the NMR structure and in the CD and ACD spectra, BChl a monomers are present in the baseplate carotenosome sample. A refined dimer structure is presented, explaining all four optical spectra.

  19. Molecular investigations of the structure and function of the protein phosphatase 1-spinophilin-inhibitor 2 heterotrimeric complex. (United States)

    Dancheck, Barbara; Ragusa, Michael J; Allaire, Marc; Nairn, Angus C; Page, Rebecca; Peti, Wolfgang


    Regulation of the major Ser/Thr phosphatase protein phosphatase 1 (PP1) is controlled by a diverse array of targeting and inhibitor proteins. Though many PP1 regulatory proteins share at least one PP1 binding motif, usually the RVxF motif, it was recently discovered that certain pairs of targeting and inhibitor proteins bind PP1 simultaneously to form PP1 heterotrimeric complexes. To date, structural information for these heterotrimeric complexes and, in turn, how they direct PP1 activity is entirely lacking. Using a combination of NMR spectroscopy, biochemistry, and small-angle X-ray scattering (SAXS), we show that major structural rearrangements in both spinophilin (targeting) and inhibitor 2 (I-2, inhibitor) are essential for the formation of the heterotrimeric PP1-spinophilin-I-2 (PSI) complex. The RVxF motif of I-2 is released from PP1 during the formation of PSI, making the less prevalent SILK motif of I-2 essential for complex stability. The release of the I-2 RVxF motif allows for enhanced flexibility of both I-2 and spinophilin in the heterotrimeric complex. In addition, we used inductively coupled plasma atomic emission spectroscopy to show that PP1 contains two metals in both heterodimeric complexes (PP1-spinophilin and PP1-I-2) and PSI, demonstrating that PSI retains the biochemical characteristics of the PP1-I-2 holoenzyme. Finally, we combined the NMR and biochemical data with SAXS and molecular dynamics simulations to generate a structural model of the full heterotrimeric PSI complex. Collectively, these data reveal the molecular events that enable PP1 heterotrimeric complexes to exploit both the targeting and inhibitory features of the PP1-regulatory proteins to form multifunctional PP1 holoenzymes.

  20. Hydrogen-related excitons and their excited-state transitions in ZnO (United States)

    Heinhold, R.; Neiman, A.; Kennedy, J. V.; Markwitz, A.; Reeves, R. J.; Allen, M. W.


    The role of hydrogen in the photoluminescence (PL) of ZnO was investigated using four different types of bulk ZnO single crystal, with varying concentrations of unintentional hydrogen donor and Group I acceptor impurities. Photoluminescence spectra were measured at 3 K, with emission energies determined to ±50 μeV, before and after separate annealing in O2, N2, and H2 atmospheres. Using this approach, several new hydrogen-related neutral-donor-bound excitons, and their corresponding B exciton, ionized donor, and two electron satellite (TES) excited state transitions were identified and their properties further investigated using hydrogen and deuterium ion implantation. The commonly observed I4 (3.36272 eV) emission due to excitons bound to multicoordinated hydrogen inside an oxygen vacancy (HO), that is present in most ZnO material, was noticeably absent in hydrothermally grown (HT) ZnO and instead was replaced by a doublet of two closely lying recombination lines I4 b ,c (3.36219, 3.36237 eV) due to a hydrogen-related donor with a binding energy (ED) of 47.7 meV. A new and usually dominant recombination line I6 -H (3.36085 eV) due to a different hydrogen-related defect complex with an ED of 49.5 meV was also identified in HT ZnO. Here, I4 b ,c and I6 -H were stable up to approximately 400 and 600 °C, respectively, indicating that they are likely to contribute to the unintentional n -type conductivity of ZnO. Another doublet I5 (3.36137, 3.36148 eV) was identified in hydrogenated HT ZnO single crystals with low Li concentrations, and this was associated with a defect complex with an ED of 49.1 meV. A broad near band edge (NBE) emission centered at 3.366 eV was associated with excitons bound to subsurface hydrogen. We further demonstrate that hydrogen incorporates on different lattice sites for different annealing conditions and show that the new features I4 b ,c, I6 -H, and I5 most likely originate from the lithium-hydrogen defect complexes L iZn-HO , A l

  1. A Molecular Dynamics Approach to Ligand-Receptor Interaction in the Aspirin-Human Serum Albumin Complex


    Alvarez, H. Ariel; McCarthy, Andrés N.; Grigera, J. Raúl


    In this work, we present a study of the interaction between human serum albumin (HSA) and acetylsalicylic acid (ASA, C9H8O4) by molecular dynamics simulations (MD). Starting from an experimentally resolved structure of the complex, we performed the extraction of the ligand by means of the application of an external force. After stabilization of the system, we quantified the force used to remove the ASA from its specific site of binding to HSA and calculated the mechanical nonequilibrium exter...

  2. Excitons in InP/InAs inhomogeneous quantum dots

    CERN Document Server

    Assaid, E; Khamkhami, J E; Dujardin, F


    Wannier excitons confined in an InP/InAs inhomogeneous quantum dot (IQD) have been studied theoretically in the framework of the effective mass approximation. A finite-depth potential well has been used to describe the effect of the quantum confinement in the InAs layer. The exciton binding energy has been determined using the Ritz variational method. The spatial correlation between the electron and the hole has been taken into account in the expression for the wavefunction. It has been shown that for a fixed size b of the IQD, the exciton binding energy depends strongly on the core radius a. Moreover, it became apparent that there are two critical values of the core radius, a sub c sub r sub i sub t and a sub 2 sub D , for which important changes of the exciton binding occur. The former critical value, a sub c sub r sub i sub t , corresponds to a minimum of the exciton binding energy and may be used to distinguish between tridimensional confinement and bidimensional confinement. The latter critical value, a ...

