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Simulace procesů v buněčných membránách / Simulation of processes in cellular membranesTimr, Štěpán January 2013 (has links)
Probing orientations of fluorescent molecules embedded in or attached to cell membranes has a great potential to reveal information on membrane structure and processes occurring in living cells. In this thesis, we first describe one- and two-photon linear dichroism measurements on a fluorescent probe embedded in a phospholipid membrane with a well- defined lipid composition. On the basis of experimental data, we determine the distribution of the angle between the one-photon transition dipole moment of the probe and the membrane normal. At the same time, we perform molecular dynamics simulations of the fluorescent probe and quantum calculations of its one-photon and two-photon absorption properties. By comparing the orientational distribution gained from experiments with that predicted by simulations, we test the ability of linear dichroism measurements to report on the orientation of a fluorescent molecule in a lipid membrane. We also examine the applicability of molecular simulations as a basis for the interpretation of experimental data.
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Anisotropické optické vlastnosti fluorescentních proteinů / Anisotropické optické vlastnosti fluorescentních proteinůRybakova, Olga January 2020 (has links)
Fluorescent proteins (FPs) are the workhorses of biological molecular imaging. Important imaging modalities (such as polarization microscopy or FRET imaging) exploit anisotropic optical properties of fluorescent proteins. In this thesis, we present the results of our polarization microscopy and X-ray diffraction experiments on FP crystals, as well as mathematical interpretation of these results, yielding information on the directionality of one- and two-photon absorption within the investigated fluorescent protein molecules. For the anisotropy of one-photon absorption, we determine the transition dipole moment (TDM) orientations in three representative fluorescent proteins. Validation with available quantum mechanical predictions values and an experimentally determined TDM orientation of the GFP gives confidence to the results obtained. For the two-photon absorption, we first test our hypothesis that two-photon absorptivity tensors of representative FPs exhibit vector-like behaviour and then examine the applicability of this simplification as a basis for the interpretation of our two-photon polarization microscopy data.
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Anisotropie de la photoluminescence dans des nanostructures organiques chirales autoassembléesGosselin, Benoit 08 1900 (has links)
Nous investiguons dans ce travail la dynamique des excitons dans une couche mince
d’agrégats H autoassemblés hélicoïdaux de molécules de sexithiophène. Le couplage intermoléculaire
(J=100 meV) place ce matériau dans la catégorie des semi-conducteurs à
couplage de type intermédiaire. Le désordre énergétique et la forte interaction électronsphonons
causent une forte localisation des excitons. Les espèces initiales se ramifient
en deux états distincts : un état d’excitons autopiégés (rendement de 95 %) et un état à
transfert de charge (rendement de 5%). À température de la pièce (293K), les processus
de sauts intermoléculaires sont activés et l’anisotropie de la fluorescence décroît rapidement
à zéro en 5 ns.
À basse température (14K), les processus de sauts sont gelés. Pour caractériser la dynamique
de diffusion des espèces, une expérience d’anisotropie de fluorescence a été
effectuée. Celle-ci consiste à mesurer la différence entre la photoluminescence polarisée
parallèlement au laser excitateur et celle polarisée perpendiculairement, en fonction du
temps. Cette mesure nous donne de l’information sur la dépolarisation des excitons, qui
est directement reliée à leur diffusion dans la structure supramoléculaire.
On mesure une anisotropie de 0,1 après 20 ns qui perdure jusqu’à 50ns. Les états à
transfert de charge causent une remontée de l’anisotropie vers une valeur de 0,15 sur
une plage temporelle allant de 50 ns jusqu’à 210 ns (période entre les impulsions laser).
Ces résultats démontrent que la localisation des porteurs est très grande à 14K,
et qu’elle est supérieure pour les espèces à transfert de charge. Un modèle numérique
simple d’équations différentielles à temps de vie radiatif et de dépolarisation constants
permet de reproduire les données expérimentales. Ce modèle a toutefois ses limitations,
notamment en ce qui a trait aux mécanismes de dépolarisation des excitons. / In this work, we investigate exciton dynamics in a thin film of sexithiophene molecules
in self-assembled chiral H-aggregate supramolecular stacks. The intermolecular coupling
energy J=100 meV places those molecules in the intermediate coupling regime.
The energetic disorder and the strong phonon-electron interactions leads to high localization
of the photoexcitations. The initial photoexcited species branches into two distinct
states : self-trapped exciton (95% yield) and charge-transfer excitons (5% yield). At
room temperature (293K), the intermolecular hopping processes are thermaly activated
and the fluorescence anisotropy goes to zero within 5 ns.
