京都大学 / 新制・課程博士 / 博士(理学) / 甲第22990号 / 理博第4667号 / 新制||理||1670(附属図書館) / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)教授 山本 潤, 教授 石田 憲二, 教授 田中 耕一郎 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

La diffraction cohérente est une technique étonnante par sa simplicité expérimentale : une source XUV cohérente illumine un échantillon unique, isolé, et la figure de diffraction de l’objet est enregistrée sur une caméra CCD. Une inversion de la figure de diffraction à une image dans l’espace réel est possible grâce à une approche basée sur des algorithmes itératifs. Les techniques d’holographie par transformée de Fourier, pour lesquelles une référence est placée à proximité de l’objet que l’on veut imager, permettent-elles la reconstruction directe de l’image, même lorsque la qualité des données expérimentales est moindre. Nous disposons dans notre laboratoire d’une source compacte XUV suffisamment intense pour réaliser ce type d’expérience. Les impulsions XUV ultrabrèves (femtoseconde à attoseconde) sont produites en sélectionnant les harmoniques d’ordre élevé d’un laser infra-rouge femtoseconde focalisé dans une cellule de gaz rare. Nous avons récemment démontré la possibilité d’utiliser cette source pour l’imagerie par diffraction cohérente avec une résolution spatiale de 78 nm. De plus, nous avons démontré expérimentalement une technique d’holographie avec référence étendue, et obtenu une résolution de 110 nm en simple tir (soit un temps d’intégration de 20 femtosecondes). Une perception d’un objet en trois dimensions nous donne une meilleure compréhension de celui-ci. A l’échelle nanométrique, les techniques d’imagerie 3D sont issues de techniques tomographiques autour de la microscopie électronique. Cependant, les nombreuses prises de vue nécessaires (sous des angles différents) rendent ces techniques caduques lors de l’étude résolue en temps de phénomènes irréversibles sur des échantillons non reproductibles. Dans ce contexte, le but de ma thèse est d’étendre les techniques d’imagerie 2D à une perception 3D d’objets nanométriques (physiques, biologiques), tout en préservant l’aspect ultrarapide. Le développement d’une nouvelle technique d’imagerie cohérent 3D en seul vue, l’ankylographie, proposée par le professeur J. Miao de UCLA [Raines et al., Nature 2010] a été effectué. Cette technique permet de reconstruire l’image 3D d’un échantillon d’après une unique image de diffraction. Son principe basique est de retrouver la profondeur d’un objet 3D par l’interférence constructive longitudinale. Cependant, cette technique d’imagerie cohérent 3D est plus exigeante en termes de qualité de données expérimentales comme en moyen informatique d’analyse et d’inversion. L’autre idée en imagerie 3D est de mimer la vision humaine en utilisant deux faisceaux X cohérents arrivant simultanément sur l’échantillon mais avec un petit angle. Dans ce schéma, on utilise des références à coté de l’objet mire (holographie) pour améliorer le rapport signal sur bruit dans la figure de diffraction (soit hologramme). On recueille ensuite deux hologrammes sur le même détecteur. L’inversion Fourier de chacun des hologrammes forme deux images issues d’une vision différente de l’objet. La parallaxe est ainsi réalisée. La reconstruction stéréo de l’objet est effectuée numériquement. Enfin, des applications de démonstration seront envisagées après ma thèse. Il s’agit d’imager des objets biologiques (nanoplanktons déjà collectés et préparés au CEA). Et nous nous intéresserons également à l’étude du mouvement 3D d’objets nanométriques (azo-polymères) sur des temps ultracourts. Une autre application importante sera d’étudier la transition de phase ultra-rapide tel que le nano-domaine magnétique où des phénomnes de désaimantation induite par des impulsion femtoseconde ont lieu. / Coherent diffraction is an amazing art by its experimental simplicity: a coherent XUV source illuminates a single, isolated sample, and