  3. Angular momentum transport with twisted exciton wave packets (United States)

    Zang, Xiaoning; Lusk, Mark T.


    A chain of cofacial molecules with CN or CN h symmetry supports excitonic states with a screwlike structure. These can be quantified with the combination of an axial wave number and an azimuthal winding number. Combinations of these states can be used to construct excitonic wave packets that spiral down the chain with well-determined linear and angular momenta. These twisted exciton wave packets can be created and annihilated using laser pulses, and their angular momentum can be optically modified during transit. This allows for the creation of optoexcitonic circuits in which information, encoded in the angular momentum of light, is converted into excitonic wave packets that can be manipulated, transported, and then reemitted. A tight-binding paradigm is used to demonstrate the key ideas. The approach is then extended to quantify the evolution of twisted exciton wave packets in a many-body, multilevel time-domain density functional theory setting. In both settings, numerical methods are developed that allow the site-to-site transfer of angular momentum to be quantified.

  4. Exciton Effects in Optical Absorption of Boron-Nitride Nanotubes

    CERN Document Server

    Harigaya, Kikuo


    Exciton effects are studied in single-wall boron-nitride (BN) nanotubes. Linear absorption spectra are calculated with changing the chiral index of the zigzag nanotubes. We consider the extended Hubbard model with atomic energies at the boron and nitrogen sites. Exciton effects are calculated using the configuration interaction technique. The Coulomb interaction dependence of the band gap, the lowest exciton energy, and the binding energy of the exciton are discussed. The optical gap of the (5,0) nanotube is about 6 eV at the onsite interaction U=2t with the hopping integral t=1.2 eV. The binding energy of the exciton is 0.50 eV for these parameters. This energy agrees well with that of other theoretical investigations. We find that the energy gap and the binding energy are almost independent of the geometries of the nanotubes. This novel property is in contrast with that of the carbon nanotubes which show metallic and semiconducting properties depending on the chiral index.

  5. Phonon-assisted absorption of excitons in Cu2O (United States)

    Schöne, Florian; Stolz, Heinrich; Naka, Nobuko


    The basic theoretical foundation for the modeling of phonon-assisted absorption spectra in direct band-gap semiconductors, introduced by Elliott 60 years ago [R. J. Elliott, Phys. Rev. 108, 1384 (1957), 10.1103/PhysRev.108.1384] using second order perturbation theory, results in a square root shaped dependency close to the absorption edge. A careful analysis of the experiments [N. Naka et al., Jpn. J. Appl. Phys. 44, 5096 (2005), 10.1143/JJAP.44.5096] reveals that for the yellow S excitons in Cu2O the lineshape does not follow that square root dependence. The reexamination of the theory shows that the basic assumptions of constant matrix elements and constant energy denominators is invalid for semiconductors with dominant exciton effects like Cu2O , where the phonon-assisted absorption proceeds via intermediate exciton states. The overlap between these and the final exciton states strongly determines the dependence of the absorption on the photon energy. To describe the experimental observed line shape of the indirect absorption of the yellow S exciton states we find it necessary to assume a momentum dependent deformation potential for the optical phonons.

  6. Spectral properties of excitons in the bilayer graphene (United States)

    Apinyan, V.; Kopeć, T. K.


    In this paper, we consider the spectral properties of the bilayer graphene with the local excitonic pairing interaction between the electrons and holes. We consider the generalized Hubbard model, which includes both intralayer and interlayer Coulomb interaction parameters. The solution of the excitonic gap parameter is used to calculate the electronic band structure, single-particle spectral functions, the hybridization gap, and the excitonic coherence length in the bilayer graphene. We show that the local interlayer Coulomb interaction is responsible for the semimetal-semiconductor transition in the double layer system, and we calculate the hybridization gap in the band structure above the critical interaction value. The formation of the excitonic band gap is reported as the threshold process and the momentum distribution functions have been calculated numerically. We show that in the weak coupling limit the system is governed by the Bardeen-Cooper-Schrieffer (BCS)-like pairing state. Contrary, in the strong coupling limit the excitonic condensate states appear in the semiconducting phase, by forming the Dirac's pockets in the reciprocal space.

  7. Spectroscopic mapping and selective electronic tuning of molecular orbitals in phosphorescent organometallic complexes – a new strategy for OLED materials

    Directory of Open Access Journals (Sweden)

    Pascal R. Ewen


    Full Text Available The improvement of molecular electronic devices such as organic light-emitting diodes requires fundamental knowledge about the structural and electronic properties of the employed molecules as well as their interactions with neighboring molecules or interfaces. We show that highly resolved scanning tunneling microscopy (STM and spectroscopy (STS are powerful tools to correlate the electronic properties of phosphorescent complexes (i.e., triplet emitters with their molecular structure as well as the local environment around a single molecule. We used spectroscopic mapping to visualize several occupied and unoccupied molecular frontier orbitals of Pt(II complexes adsorbed on Au(111. The analysis showed that the molecules exhibit a peculiar localized strong hybridization that leads to partial depopulation of a dz² orbital, while the ligand orbitals are almost unchanged. We further found that substitution of functional groups at well-defined positions can alter specific molecular orbitals without influencing the others. The results open a path toward the tailored design of electronic and optical properties of triplet emitters by smart ligand substitution, which may improve the performance of future OLED devices.

