Fluorescence correlation spectroscopy reveals fast optical excitation-driven intramolecular dynamics of yellow fluorescent proteins

Fast excitation-driven fluctuations in the fluorescence emission of yellow-shifted green fluorescent protein mutants T203Y and T203F, with S65G/S72A, are discovered in the 10−6–10−3-s time range, by using fluorescence correlation spectroscopy at 10−8 M. This intensity-dependent flickering is conspicuous at high pH, with rate constants independent of pH and viscosity with a minor temperature effect. The mean flicker rate increases linearly with excitation intensity for at least three decades, but the mean dark fraction of the molecules undergoing these dynamics is independent of illumination intensity over ≈6 × 102 to 5 × 106 W/cm2. These results suggest that optical excitation establishes an equilibration between two molecular states of different spectroscopic properties that are coupled only via the excited state as a gateway. This reversible excitation-driven transition has a quantum efficiency of ≈10−3. Dynamics of external protonation, reversibly quenching the fluorescence, are also observed at low pH in the 10- to 100-μs time range. The independence of these two bright–dark flicker processes implies the existence of at least two separate dark states of these green fluorescent protein mutants. Time-resolved fluorescence measurements reveal a single exponential decay of the excited state population with 3.8-ns lifetime, after 500-nm excitation, that is pH independent. Our fluorescence correlation spectroscopy results are discussed in terms of recent theoretical studies that invoke isomerization of the chromophore as a nonradiative channel of the excited state relaxation.

Monitoring the GAP catalyzed H-Ras GTPase reaction at atomic resolution in real time

The molecular reaction mechanism of the GTPase-activating protein (GAP)-catalyzed GTP hydrolysis by Ras was investigated by time resolved Fourier transform infrared (FTIR) difference spectroscopy using caged GTP (P3-1-(2-nitro)phenylethyl guanosine 5′-O-triphosphate) as photolabile trigger. This approach provides the complete GTPase reaction pathway with time resolution of milliseconds at the atomic level. Up to now, one structural model of the GAP⋅Ras⋅GDP⋅AlFx transition state analog is known, which represents a “snap shot” along the reaction-pathway. As now revealed, binding of GAP to Ras⋅GTP shifts negative charge from the γ to β phosphate. Such a shift was already identified by FTIR in GTP because of Ras binding and is now shown to be enhanced by GAP binding. Because the charge distribution of the GAP⋅Ras⋅GTP complex thus resembles a more dissociative-like transition state and is more like that in GDP, the activation free energy is reduced. An intermediate is observed on the reaction pathway that appears when the bond between β and γ phosphate is cleaved. In the intermediate, the released Pi is strongly bound to the protein and surprisingly shows bands typical of those seen for phosphorylated enzyme intermediates. All these results provide a mechanistic picture that is different from the intrinsic GTPase reaction of Ras. FTIR analysis reveals the release of Pi from the protein complex as the rate-limiting step for the GAP-catalyzed reaction. The approach presented allows the study not only of single proteins but of protein–protein interactions without intrinsic chromophores, in the non-crystalline state, in real time at the atomic level.

Fotofísica de enodionas

Em 1906, Albrecht obteve a primeira enodiona conhecida, ao reagir benzoquinona com ciclopentadieno. A estrutura desta enodiona somente foi elucidada em 1928, por Diels e Alder que, entretanto, perceberam ser possív.el existirem dois diferentes isômeros para o composto em questão: endo e exo. A descoberta, em 1958, da reação de fotocilização deste aduto de Diels-Alder, por Cookson e colaboradores, demonstrou que se tratava do isômero endo e esta reação passou a ser utilizada para se comprovar a configuração endo de vários compostos de estrutura análoga. Porém, apesar de sua importância histórica como método para comprovar a configuração dos adutos de Diels-Alder, os dados disponíveis até hoje são insuficientes para o esclarecimento dos processos subjacentes à fotociclização desses compostos, especialmente porque hoje sabemos que existem adutos de configuração endo que não fotociclizam. Visando aumentar o conhecimento sobre o comportamento destes adutos frente à reação de fotociclização, determinaram-se seus espectros de absorção (na região do UVNisível) e de emissão de luminescência e concluiu-se, com base em nossos resultados e daqueles relatados na literatura, que o fato de não ocorrer a fotociclização de alguns adutos de configuração endo não depende exclusivamente da estabilidade dos estados excitados envolvidos, ainda que essa característica e a natureza destes certamente afete os rendimentos quânticos da reação. Antes, parece-nos que estruturas que permitam deslocalizar um dos elétrons do birradical intermediariamente formado neste processo propiciam a reversão deste intermediário ao reagente, ao invés de se formar o produto de fotociclização. Alem disso, reinvestigamos a reação de fotoisomerização endo → exo do aduto de benzoquinona e ciclopentadieno, por irradiação em etanol/trietil-amina, relatada por Pandey e colaboradores em 1990, tendo verificado que tal isomerização não ocorre nas condições descritas na literatura, obtendo-se, ao invés disso, principalmente o tautômero aromático da enodiona e seu produto de fotociclização. Por outro lado, descobrimos que, deixar em repouso, no escuro, o aduto de benzoquinona e ciclopentadieno em etanol/trietil-amina conduz,a um dímero deste aduto, não descrito previamente.