the diffraction pattern of the object is recorded by a CCD camera. An inversion of the diffraction pattern to an image in real space is possible through an approach based on iterative algorithms. The techniques for Fourier transform holography, for which reference is placed near the object to be imaged, allow the direct reconstruction of the image, even when the quality of the experimental data is worse. We have a laboratory sufficiently intense compact XUV source for this type of experience. The ultrashort XUV pulses (from femtosecond to attosecond) are produced by selecting high order harmonics of a femtosecond infrared laser which is focused into a cell of rare gas. We recently demonstrated the feasibility of using this source for coherent diffraction imaging with a spatial resolution of 78 nm. Furthermore, we demonstrated experimentally a holographic technique with extended reference and obtained a resolution of 110 nm in single shot (i.e. an integration time of 20 femtoseconds). A perception of an object in three dimensions gives us a better understanding thereof. A nanoscale 3D imaging techniques are from tomographic techniques of electron microscopy. However, many shots required (from different angles) make these techniques obsolete during the study time-resolved irreversible phenomena on non-reproducible samples. In this context, the aim of my thesis is to extend the 2D imaging techniques for 3D perception of nanoscale (physical, biological ) objects, while preserving the ultrafast appearance. The development of a new technology of 3D coherent imaging in single view, named ‘ankylography’, proposed by Professor Miao J. UCLA [Raines et al., Nature 2010] was made in progress. This technique allows reconstructing a 3D image of the sample after a single diffraction image. Its basic principle is to find the depth of a 3D object by the longitudinal constructive interference. However, this technique is more requested in both the quality of experimental data and the computer hardware and analysis. The other idea for 3D imaging is to imitate human vision using two coherent beams X arriving simultaneously on the sample but with a small angle. In this scheme, we use references near the target object (i.e. holography) to improve the signal to noise ratio in the diffraction pattern (hologram). Two holograms are then collected on the same detector. The inverse Fourier of each hologram forms two images from different views of the object. Parallax is thus produced. The stereo reconstruction of the object is performed by computer. Finally, the demonstration of applications will be considered after my thesis. This imaging of biological objects (such as nanoplanktons already collected and prepared CEA). And we are also interested in the study of 3D nanoscale objects (azo-polymers) movement on ultrashort time. Furthermore, another important application will be to study the ultra-fast phase transition such as nano-magnetic field where demagnetization phenomena induced by femtosecond pulse occurs.

In the last decade, there has been tremendous progress in the field of ultrashort-pulse measurement. However, this effort has focused mostly on the temporal behavior of 100-fs, 800-nm ultrashort pulse, ignoring other pulse lengths, wavelengths, and the very common space-time couplings or so called spatio-temporal distortions. In this thesis work, I do an extensive study of spatio-temporal distortions and their measurement using Frequency Resolved Optical Gating (FROG) and its relatives. I clarify some ambiguities in the descriptions of these effects in the existing theory and establish a more general description of such distortions in ultrashort pulses. I also extend these measurement techniques to different wavelengths and pulse lengths. Specifically, I develop measurement devices for few-cycle NIR pulses, weak and narrowband fiber laser pulses, long (several-ps) NIR pulses, and visible pulses from NOPAs.