  8. Dirac cones and Dirac saddle points of bright excitons in monolayer transition metal dichalcogenides. (United States)

    Yu, Hongyi; Liu, Gui-Bin; Gong, Pu; Xu, Xiaodong; Yao, Wang


    In monolayer transition metal dichalcogenides, tightly bound excitons have been discovered with a valley pseudospin optically addressable through polarization selection rules. Here, we show that this valley pseudospin is strongly coupled to the exciton centre-of-mass motion through electron-hole exchange. This coupling realizes a massless Dirac cone with chirality index I = 2 for excitons inside the light cone, that is, bright excitons. Under moderate strain, the I = 2 Dirac cone splits into two degenerate I = 1 Dirac cones, and saddle points with a linear Dirac spectrum emerge. After binding an extra electron, the charged exciton becomes a massive Dirac particle associated with a large valley Hall effect protected from intervalley scattering. Our results point to unique opportunities to study Dirac physics, with exciton's optical addressability at specifiable momentum, energy and pseudospin. The strain-tunable valley-orbit coupling also implies new structures of exciton condensates, new functionalities of excitonic circuits and mechanical control of valley pseudospin.

  9. Excitonic, vibrational, and van der Waals interactions in electron energy loss spectroscopy. (United States)

    Mizoguchi, T; Miyata, T; Olovsson, W


    The pioneer, Ondrej L. Krivanek, and his collaborators have opened up many frontiers for the electron energy loss spectroscopy (EELS), and they have demonstrated new potentials of the EELS method for investigating materials. Here, inspired by those achievements, we show further potentials of EELS based on the results of theoretical calculations, that is excitonic and van der Waals (vdW) interactions, as well as vibrational information of materials. Concerning the excitonic interactions, we highlight the importance of the two-particle calculation to reproduce the low energy-loss near-edge structure (ELNES), the Na-L 2,3 edge of NaI and the Li-K edge of LiCl and LiFePO 4 . Furthermore, an unusually strong excitonic interaction at the O-K edge of perovskite oxides, SrTiO 3 and LaAlO 3 , is shown. The effect of the vdW interaction in the ELNES is also investigated, and we observe that the magnitude of the vdW effect is approximately 0.1eV in the case of the ELNES from a solid and liquid, whereas its effect is almost negligible in the case of the ELNES from the gaseous phase owing to the long inter-molecular distance. In addition to the "static" information, the influence of the "dynamic" behavior of atoms in materials to EELS is also investigated. We show that measurements of the infrared spectrum are possible by using a modern monochromator system. Furthermore, an estimation of the atomic vibration in core-loss ELNES is also presented. We show the acquisition of vibrational information using the ELNES of liquid methanol and acetic acid, solid Al 2 O 3 , and oxygen gas. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Fluorescence enhancement of the aflatoxin B{sub 1} by forming inclusion complexes with some cyclodextrins and molecular modeling study

    Energy Technology Data Exchange (ETDEWEB)

    Aghamohammadi, Mohammad [Department of Chemistry, Faculty of Science, Tarbiat Modarres University, P.O. Box 14115-111, Tehran (Iran, Islamic Republic of); Alizadeh, Naader [Department of Chemistry, Faculty of Science, Tarbiat Modarres University, P.O. Box 14115-111, Tehran (Iran, Islamic Republic of)], E-mail:


    The interaction between the aflatoxin B{sub 1} (AFB{sub 1}) and three cyclodextrins, {alpha}-cyclodextrin ({alpha}-CD), {beta}-cyclodextrin ({beta}-CD) and heptakis-2,6-dimethyl-o-{beta}-cyclodextrin (ome-CD), was studied by spectrofluorescence technique. It was found that the inclusion association behavior occurs for the complexes of cyclodextrins with AFB{sub 1}. The fluorescence of AFB{sub 1} is generally enhanced in the complexes with cyclodextrins in aqueous solutions. The inclusion complex constants of the three types of cyclodextrins at different temperatures were evaluated from Benesi-Hildebrand plot and also by non-linear regression analysis. These cyclodextrins can only form the 1:1 (host:guest) inclusion complex in the studied temperature range of 20-50 deg. C. The enthalpy ({delta}H{sup o}) and entropy ({delta}S{sup o}) changes of complexation were extracted from the temperature dependency of complex formation constants (K). Temperature-dependent measurements showed that the association step is controlled by enthalpy-entropy compensation effect. The use of ome-CD generally resulted in the greatest fluorescence intensity. On the other hand, the discrepancy between the exhibited enhanced fluorescence and thermodynamic parameters ({delta}G{sup o}) is proposed to be different only by the orientation of the AFB{sub 1} within the cyclodextrin cavity. To find the most favorable structure, the geometry of complex was investigated by molecular modeling approach employing the semiemperical HF-SCF calculations.

  11. Spectroscopic and molecular modeling based approaches to study on the binding behavior of DNA with a copper (II) complex. (United States)

    Vahdati Rad, Fatemeh; Housaindokht, Mohammad Reza; Jalal, Razieh; Eshtiagh Hosseini, Hossein; Verdian Doghaei, Asma; Sadeghi Goghari, Sadegh


    Blocking the division of tumor cells by small-molecules is currently of great interest for the design of new antitumor drugs. The interaction of a new metal complex with DNA was investigated through several techniques. Absorption spectroscopy and gel electrophoresis studies on the interaction of the Cu-complex of (2a-4mpyH)2 [Cu(pyzdc)2 (H2O)2].6 H2O with DNA have shown that this complex can bind to CT-DNA with binding constant 3.99 × 10(5) M(-1). The cyclic voltammetry (CV) responses of the metal complex in the presence of CT-DNA have shown that the metal complex can bind to CT-DNA through partial intercalation mode and this is consistent with molecular docking analysis, quenching process and thermal denaturation experiments. The cytotoxicity of this complex has been evaluated by MTT assay. The results of cell viability assay on DU145 cell line revealed that the metal complex had cytotoxic effects.