Spin splitting in a polarized quasi-two-dimensional exciton gas

We have observed a large spin splitting between "spin" +1 and -1 heavy-hole excitons, having unbalanced populations, in undoped GaAs/AlAs quantum wells in the absence of any external magnetic field. Time-resolved photoluminescence spectroscopy, under excitation with circularly polarized light, reveals that, for high excitonic density and short times after the pulsed excitation, the emission from majority excitons lies above that of minority ones. The amount of the splitting, which can be as large as 50% of the binding energy, increases with excitonic density and presents a time evolution closely connected with the degree of polarization of the luminescence. Our results are interpreted on the light of a recently developed model, which shows that, while intraexcitonic exchange interaction is responsible for the spin relaxation processes, exciton-exciton interaction produces a breaking of the spin degeneracy in two-dimensional semiconductors.

Investigations of infra-red spectra ...

Pt. V-VII have title: Supplementary investigations of infra-red spectra.

Energy transfer dynamics of nanocrystal-polymer composites

Steady-state and time-resolved photoluminescence spectroscopy are used to examine the photoluminescent properties of nanocrystal-polymer composites consisting of colloidal PbS nanocrystals blended with poly(2-methoxy-5(2-ethylhexyloxy)-p-phenylene vinylene). Quenching of the emission from the conjugated polymer due to the PbS nanocrystals is observed along with band edge emission from the ligand capped PbS nanocrystals. A decrease in the photoluminescence lifetime of MEH-PPV is also observed in the thin film nanocrystal-polymer composite materials. Photoluminescence excitation spectroscopy of the PbS nanocrystal emission from the composite shows features attributed to MEH-PPV providing evidence of a Forster transfer process.

Quantitative fluorescence spectra and quantum yield map of synthetic pheomelanin

Spectroscopic studies of pheomelanin and its constituents have been sparse. These data present what is by far the most complete description of the fluorescence characteristics of synthetic pheomelanin. Emission spectra between 260 and 600 nm were acquired,for excitation wavelengths between 250 and 500 nm at 1-nm intervals. A quantum yield map is also presented, correcting the fluorescence intensities for differences in species concentration and molar absorptivity. These fluorescence features exhibit interesting similarities and differences to eumelanin, and these data are interpreted with respect to possible chemical structures. Overall, these data suggest that pheomelanin oligomers may be more tightly coupled than those of eumelanin. Finally, the quantum yield is shown to be on the order of 10(-4) and exhibit a complex dependence on excitation energy, varying by a factor of 4 across the energies employed here. (c) 2006 Wiley Periodicals, Inc.

Asymptotic theory of time varying networks with memory and heterogeneous activation pattern

In this thesis work we develop a new generative model of social networks belonging to the family of Time Varying Networks. The importance of correctly modelling the mechanisms shaping the growth of a network and the dynamics of the edges activation and inactivation are of central importance in network science. Indeed, by means of generative models that mimic the real-world dynamics of contacts in social networks it is possible to forecast the outcome of an epidemic process, optimize the immunization campaign or optimally spread an information among individuals. This task can now be tackled taking advantage of the recent availability of large-scale, high-quality and time-resolved datasets. This wealth of digital data has allowed to deepen our understanding of the structure and properties of many real-world networks. Moreover, the empirical evidence of a temporal dimension in networks prompted the switch of paradigm from a static representation of graphs to a time varying one. In this work we exploit the Activity-Driven paradigm (a modeling tool belonging to the family of Time-Varying-Networks) to develop a general dynamical model that encodes fundamental mechanism shaping the social networks' topology and its temporal structure: social capital allocation and burstiness. The former accounts for the fact that individuals does not randomly invest their time and social interactions but they rather allocate it toward already known nodes of the network. The latter accounts for the heavy-tailed distributions of the inter-event time in social networks. We then empirically measure the properties of these two mechanisms from seven real-world datasets and develop a data-driven model, analytically solving it. We then check the results against numerical simulations and test our predictions with real-world datasets, finding a good agreement between the two. Moreover, we find and characterize a non-trivial interplay between burstiness and social capital allocation in the parameters phase space. Finally, we present a novel approach to the development of a complete generative model of Time-Varying-Networks. This model is inspired by the Kaufman's adjacent possible theory and is based on a generalized version of the Polya's urn. Remarkably, most of the complex and heterogeneous feature of real-world social networks are naturally reproduced by this dynamical model, together with many high-order topological properties (clustering coefficient, community structure etc.).