Orientador: Carlos Henrique de Brito Cruz / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin / Made available in DSpace on 2018-09-27T13:12:22Z (GMT). No. of bitstreams: 1 PadilhaJunior_LazaroAurelio_D.pdf: 3832856 bytes, checksum: ee1e342cd7bc49e51127fe13ee9ed626 (MD5) Previous issue date: 2006 / Resumo: Nesta tese as propriedades ópticas lineares e não-lineares em pontos quânticos de semicondutores de band-gap diretos, CdTe e CdSe, são estudados em escala temporal de femtossegundos, especialmente aquelas propriedades importantes para aplicações em chaveamento totalmente óptico, como o tempo de resposta e a susceptibilidade de terceira ordem. Os processos de recombinação de elétrons fotoexcitados são investigados assim como seus tempos de resposta, usando um modelo teórico que considera a influência dos estados de armadilhas de superfície e da recombinação Auger. As propriedades ópticas não lineares de terceita ordem, absorção de dois fótons e efeito Kerr óptico, são estudados através de diferente técnicas experimentais: Z-scan, bombeio e prova e foto-luminescência excitada por dois fótons. Forte influência do tamanho dos nanocristais é observada, especialmente nos espectros de absorção de dois-fótons. Modelos teóricos baseados na aproximação de massa efetiva e no modelo p k de Kane são usados para descrever a influência do confinamento quântico nos processos de absorção de dois-fótons degenerados e não-degenerados. A importância da mistura das bandas de buracos é observada no ajuste teórico dos espectros de absorção de dois fótons. Finalmente, chaves totalmente ópticas operando por saturação de absorção e por controle de polarização são demonstradas para pontos quânticos de CdTe em matriz vítrea / Abstract: In this thesis the linear and non-linear optical properties of direct band-gap semiconductors, CdTe and CdSe, quantum dots are studied at femtosecond time scale, mainly those properties important for applications in all-optical switching such as response time and third order susceptibility. The photo-excited electron recombination processes are investigated as well their response time using a theoretical model considering the influence of the surface trapping states and the Auger recombination. The third order nonlinear optical properties, two-photon absorption and optical Kerr effect, are studied by different experimental techniques: Z-scan, pump and probe and two-photon induced photo-luminescence. Strong influence from the nanocrystals size is observed, especially on the two-photon absorption spectra. Theoretical models based on the effective mass approximation and Kane¿s p k model are used to describe the influence of the quantum confinement on the degenerate and non-degenerate two-photon absorption processes. The importance of the hole band mixing is easily seen from the two-photon absorption fitting. Finally, all-optical switching by absorption saturation and polarization control are demonstrated for CdTe quantum dots in doped glass / Doutorado / Propriedades Óticas e Espectroscopia da Matéria Condensada ; Outras Inter. da Matéria Com. Rad. e Part / Doutor em Ciências

La structuration des liquides près d'interfaces est liée aux forces d'interactions liquides/interface à des distances de quelques dimensions moléculaires. Cet effet universel joue un rôle primordial dans divers domaines tels que le transport de chaleur, le transport de particules à travers les membranes biologiques, la nanofluidique, la microbiologie et la nanorhéologie.Le but principal de cette thèse est de réaliser l'échographie par laser de liquides nanostructurés près d'une interface, afin de mieux comprendre les propriétés physiques de liquides confinés à des échelles moléculaires. La méthode utilisée est la technique d'acoustique picoseconde, qui est une technique tout optique impliquant des lasers impulsionnels pour la génération et la détection d'ultrasons picosecondes. Nous avons adapté la technique pour étudier les propriétés acoustiques longitudinales à haute fréquence des liquides ultra-minces. Les résultats de la diffusion de Brillouin dans le domaine temporel sont utilisés pour déterminer le profil de distribution de la température dans le volume de liquide étudié qui peut être extrapolé aux dimensions nanométriques. Les résultats sur le changement de la fréquence de Brillouin aussi bien que sur l’atténuation acoustique en fonction de la puissance du laser donnent un aperçu de la relation entre les propriétés thermiques et mécaniques des liquides. L'analyse de Fourier des résultats pour différentes épaisseurs de liquide donnent