  12. Dephasing in the quasi-two-dimensional exciton-biexciton system

    DEFF Research Database (Denmark)

    Langbein, Wolfgang Werner; Hvam, Jørn Märcher


    The polarization decay in the exciton-biexciton system of a homogeneously broadened single quantum well is studied by transient four-wave mixing. All three decay rates in the exciton-biexciton three-level system are deduced. The relation between the rates unravels correlations between scattering...... excitons and biexcitons are mutually uncorrelated. In contrast, the biexciton phonon scattering is twice as fast and correlated to exciton-phonon scattering, indicating the interaction with similar phonon modes....

  13. Inclusion complexes of cefuroxime axetil with β-cyclodextrin: Physicochemical characterization, molecular modeling and effect of l-arginine on complexation

    Directory of Open Access Journals (Sweden)

    Sarika Sapte


    Full Text Available The inclusion complexes of poorly water-soluble cephalosporin, cefuroxime axetil (CFA, were prepared with β-cyclodextrin (βCD with or without addition of l-arginine (ARG to improve its physicochemical properties. We also investigated the effect of ARG on complexation efficiency (CE of βCD towards CFA in an aqueous medium through phase solubility behaviour according to Higuchi and Connors. Although phase solubility studies showed AL (linear type of solubility curve in presence and absence of ARG, the CE and association constant (Ks of βCD towards CFA were significantly promoted in presence of ARG, justifying its use as a ternary component. The solid systems of CFA with βCD were obtained by spray drying technique with or without incorporation of ARG and characterized by differential scanning calorimetry (DSC, X-ray powder diffractometry (XRPD, scanning electron microscopy (SEM, and saturation solubility and dissolution studies. The molecular modeling studies provided a better insight into geometry and inclusion mode of CFA inside βCD cavity. The solubility and dissolution rate of CFA were significantly improved upon complexation with βCD as compared to CFA alone. However, ternary system incorporated with ARG performed better than binary system in physicochemical evaluation. In conclusion, ARG could be exploited as a ternary component to improve the physicochemical properties of CFA via βCD complexation.

  14. Molecular complexes of MoO/sub 2/Cl/sub 2/ with aromatic and heterocyclic azomethines

    Energy Technology Data Exchange (ETDEWEB)

    Abramenko, V.L.; Garnovskij, A.D.; Surpina, L.V. (Voroshilovgradskij Mashinostroitel' nyj Inst. (Ukrainian SSR); Rostovskij-na-Donu Inst. Sel' skokhozyajstvennogo Mashinostroeniya (USSR))


    Earlier unknown MoO/sub 2/Cl/sub 2/xnL(2) molecular complexes (n=0.5, 1, 2; L=Schitt bases (SB) from banzoic (L/sup 1/), Si cylic, ..beta..-oxynaphthoic aldehydes and aromatic, aliphatic, heterocyclic mono- and diamines) are prepared by MoO/sub 2/Cl/sub 2/ (1) interaction with SB in organic solvents. Complex composition is determined by ligand nature. The prepared compounds are finely crystalline substances easily hydrolized in water, unsoluble in most solvents. Increase of frequency of C=N-bond valent oscillations by 10-40 cm/sup -1/ as compared with its position in L spectrum is observed in IR spectra 2 that points out molybdenum coordination by azomethine atom of nitrogen. Bands of Ph-O valent oscillations (1280-1300 cm/sup -1/) and OH/sup -/ (2800-3200 cm/sup -1/) under complexing are not practically shifted that testifies to conservation of intramolecular hydrogen bond in coordinated molecules of the ligands. The mentioned peculiarities in IR spectra permitted to attribute 2 to molecular type complexes with donor-acceptor bond N ..-->.. Mo(6). According to conductometric measurements 2 are 1:2 electrolytes in MeOH and dimethylformamide solutions and they are subjected to the reaction of the main solvolysis.

  15. Distinct Regions within the Erlins Are Required for Oligomerization and Association with High Molecular Weight Complexes*S⃞ (United States)

    Hoegg, Maja B.; Browman, Duncan T.; Resek, Mary E.; Robbins, Stephen M.


    The group of stomatin/prohibitin/flotillin/HflK/C (SPFH) domain-containing proteins comprise members of diverse subcellular localization and function. Association with detergent-resistant membranes (DRMs) and the propensity to form oligomers are two common properties of SPFH domain proteins and likely important for the function of these proteins. Our laboratory recently discovered two novel members of this protein group, which, based on their endoplasmic reticulum (ER) localization and association with DRMs, were named ER lipid raft-associated protein (erlin)-1 and -2. Here we characterized erlin oligomerization and identified domains within the erlins responsible for oligomerization and DRM association. Using co-immunoprecipitation and sucrose density gradient centrifugation approaches on endogenous and ectopically expressed erlin proteins, we found that they formed homo- and hetero-oligomers and were part of large multimeric complexes. These properties were independent of their DRM association. By analyzing truncation and point mutants of erlin-2 we discovered that interaction between erlin monomers (oligomerization) and association with high molecular weight complexes require distinct regions within the protein. Although oligomerization and DRM association were mediated by a region immediately downstream of the SPFH domain (residues 228–300), integration into high molecular weight complexes was absolutely dependent on a phenylalanine residue C-terminal of this region (Phe-305), which lies within a short stretch of hydrophobic residues. Our data demonstrate that lower order oligomerization and incorporation into multimeric complexes are two separate biochemical properties of the erlins, because they are mediated by distinct regions. PMID:19131330