At low temperature (14K), hopping processes are frozen. To characterize exciton diffusion
mechanisms, a fluorescence anisotropy experiment has been done. This measurement
consists of monitoring the difference between the parallel and perpendicular composants
of the photoluminescence (with respect to the laser beam), as a function of time.
The fluorescence anisotropy gives us information about the depolarization of the excitons,
which is directly connected with their diffusion within the supramolecular stack.
We measure an anisotropy of 0,1 after 20 ns which stays constant for 50 ns. Chargetransfer
states induce a rise of the anisotropy up to 0,15 between 50 ns and 210 ns (the
period between adjacent laser pulses). Those measurements shows that exciton localization
is very strong at 14K and higher for the charge-transfer states than the self-trapped
ones. A simple mathematical model based on the resolution of a system of differential
equations with constants radiative and depolarization lifetimes can reproduce the experimental
data. This model has some limitations, especially for the description of the
depolarization mechanisms of the self-trapped excitons.
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Anisotropie de la photoluminescence dans des nanostructures organiques chirales autoassembléesGosselin, Benoit 08 1900 (has links)
Nous investiguons dans ce travail la dynamique des excitons dans une couche mince
d’agrégats H autoassemblés hélicoïdaux de molécules de sexithiophène. Le couplage intermoléculaire
(J=100 meV) place ce matériau dans la catégorie des semi-conducteurs à
couplage de type intermédiaire. Le désordre énergétique et la forte interaction électronsphonons
causent une forte localisation des excitons. Les espèces initiales se ramifient
en deux états distincts : un état d’excitons autopiégés (rendement de 95 %) et un état à
transfert de charge (rendement de 5%). À température de la pièce (293K), les processus
de sauts intermoléculaires sont activés et l’anisotropie de la fluorescence décroît rapidement
à zéro en 5 ns.
À basse température (14K), les processus de sauts sont gelés. Pour caractériser la dynamique
de diffusion des espèces, une expérience d’anisotropie de fluorescence a été
effectuée. Celle-ci consiste à mesurer la différence entre la photoluminescence polarisée
parallèlement au laser excitateur et celle polarisée perpendiculairement, en fonction du
temps. Cette mesure nous donne de l’information sur la dépolarisation des excitons, qui
est directement reliée à leur diffusion dans la structure supramoléculaire.
On mesure une anisotropie de 0,1 après 20 ns qui perdure jusqu’à 50ns. Les états à
transfert de charge causent une remontée de l’anisotropie vers une valeur de 0,15 sur
une plage temporelle allant de 50 ns jusqu’à 210 ns (période entre les impulsions laser).
Ces résultats démontrent que la localisation des porteurs est très grande à 14K,
et qu’elle est supérieure pour les espèces à transfert de charge. Un modèle numérique
simple d’équations différentielles à temps de vie radiatif et de dépolarisation constants
permet de reproduire les données expérimentales. Ce modèle a toutefois ses limitations,
notamment en ce qui a trait aux mécanismes de dépolarisation des excitons. / In this work, we investigate exciton dynamics in a thin film of sexithiophene molecules
in self-assembled chiral H-aggregate supramolecular stacks. The intermolecular coupling
energy J=100 meV places those molecules in the intermediate coupling regime.
The energetic disorder and the strong phonon-electron interactions leads to high localization
of the photoexcitations. The initial photoexcited species branches into two distinct
states : self-trapped exciton (95% yield) and charge-transfer excitons (5% yield). At
room temperature (293K), the intermolecular hopping processes are thermaly activated
and the fluorescence anisotropy goes to zero within 5 ns.
At low temperature (14K), hopping processes are frozen. To characterize exciton diffusion
mechanisms, a fluorescence anisotropy experiment has been done. This measurement
consists of monitoring the difference between the parallel and perpendicular composants
of the photoluminescence (with respect to the laser beam), as a function of time.
The fluorescence anisotropy gives us information about the depolarization of the excitons,
which is directly connected with their diffusion within the supramolecular stack.
We measure an anisotropy of 0,1 after 20 ns which stays constant for 50 ns. Chargetransfer
states induce a rise of the anisotropy up to 0,15 between 50 ns and 210 ns (the
period between adjacent laser pulses). Those measurements shows that exciton localization
is very strong at 14K and higher for the charge-transfer states than the self-trapped
ones. A simple mathematical model based on the resolution of a system of differential
equations with constants radiative and depolarization lifetimes can reproduce the experimental
data. This model has some limitations, especially for the description of the
depolarization mechanisms of the self-trapped excitons.