l'information sur la vitesse du son et de l’atténuation aux fréquences GHz. Ce nouveau schéma expérimental est une première étape vers la compréhension des liquides confinés mesuré par l'échographie d'ultrasons aux fréquences GHz. / The phenomenon of liquid structuring near interfaces is related to the liquid/interface interaction forces at distances of some molecular dimensions. Despite the fact that this universal structuring effect plays a key role in various fields such as heat transport, particle transport through biological membranes, nanofluidics, microbiology and nanorheology, the experimental investigation of liquid structuring remainschallenging.The aim of this PhD thesis is the experimental study of the structuring/ordering of liquids at nanoscale distances from their interfaces with solids. In this context, we have adapted the experimental technique of picosecond laser ultrasonics to investigate high-frequency longitudinal acoustic properties of ultrathin liquids confined between solid surfaces of different types. At first, we will present results of time-domain Brillouin scattering (TDBS) used to determine the temperature distribution profile in the investigated liquid volume which can be extrapolated to nanometer dimensions. Results for the evolution of the extracted Brillouin scattering frequencies and attenuation rates recorded at different laser powers give insight to the intrinsic relationship between thermal and mechanical properties of liquids. Second, we will describe our results for the measurements of mechanical properties of ultrathin liquids with a nanometric resolution. Fourier analysis of the recorded TDBS signals for different liquid thicknesses yield the value of the longitudinal speed of sound and attenuation at GHz frequencies. This novel TDBS experimental scheme is a first step towards the understanding of confined liquids measured by GHz ultrasonic probing.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2017-04-27T13:00:02Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese_Euclides_Almeida_Fisica.pdf: 5907240 bytes, checksum: 503a5b57e757a03f24206d4d3d26032c (MD5) / Made available in DSpace on 2017-04-27T13:00:02Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese_Euclides_Almeida_Fisica.pdf: 5907240 bytes, checksum: 503a5b57e757a03f24206d4d3d26032c (MD5) Previous issue date: 2012-07-30 / CNPQ / O principal objetivo deste trabalho foi investigar fenômenos ópticos ultrarrápidos em sistemas nanoestruturados empregando diferentes técnicas espectroscópicas não lineares, tanto no domínio do tempo quanto no domínio da frequência. Para fornecer uma base adequada que permita entender os experimentos feitos nessa tese, os princípios físicos das espectroscopias ópticas não lineares são apresentados. Inicialmente é apresentada uma descrição da função resposta não linear no domínio do tempo. A evolução temporal da polarização óptica, que gera o sinal espectroscópico, é descrita em detalhes usando uma teoria de perturbação diagramática. Técnicas ópticas não lineares são apresentadas, tais como eco de fótons, bombeamento-e-sonda e hole burning, assim como o comportamento dinâmico de um material pode ser interpretado a partir do sinal gerado. A técnica de mistura degenerada de quatro ondas com luz incoerente foi usada para investigar, pela primeira vez, o defasamento ultrarrápido de éxcitons em uma vitrocerâmica contendo nanocristais de niobato de sódio. O tempo de defasamento medido (T2 = 20 fs) indica qu empregada para investigar processos de transferência de carga em colóides com nanopartículas de TiO2 e rodamina 6G. O comportamento do sinal de depleção transiente é comparado com o observado para a rodamina livre suspensa em etanol. A análise dos resultados permitiu atribuir o comportamento de depleção à transferência de carga de estados excitados termalizados das moléculas de corante para a banda de condução do semicondutor e a transferência no sentido inverso do semicondutor para as moléculas. / The main objective of this work was the investigation of ultrafast optical phenomena in selected nanostructured systems employing different nonlinear spectroscopic techniques, either in the time or the frequency domain. To provide an appropriate background to understand the performed experiments the principles of nonlinear optical spectroscopies are presented. Initially a description of the nonlinear optical response function in the time domain is given. The time evolution of the optical polarization, that gives rise to the spectroscopic signal, is described in detail using a diagrammatic