  16. On the relation between local and charge-transfer exciton bindingenergies in organic photovoltaic materials

    NARCIS (Netherlands)

    de Gier, Hilde Dorothea; Braam, Henderika; Havenith, Remco


    In organic photovoltaic devices two types of excitons can be generated for which different binding energies can be defined: the binding energy of the local exciton generated immediately after light absorption on the polymer and the binding energy of the charge-transfer exciton generated through the

  17. Study on inclusion complexation between plant growth regulator 6-benzylaminopurine and β-cyclodextrin: Preparation, characterization and molecular modeling (United States)

    Ge, Xia; He, Jiang; Yang, Ying; Qi, Fengming; Huang, Zheng; Lu, Ruihua; Huang, Lizhen; Yao, Xiaojun


    An inclusion complex between the plant growth regulator 6-benzylaminopurine (6-BA) and β-cyclodextrin (β-CD) was prepared. A 1:1 host-guest stoichiometry was conformed by elemental analysis and Job's plot. From phase solubility diagram, a calculated apparent stability constant was 259.49 L/mol. The obtained complex was found to significantly improve the water solubility of 6-BA, and there was a 4.1-fold increase in the presence of 12 mmol/L β-CD as compared with the free 6-BA. Thermoanalysis, NMR and IR spectra were applied to characterize the complex. 1H NMR and ROESY results indicated that the benzene ring of 6-BA was included into the β-CD cavity, which was in agreement with the most predominant configuration optimized by molecular modeling.

  18. Excitonic connectivity between photosystem II units: what is it, and how to measure it? (United States)

    Stirbet, Alexandrina


    In photosynthetic organisms, light energy is absorbed by a complex network of chromophores embedded in light-harvesting antenna complexes. In photosystem II (PSII), the excitation energy from the antenna is transferred very efficiently to an active reaction center (RC) (i.e., with oxidized primary quinone acceptor Q(A)), where the photochemistry begins, leading to O2 evolution, and reduction of plastoquinones. A very small part of the excitation energy is dissipated as fluorescence and heat. Measurements on chlorophyll (Chl) fluorescence and oxygen have shown that a nonlinear (hyperbolic) relationship exists between the fluorescence yield (Φ(F)) (or the oxygen emission yield, (Φ(O2)) and the fraction of closed PSII RCs (i.e., with reduced Q(A)). This nonlinearity is assumed to be related to the transfer of the excitation energy from a closed PSII RC to an open (active) PSII RC, a process called PSII excitonic connectivity by Joliot and Joliot (CR Acad Sci Paris 258: 4622-4625, 1964). Different theoretical approaches of the PSII excitonic connectivity, and experimental methods used to measure it, are discussed in this review. In addition, we present alternative explanations of the observed sigmoidicity of the fluorescence induction and oxygen evolution curves.

  19. Molecular features governing the stability and specificity of functional complex formation by Mycobacterium tuberculosis CFP-10/ESAT-6 family proteins. (United States)

    Lightbody, Kirsty L; Ilghari, Dariush; Waters, Lorna C; Carey, Gemma; Bailey, Mark A; Williamson, Richard A; Renshaw, Philip S; Carr, Mark D


    The Mycobacterium tuberculosis complex CFP-10/ESAT-6 family proteins play essential but poorly defined roles in tuberculosis pathogenesis. In this article we report the results of detailed spectroscopic studies of several members of the CFP-10/ESAT-6 family. This work shows that the CFP-10/ESAT-6 related proteins, Rv0287 and Rv0288, form a tight 1:1 complex, which is predominantly helical in structure and is predicted to closely resemble the complex formed by CFP-10 and ESAT-6. In addition, the Rv0287.Rv0288 complex was found to be significantly more stable to both chemical and temperature induced denaturation than CFP-10.ESAT-6. This approach demonstrated that neither Rv0287.Rv0288 nor the CFP-10.ESAT-6 complexes are destabilized at low pH (4.5), indicating that even in low pH environments, such as the mature phagosome, both Rv0287.Rv0288 and CFP-10.ESAT-6 undoubtedly function as complexes rather than individual proteins. Analysis of the structure of the CFP-10.ESAT-6 complex and optimized amino acid sequence alignments of M. tuberculosis CFP-10/ESAT-6 family proteins revealed that residues involved in the intramolecular contacts between helices are conserved across the CFP-10/ESAT-6 family, but not those involved in primarily intermolecular contacts. This analysis identified the molecular basis for the specificity and stability of complex formation between CFP-10/ESAT-6 family proteins, and indicates that the formation of functional complexes with key roles in pathogenesis will be limited to genome partners, or very closely related family members, such as Rv0287/Rv0288 and Rv3019c/Rv3020c.

  20. MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories

    KAUST Repository

    Abdel-Azeim, Safwat


    Background: Molecular Dynamics ( MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. Results: On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. Conclusions: MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.