Periodic polymer photonic bandgap structures for on-chip optical cavities

Integrated on-chip optical platforms enable high performance in applications of high-speed all-optical or electro-optical switching, wide-range multi-wavelength on-chip lasing for communication, and lab-on-chip optical sensing. Integrated optical resonators with high quality factor are a fundamental component in these applications. Periodic photonic structures (photonic crystals) exhibit a photonic band gap, which can be used to manipulate photons in a way similar to the control of electrons in semiconductor circuits. This makes it possible to create structures with radically improved optical properties. Compared to silicon, polymers offer a potentially inexpensive material platform with ease of fabrication at low temperatures and a wide range of material properties when doped with nanocrystals and other molecules. In this research work, several polymer periodic photonic structures are proposed and investigated to improve optical confinement and optical sensing. We developed a fast numerical method for calculating the quality factor of a photonic crystal slab (PhCS) cavity. The calculation is implemented via a 2D-FDTD method followed by a post-process for cavity surface energy radiation loss. Computational time is saved and good accuracy is demonstrated compared to other published methods. Also, we proposed a novel concept of slot-PhCS which enhanced the energy density 20 times compared to traditional PhCS. It combines both advantages of the slot waveguide and photonic crystal to localize the high energy density in the low index material. This property could increase the interaction between light and material embedded with nanoparticles like quantum dots for active device development. We also demonstrated a wide range bandgap based on a one dimensional waveguide distributed Bragg reflector with high coupling to optical waveguides enabling it to be easily integrated with other optical components on the chip. A flexible polymer (SU8) grating waveguide is proposed as a force sensor. The proposed sensor can monitor nN range forces through its spectral shift. Finally, quantum dot - doped SU8 polymer structures are demonstrated by optimizing spin coating and UV exposure. Clear patterns with high emission spectra proved the compatibility of the fabrication process for applications in optical amplification and lasing.

Energy transfer rates and population inversion investigation of sup(1)Gsub(4) and sup(1)Dsub(2) excited states of Tmsup(3+) in Yb:Tm:Nd:KYsub(3)Fsub(10) crystals

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

It’s a Trap! Unravelling Reversible Charge Trapping in Nanocrystals Through Single Particle and Ensemble Studies

Thesis (Ph.D.)--University of Washington, 2016-08

Dynamics of coupled modes in two-section semiconductor lasers with saturable absorption

Semiconductor lasers have the potential to address a number of critical applications in advanced telecommunications and signal processing. These include applications that require pulsed output that can be obtained from self-pulsing and mode-locked states of two-section devices with saturable absorption. Many modern applications place stringent performance requirements on the laser source, and a thorough understanding of the physical mechanisms underlying these pulsed modes of operation is therefore highly desirable. In this thesis, we present experimental measurements and numerical simulations of a variety of self-pulsation phenomena in two-section semiconductor lasers with saturable absorption. Our theoretical and numerical results will be based on rate equations for the field intensities and the carrier densities in the two sections of the device, and we establish typical parameter ranges and assess the level of agreement with experiment that can be expected from our models. For each of the physical examples that we consider, our model parameters are consistent with the physical net gain and absorption of the studied devices. Following our introductory chapter, the first system that we consider is a two-section Fabry-Pérot laser. This example serves to introduce our method for obtaining model parameters from the measured material dispersion, and it also allows us to present a detailed discussion of the bifurcation structure that governs the appearance of selfpulsations in two-section devices. In the following two chapters, we present two distinct examples of experimental measurements from dual-mode two-section devices. In each case we have found that single mode self-pulsations evolve into complex coupled dualmode states following a characteristic series of bifurcations. We present optical and mode resolved power spectra as well as a series of characteristic intensity time traces illustrating this progression for each example. Using the results from our study of a twosection Fabry-Pérot device as a guide, we find physically appropriate model parameters that provide qualitative agreement with our experimental results. We highlight the role played by material dispersion and the underlying single mode self-pulsing orbits in determining the observed dynamics, and we use numerical continuation methods to provide a global picture of the governing bifurcation structure. In our concluding chapter we summarise our work, and we discuss how the presented results can inform the development of optimised mode-locked lasers for performance applications in integrated optics.