perturbation theory. Nonlinear optical techniques are discussed such as photon echoes, pump-and-probe and hole-burning, as well as how the dynamical behavior of a material can be interpreted from the generated signals. The degenerate four-wave mixing technique with incoherent light was used to investigate for the first time the ultrafast dephasing of excitons in a glass-ceramic containing sodium niobate nanocrystals. The short dephasing time measured (T2 = 20 fs) indicates that different dephasing channels contribute for the excitonic dephasing, namely: electron-electron scattering, electron-phonon coupling and fast trapping of electrons in defects on the nanocrystals interface. Low-temperature luminescence experiments were also performed to measure excitonic and trap states lifetimes. The persistent spectral holeburning technique was applied to measure localized surface plasmons dephasing times in colloidal silver nanoparticles capped with different stabilizing molecules. The dependence of T2 with three different stabilizers was demonstrated and theoretically analyzed. The results show that the dephasing times are shorter than the theoretically calculated T2 using the bulk dielectric functions of the metal. This discrepancy is attributed to changes in the electronic density of states at the nanoparticles interface caused by the presence of the stabilizers. Ab-initio calculations based on the Density Functional Theory were performed to further understand the interaction between the nanoparticles and stabilizing agents. The femtosecond transient absorption technique was employed to study the ultrafast dynamics of in-gap states in a glassceramics containing sodium niobate nanocrystals. Two main temporal components were found for the excited state absorption signal: a fast component, with decay time of ≈ 1 ps, and a slower component which is attributed to deep trap states. This slower component is responsible for the excited state absorption contribution in optical limiting experiments previously reported in the literature. The dynamics of the optical limiting in this sample was also studied, in the millisecond range, exciting the sample with a train of femtosecond pulses. The optical limiting behavior reflects the dynamics of population in the excited and trap states and this dynamics was modeled using rate equations for the electronic states’ populations. Finally, the pump-andprobe transient absorption technique was employed to investigate charge-transfer processes in colloids with rhodamine 6G and TiO2 nanoparticles. The transient bleaching signal behavior is compared with the one observed for unlinked rhodamine 6G dissolved in ethanol. The analysis of the results allowed the attribution of the bleaching behavior to charge-transfer from thermalized excited states of the dye molecules to the semiconductor conduction band and to the back charge-transfer from the semiconductor to the molecules.

La technique d’optique ultra-rapide pompe-sonde, qui repose sur l’emploi de lasers à impulsion ultracourte(femtoseconde), permet de déclencher et étudier des processus ultrarapides dans la matière. L’acoustique picoseconde concerne pour sa part l’étude des processus de génération et détection de phonons acoustiques haute fréquence ainsi quel’analyse des nanomatériaux avec ces phonons (nanoéchographie). Les travaux de recherche de cette thèse avaient pourbut l’étude des couplages électronphonon acoustique dans le matériau ferroélectrique BiFeO3 par acoustique ultrarapide. Nous avons pu mettre en évidence que selon l’orientation du cristal photoexcité, l’émission des phonons acoustiques cohérents longitudinaux (LA) et transverses (TA) pouvait être modulée. De manière spectaculaire, nous avons purévéler un couplage électron-phonon acoustique transverse très efficace comme cela n’avait jamais été observé jusqu’alors dans les métaux, semiconducteurs ou nanostructures artificielles. Une étude détaillée indique que le mécanismepiézoélectrique inverse semble être le moteur de ce couplage électron-phonon (Lejman et al, Nature Communications, 2014). Dans une seconde partie, nous avons montré que BFO, ainsi qu’un autre ferroélectrique biréfringent LiNbO3 (LNO), peuvent être utilisés pour la conversion de mode ultra-rapide par processus acousto-optique (manipulation de la polarisation de la lumière à l’échelle de la picoseconde avec des phonons acoustiques). Cet effet, jamais mis enévidence jusqu’alors dans le domaine GHz, pourrait potentiellement être exploité dans de nouveaux dispositifs photoniques/phononiques pour des modulations acousto-optiques