  1. Facile and Selective Synthetic Approach for Ruthenium Complexes Utilizing a Molecular Sieve Effect in the Supporting Ligand

    Directory of Open Access Journals (Sweden)

    Dai Oyama


    Full Text Available It is extremely important for synthetic chemists to control the structure of new compounds. We have constructed ruthenium-based mononuclear complexes with the tridentate 2,6-di(1,8-naphthyridin-2-ylpyridine (dnp ligand to investigate a new synthetic approach using a specific coordination space. The synthesis of a family of new ruthenium complexes containing both the dnp and triphenylphosphine (PPh3 ligands, [Ru(dnp(PPh3(X(L]n+ (X = PPh3, NO2−, Cl−, Br−; L = OH2, CH3CN, C6H5CN, SCN−, has been described. All complexes have been spectroscopically characterized in solution, and the nitrile complexes have also been characterized in the solid state through single-crystal X-ray diffraction analysis. Dnp in the present complex system behaves like a “molecular sieve” in ligand replacement reactions. Both experimental data and density functional theory (DFT calculations suggest that dnp plays a crucial role in the selectivity observed in this study. The results provide useful information toward elucidating this facile and selective synthetic approach to new transition metal complexes.

  2. Incomplete Exciton Harvesting from Fullerenes in Bulk Heterojunction Solar Cells

    KAUST Repository

    Burkhard, George F.


    We investigate the internal quantum efficiencies (IQEs) of high efficiency poly-3-hexylthiophene:[6,6]-phenyl-C61-butyric acid methyl ester (P3HT:PCBM) solar cells and find them to be lower at wavelengths where the PCBM absorbs. Because the exciton diffusion length in PCBM is too small, excitons generated in PCBM decay before reaching the donor-acceptor interface. This result has implications for most state of the art organic solar cells, since all of the most efficient devices use fullerenes as electron acceptors. © 2009 American Chemical Society.

  3. Exciton localization-delocalization transition in an extended dendrimer

    Energy Technology Data Exchange (ETDEWEB)

    Pouthier, Vincent, E-mail: [Institut UTINAM, Université de Franche-Comté, CNRS UMR 6213, 25030 Besançon Cedex (France)


    Exciton-mediated quantum state transfer between the periphery and the core of an extended dendrimer is investigated numerically. By mapping the dynamics onto that of a linear chain, it is shown that a localization-delocalization transition arises for a critical value of the generation number G{sub c} ≈ 5. This transition originates in the quantum interferences experienced by the excitonic wave due to the multiple scatterings that arise each time the wave tunnels from one generation to another. These results suggest that only small-size dendrimers could be used for designing an efficient quantum communication protocol.

  4. Defect Structure of Localized Excitons in a WSe2 Monolayer

    KAUST Repository

    Zhang, Shuai


    The atomic and electronic structure of intrinsic defects in a WSe2 monolayer grown on graphite was revealed by low temperature scanning tunneling microscopy and spectroscopy. Instead of chalcogen vacancies that prevail in other transition metal dichalcogenide materials, intrinsic defects in WSe2 arise surprisingly from single tungsten vacancies, leading to the hole (p-type) doping. Furthermore, we found these defects to dominate the excitonic emission of the WSe2 monolayer at low temperature. Our work provided the first atomic-scale understanding of defect excitons and paved the way toward deciphering the defect structure of single quantum emitters previously discovered in the WSe2 monolayer.

  5. Excitonic surface polaritons in luminescence from ZnTe crystals

    Energy Technology Data Exchange (ETDEWEB)

    Brodin, M.S.; Bandura, V.M.; Matsko, M.G. (AN Ukrainskoj SSR, Kiev. Inst. Fiziki)


    The form and structure of reflection and exciton-polariton luminescence spectra of ZnTe crystals are studied in the region of the ground (n = 1) exciton state. The longitudinal-transverse splitting magnitude LT/ is determined from the shape of the reflection spectra. A detected doublet structure of an emission band from the lower polariton branch is associated with the k-linear term. The evolution of bulk and surface polariton luminescence spectra versus temperature and wavelength of the exciting light is investigated.

  6. One-dimensional models of excitons in carbon nanotubes

    DEFF Research Database (Denmark)

    Cornean, Horia Decebal; Duclos, Pierre; Pedersen, Thomas Garm


    Excitons in carbon nanotubes may be modeled by two oppositely charged particles living on the surface of a cylinder. We derive three one-dimensional effective Hamiltonians which become exact as the radius of the cylinder vanishes. Two of them are solvable.......Excitons in carbon nanotubes may be modeled by two oppositely charged particles living on the surface of a cylinder. We derive three one-dimensional effective Hamiltonians which become exact as the radius of the cylinder vanishes. Two of them are solvable....

  7. Realization of an all optical exciton-polariton router

    Energy Technology Data Exchange (ETDEWEB)

    Marsault, Félix; Nguyen, Hai Son; Tanese, Dimitrii; Lemaître, Aristide; Galopin, Elisabeth; Sagnes, Isabelle; Amo, Alberto [Laboratoire de Photonique et de Nanostructures, LPN/CNRS, Route de Nozay, 91460 Marcoussis (France); Bloch, Jacqueline, E-mail: [Laboratoire de Photonique et de Nanostructures, LPN/CNRS, Route de Nozay, 91460 Marcoussis (France); Physics Department, Ecole Polytechnique, F-91128 Palaiseau Cedex (France)


    We report on the experimental realization of an all optical router for exciton-polaritons. This device is based on the design proposed by Flayac and Savenko [Appl. Phys. Lett. 103, 201105 (2013)], in which a zero-dimensional island is connected through tunnel barriers to two periodically modulated wires of different periods. Selective transmission of polaritons injected in the island, into either of the two wires, is achieved by tuning the energy of the island state across the band structure of the modulated wires. We demonstrate routing of ps polariton pulses using an optical control beam which controls the energy of the island quantum states, thanks to polariton-exciton interactions.