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Estudo teórico da forma de linha de absorção do poli(p-fenileno vinileno)Silva, Marcelo Castanheira da 05 November 2013 (has links)
Fundação de Amparo a Pesquisa do Estado de Minas Gerais / In this work we made a theoretical study of absorption line-shape of poly (pphenylene
vinylene) (PPV). The model was applied in films processed by techniques:
spin-coating (SC), layer-by-layer (LbL), and Langmuir-Blodgett (LB). The probability
of electronic transitions was calculated based on the molecular model of excitons,
Franck-Condon states, Gaussian distribution of non-entangled chains with conjugate
degree n, semi-empirical parameterization of energy gap, electric dipole moment, and
electron-vibrational mode coupling. Based on the approach of the energy gap functional
dependence 1/n, the inclusion of the non-homogeneity energy dispersion 1/n2 is
essential to obtain good experimental data agreement, mainly, where the absorption
spectra display peaks width of about 65 meV. For unresolved absorption spectra, such
as those observed for a large number of conjugated polymers processed via spin-coating
technique, for example, the non-homogeneity energy dispersion parameterization is not
significant. We develop a model to describe the possible chemical reactions of
conversion of poly(xylyliden tetrahydrothiophenium chloride) (PTHT) monomers to
PPV monomers and PPV monomers in others monomers of different degrees of
conjugation. The dependence 1/n of the functional energy gap was compared with
experimental data oligomers and calculations optimized geometry by Density
Functional Theory (DFT). Effects of exciton confinement were considered in the
transition dipole moment functional. Simulations to calculate the oscillator strength of
the absorption spectra in PPV oligomers indicate that the HOMO-LUMO state prevails
over other excited states. Results obtained from the use of the distribution of the random
walk are as good as those achieved by the use of Gaussian distribution of conjugated
segments in simulations of absorption spectra of the PPV. The use of transition dipole
moment functional, which includes the effect of exciton confinement together with the
distribution of the random walk provide good results in adjustments theoretical
absorption spectra of PPV with more consistent physical parameters. / Nesse trabalho fizemos um estudo teórico da forma de linha de absorção do
poli(p-fenileno vinileno) (PPV). O modelo foi aplicado em filmes processados pelas
técnicas: spin-coating (SC), layer-by-layer (LbL) e Langmuir-Blodgett (LB). A
probabilidade de transição eletrônica foi calculada com base no modelo do exciton
molecular, estados de Franck-Condon, distribuição Gaussiana de cadeias não
emaranhadas com grau de conjugação n, parametrização semi-empírica do gap de
energia, do momento de dipolo elétrico e do acoplamento eletrônico vibracional.
Baseamos na aproximação do funcional do gap de energia de dependência 1/n, a
inclusão da dispersão de energia não homogênea 1/n2, que é essencial para se obter uma
boa concordância com os dados experimentais, principalmente em casos, onde o
espectro de absorção apresenta picos com largura de aproximadamente 65 meV. Em
espectros de filmes pouco definidos, tais como os processados pela técnica spin-coating,
a dispersão de energia não homogênea não é significativa. Desenvolvemos um modelo
para descrever as possíveis reações químicas de conversão de monômeros de poli-
(cloreto de xilideno tetrahidrotiofeno) (PTHT) em PPV e de monômeros de PPV em
outros de diferentes graus de conjugação. A dependência 1/n do funcional do gap de
energia foi comparada com dados experimentais de oligômeros de PPV e cálculos
otimizados da geometria pela Teoria do Funcional da Densidade (DFT). Efeitos de
confinamento de exciton foram considerados no funcional do momento de dipolo de
transição eletrônica. Simulações feitas para calcular a força de oscilador no espectro de
absorção em oligômeros de PPV indicam que o estado HOMO-LUMO prevalece sobre
outros estados excitados. Resultados obtidos pelo uso da distribuição do passeio
aleatório são tão bons quanto aos realizados pelo uso da distribuição Gaussiana de
segmentos conjugados em simulações de espectros de absorção do PPV. O uso do
funcional do momento de dipolo de transição, que inclui efeito de confinamento de
excitons, junto com a distribuição do passeio aleatório propiciam bons resultados nos
ajustes teóricos de espectros de absorção do PPV com parâmetros físicos mais
consistentes. / Doutor em Física
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