Functional surface chemistry of carbon-based nanostructures

The recently discovered abilities to synthesize single-walled carbon nanotubes and prepare single layer graphene have spurred interest in these sp2-bonded carbon nanostructures. In particular, studies of their potential use in electronic devices are many as silicon integrated circuits are encountering processing limitations, quantum effects, and thermal management issues due to rapid device scaling. Nanotube and graphene implementation in devices does come with significant hurdles itself. Among these issues are the ability to dope these materials and understanding what influences defects have on expected properties. Because these nanostructures are entirely all-surface, with every atom exposed to ambient, introduction of defects and doping by chemical means is expected to be an effective route for addressing these issues. Raman spectroscopy has been a proven characterization method for understanding vibrational and even electronic structure of graphene, nanotubes, and graphite, especially when combined with electrical measurements, due to a wealth of information contained in each spectrum. In Chapter 1, a discussion of the electronic structure of graphene is presented. This outlines the foundation for all sp2-bonded carbon electronic properties and is easily extended to carbon nanotubes. Motivation for why these materials are of interest is readily gained. Chapter 2 presents various synthesis/preparation methods for both nanotubes and graphene, discusses fabrication techniques for making devices, and describes characterization methods such as electrical measurements as well as static and time-resolved Raman spectroscopy. Chapter 3 outlines changes in the Raman spectra of individual metallic single-walled carbon nantoubes (SWNTs) upon sidewall covalent bond formation. It is observed that the initial degree of disorder has a strong influence on covalent sidewall functionalization which has implications on developing electronically selective covalent chemistries and assessing their selectivity in separating metallic and semiconducting SWNTs. Chapter 4 describes how optical phonon population extinction lifetime is affected by covalent functionalization and doping and includes discussions on static Raman linewidths. Increasing defect concentration is shown to decrease G-band phonon population lifetime and increase G-band linewidth. Doping only increases G-band linewidth, leaving non-equilibrium population decay rate unaffected. Phonon mediated electron scattering is especially strong in nanotubes making optical phonon decay of interest for device applications. Optical phonon decay also has implications on device thermal management. Chapter 5 treats doping of graphene showing ambient air can lead to inadvertent Fermi level shifts which exemplifies the sensitivity that sp2-bonded carbon nanostructures have to chemical doping through sidewall adsorption. Removal of this doping allows for an investigation of electron-phonon coupling dependence on temperature, also of interest for devices operating above room temperature. Finally, in Chapter 6, utilizing the information obtained in previous chapters, single carbon nanotube diodes are fabricated and characterized. Electrical performance shows these diodes are nearly ideal and photovoltaic response yields 1.4 nA and 205 mV of short circuit current and open circuit voltage from a single nanotube device. A summary and discussion of future directions in Chapter 7 concludes my work.

A comparative study of the photophysics and photochemistry of 4-chlorophenol adsorbed on silicalite and beta-cyclodextrin

The photochemistry and photophysics of 4-chlorophenol (4-CP) were studied onto two model solid supports, silicalite and beta-cyclodextrin (beta-Cl)), using time resolved diffuse reflectance techniques and product degradation analysis. The results have shown that the photochemistry and photophysics of 4-CP are different from solution and depend on the solid. Ground state diffuse reflectance and time resolved luminescence demonstrated the inclusion of the probe in both substrates. 4-CP exhibits room temperature luminescence in both hosts, being structured and much more intense in beta-CD. The emission was assigned to phosphorescence of the inclusion complex. Transient absorption demonstrated the formation of the unsubstituted phenoxyl radical and of 4-chlorophenoxyl radical in beta-CD. In silicalite only the later was detected. The studies of the photodegradation products indicate that phenol is the main photoproduct in beta-CD. In silicalite the chromatographic analysis indicates the presence of products that involve the ring cleavage. (C) 2002 Elsevier Science B.V. All rights reserved.