  8. Molecular Fluoride-Bridged 3d-4f Complexes and Their Magnetic Properties

    DEFF Research Database (Denmark)

    Pedersen, K. S.; Bendix, J.


    be utilized efficiently in tailored synthesis of polynuclear complexes and extended structures. In particular, the strong affinity of the lanthanides for fluoride makes it a good choice for directed synthesis of mixed lanthanide-transition metal complexes. Despite the competition from formation of lanthanide...

  9. Peanut Allergen Ara h 1 Interacts with Proanthocyanidins into Higher Molecular Weight Complexes

    NARCIS (Netherlands)

    Boxtel, van E.L.; Broek, van den L.A.M.; Koppelman, S.J.; Vincken, J.P.; Gruppen, H.


    Mildly extracted peanut allergen Ara h 1 was previously reported to occur as an oligomeric complex. In this paper we describe how the protein in this oligomeric complex interacts noncovalently with phenolic compounds of the proanthocyanidin type. These interactions are being disrupted during anion

  10. Molecular modelling of rare earth element complexation in subduction zone fluids

    NARCIS (Netherlands)

    van Sijl, J.; Allan, N.L.; Davies, G.R.; van Westrenen, W.


    Complexation of (trace) elements in fluids plays a critical role in determining element mobility in subduction zones, but to date, the atomic-scale processes controlling elemental solubilities are poorly understood. As a first step towards computer simulation of element complexation in subduction

  11. Synthesis of sp3-rich scaffolds for molecular libraries through complexity-generating cascade reactions

    DEFF Research Database (Denmark)

    Flagstad, Thomas; Min, Geanna; Bonnet, K.


    An efficient strategy for the synthesis of complex small molecules from simple building blocks is presented. Key steps of the strategy include tandem Petasis and Diels–Alder reactions, and divergent complexity-generating cyclization cascades from a key dialdehyde intermediate. The methodology...

  12. Peanut allergen Ara h 1 interacts with proanthocyanidins into higher molecular weight complexes

    NARCIS (Netherlands)

    Boxtel, E.L. van; Broek, L.A.M. van den; Koppelman, S.J.; Vincken, J.-P.; Gruppen, H.


    Mildly extracted peanut allergen Ara h 1 was previously reported to occur as an oligomeric complex. In this paper we describe how the protein in this oligomeric complex interacts noncovalently with phenolic compounds of the proanthocyanidin type. These interactions are being disrupted during anion

  13. Controlling excitons. Concepts for phosphorescent organic LEDs at high brightness

    Energy Technology Data Exchange (ETDEWEB)

    Reineke, Sebastian


    This work focusses on the high brightness performance of phosphorescent organic light-emitting diodes (OLEDs). The use of phosphorescent emitter molecules in OLEDs is essential to realize internal electron-photon conversion efficiencies of 100 %. However, due to their molecular nature, the excited triplet states have orders of magnitude longer time constants compared to their fluorescent counterparts which, in turn, strongly increases the probability of bimolecular annihilation. As a consequence, the efficiencies of phosphorescent OLEDs decline at high brightness - an effect known as efficiency roll-off, for which it has been shown to be dominated by triplet-triplet annihilation (TTA). In this work, TTA of the archetype phosphorescent emitter Ir(ppy){sub 3} is investigated in time-resolved photoluminescence experiments. For the widely used mixed system CBP:Ir(ppy){sub 3}, host-guest TTA - an additional unwanted TTA channel - is experimentally observed at high excitation levels. By using matrix materials with higher triplet energies, this effect is efficiently suppressed, however further studies show that the efficiency roll-off of Ir(ppy)3 is much more pronounced than predicted by a model based on Foerster-type energy transfer, which marks the intrinsic limit for TTA. These results suggest that the emitter molecules show a strong tendency to form aggregates in the mixed film as the origin for enhanced TTA. Transmission electron microscopy images of Ir(ppy){sub 3} doped mixed films give direct proof of emitter aggregates. Based on these results, two concepts are developed that improve the high brightness performance of OLEDs. In a first approach, thin intrinsic matrix interlayers are incorporated in the emission layer leading to a one-dimensional exciton confinement that suppresses exciton migration and, consequently, TTA. The second concept reduces the efficiency roll-off by using an emitter molecule with slightly different chemical structure, i.e. Ir(ppy){sub 2

  14. Cytogenetic and molecular markers reveal the complexity of the genus Piabina Reinhardt, 1867 (Characiformes: Characidae

    Directory of Open Access Journals (Sweden)

    Marlon Felix Pazian

    Full Text Available Cytogenetic and molecular analyses were carried out in fish representative of the genus Piabina. This study specifically involved the species P. argentea and P. anhembi collected from areas of the Paranapanema and Tietê River basins, Brazil. Our findings suggest that fish classified as Piabina argentea in the Paranapanema and Tietê Rivers may represent more than one species. The samples analyzed differed by cytogenetic particularities and molecular analyses using partial sequences of the genes COI and CytB as genetic markers revealed three distinct groups of P. argentea with genetic distances sufficient to support the conclusion that the three samples analyzed are three distinct taxonomic units.

  15. Discovery of Novel Complex Metal Hydrides for Hydrogen Storage through Molecular Modeling and Combinatorial Methods

    Energy Technology Data Exchange (ETDEWEB)

    Lesch, David A; Adriaan Sachtler, J.W. J.; Low, John J; Jensen, Craig M; Ozolins, Vidvuds; Siegel, Don; Harmon, Laurel


    UOP LLC, a Honeywell Company, Ford Motor Company, and Striatus, Inc., collaborated with Professor Craig Jensen of the University of Hawaii and Professor Vidvuds Ozolins of University of California, Los Angeles on a multi-year cost-shared program to discover novel complex metal hydrides for hydrogen storage. This innovative program combined sophisticated molecular modeling with high throughput combinatorial experiments to maximize the probability of identifying commercially relevant, economical hydrogen storage materials with broad application. A set of tools was developed to pursue the medium throughput (MT) and high throughput (HT) combinatorial exploratory investigation of novel complex metal hydrides for hydrogen storage. The assay programs consisted of monitoring hydrogen evolution as a function of temperature. This project also incorporated theoretical methods to help select candidate materials families for testing. The Virtual High Throughput Screening served as a virtual laboratory, calculating structures and their properties. First Principles calculations were applied to various systems to examine hydrogen storage reaction pathways and the associated thermodynamics. The experimental program began with the validation of the MT assay tool with NaAlH4/0.02 mole Ti, the state of the art hydrogen storage system given by decomposition of sodium alanate to sodium hydride, aluminum metal, and hydrogen. Once certified, a combinatorial 21-point study of the NaAlH4 LiAlH4Mg(AlH4)2 phase diagram was investigated with the MT assay. Stability proved to be a problem as many of the materials decomposed during synthesis, altering the expected assay results. This resulted in repeating the entire experiment with a mild milling approach, which only temporarily increased capacity. NaAlH4 was the best performer in both studies and no new mixed alanates were observed, a result consistent with the VHTS. Powder XRD suggested that the reverse reaction, the regeneration of the

  16. Synthesis, Characterization, Molecular Modeling, and DNA Interaction Studies of Copper Complex Containing Food Additive Carmoisine Dye. (United States)

    Shahabadi, Nahid; Akbari, Alireza; Jamshidbeigi, Mina; Khodarahmi, Reza


    A copper complex of carmoisine dye; [Cu(carmoisine)2(H2O)2]; was synthesized and characterized by using physico-chemical and spectroscopic methods. The binding of this complex with calf thymus (ct) DNA was investigated by circular dichroism, absorption studies, emission spectroscopy, and viscosity measurements. UV-vis results confirmed that the Cu complex interacted with DNA to form a ground-state complex and the observed binding constant (2× 10(4) M(-1)) is more in keeping with the groove bindings with DNA. Furthermore, the viscosity measurement result showed that the addition of complex causes no significant change on DNA viscosity and it indicated that the intercalation mode is ruled out. The thermodynamic parameters are calculated by van't Hoff equation, which demonstrated that hydrogen bonds and van der Waals interactions played major roles in the reaction. The results of circular dichroism (CD) suggested that the complex can change the conformation of DNA from B-like form toward A-like conformation. The cytotoxicity studies of the carmoisine dye and its copper complex indicated that both of them had anticancer effects on HT-29 (colon cancer) cell line and they may be new candidates for treatment of the colon cancer.

  17. Predicting Viscosity of Complex Lubricant Molecules with Ester Functional Groups using Nonequilibrium Molecular Dynamics Simulations. (United States)

    Sabuj, M. A.; Rai, Neeraj

    The knowledge of transport properties (viscosity and diffusion) are important for a number of wide range of industrial applications. Although molecular simulations have made tremendous progress in the last decade in predicting thermodynamic and transport properties based only on molecular structure, predicting viscosities with good accuracy has remained a significant challenge. Here, we use nonequilibrium molecular dynamics simulation (NEMD) to predict shear viscosity of four different but structurally similar pentaerythritol ester (PE) molecules at five different temperatures and five different pressures using the TraPPE-UA force field. Our calculations shows that TraPPE force field can predict shear viscosity values within 10 ∖% of experimental measurements. Furthermore, PE molecules absorb moistures from atmosphere; therefore, the change of viscosity was calculated in the presence of 5, 10 and 25 mole ∖% of water. Structural analysis was provided to get molecular insights and relative order of viscosity. The free volume concept can predict the pressure dependence of viscosity very well, a quantitative and rigorous analysis of the pressure dependence of viscosity was provided in terms of the free volume of the liquid. Effort sponsored by the Engineering Research & Development Center under Cooperative Agreement number W912HZ-15-2-0004.

  18. [pi] Backbonding in Carbonyl Complexes and Carbon-Oxygen Stretching Frequencies: A Molecular Modeling Exercise (United States)

    Montgomery, Craig D.


    An exercise is described that has illustrated the effect of various factors on [pi] backbonding to carbonyl ligands, where the students can view the molecular orbitals corresponding to the M-CO [pi] interaction as well as the competing interaction between the metal and co-ligands. The visual and hands-on nature of the modeling exercise has helped…

  19. Foam properties of proteins, low molecular weight surfactants and their complexes

    NARCIS (Netherlands)

    Lech, F.J.


    This thesis shows the effects that the addition of low molecular weight surfactants (LWMS) to proteins has on the foam stability of the mixture. For this, the bulk, interfacial, thin liquid films and foam properties are determined for different protein-LWMS mixtures at different molar ratios (MR).

  20. Complexity in Dioryctria zimmermani Species Group: Incongruence Between Species Limits and Molecular Diversity (United States)

    Amanda D. Roe; Daniel R. Miller; Susan J. Weller


    Dioryctria (Zeller 1846) (Lepidoptera: Pyralidae: Phycitinae) moths, commonlyknown as coneworms, are a group of important coniferous pests. InterspeciÞc overlap of molecular, morphological, and behavioral traits has made identiÞcation and delimitation of these species problematic, impeding their management and control. In particular, delimitation of members of the...