à haute cadence. / Ultrafast optical pump-probe technique, by exploiting ultrashort laser pulses (femtosecond), allows to initiate and monitor ultrafast processes in matter. Picosecond acoustics is a research field that focuses on the generation and detection mechanisms of high frequency coherent acoustic phonons in different media, as well as on their application in testing of nanomaterials and nanostructures. This PhDs research project was devoted to study of electron-acoustic phonon coupling in ferroelectric BiFeO3 (bismuth ferrite, BFO) by ultrafast acoustics. We have evidenced that depending on the BFO crystal orientation it was possible to tune the coherent phonons spectrum with in particular variable amplitude of longitudinal (LA) and transverse (TA) acoustic modes. In some grains with particular crystallographic orientations much stronger TA than LA signal was observed. Spectacularly, we have revealed an efficient coupling between electron and transverse acousticphonon. Such high ratio never reported before in any metal, semiconductor or nanostructure before, can be principally attributed to the photoinduced inverse piezoelectric effect (Lejman et al Nature Communications 2014). In a second part, we have shown that BFO as well as another birefringent ferroelectric LiNbO3 (LNO) can be used for ultrafast acousto-optic modeconversion (manipulation of light polarization at the picosecond time scale with coherent acoustic phonons). This effect, never reported at GHz up to now, can be potentially applied in photonics for ultrafast manipulation of light polarization bycoherent acoustic phonons in next generation photonic/phononic devices.

L’acoustique picoseconde est une technique qui permet de générer et de détecter des ondes acoustiques de longueur d’onde submicrométrique par l’utilisation d’impulsions lumineuses ultrarapides (100 fs). Si la technique commence à être appliquée industriellement pour le contrôle non-destructif de films solides micrométriques, comme les microprocesseurs, très peu d’études concernent son application aux milieux liquides ou mous, malgré son potentiel unique pour les mesures acoustiques très hautes fréquences (supérieur à la dizaine de GHz). Ce travail de thèse dresse un premier panorama d’applications possibles de la technique d’acoustique picoseconde pour l’étude d’une cellule biologique unique, dont l’épaisseur peut être d’une centaine de nanomètres à quelques micromètres. Les résolutions atteintes permettent des applications pour l’imagerie et la tomographie acoustique d’une cellule unique par la détermination locale de ses propriétés physiques. Un modèle de simulation analytique est développé pour aider à la compréhension des signaux détectés et pour la résolution du problème inverse. La génération acoustique est simulée en résolvant les équations couplées de diffusion de la chaleur et de la propagation acoustique. La détection optique est ensuite étudiée en résolvant l’équation de Maxwell où les phénomènes thermiques et acoustiques perturbent l’indice optique du matériau. Pour les besoins expérimentaux, une enceinte biologique, étanche et thermostatée, est conçue. De même, le montage laser est adapté pour permettre une détection bicolore de l’onde acoustique se propageant dans la cellule. Enfin, un microscope combinant la visualisation des cellules par épifluorescence au dispositif laser expérimental est développé. Ce dernier permet de localiser précisément les éléments subcellulaires de la cellule, pour ensuite les étudier par acoustique picoseconde. La démonstration du potentiel de la méthode pour l’imagerie cellulaire et l’évaluation de sa sensibilité est faite sur cellule végétale. Ensuite, une mesure quantitative des propriétés viscoélastiques de cellules ostéoblastes (MC3T3-E1), adhérentes sur un matériau mimant une prothèse de titane, est réalisée. Puis, l’effet du peptide RGD et de la protéine BMP-2 sur les propriétés viscoélastiques de la cellule ostéoblaste est quantifié. Ce travail est réalisé en partenariat avec une équipe de recherche en bio-ingénierie et reconstruction tissulaire, l’U577. / The picosecond ultrasonics technique is well suited to generate and to probe acoustic waves of submicromic wavelength using ultrafast light pulses (100 fs). If the technique starts to be used for non-destructive testing in industry, for micrometric solid films (microprocessor) for example, very few applications concern liquids or soft media, despite its unique potential for acoustic measurements at very high acoustic frequencies (up to ten GHz). This PhD study gives a first comprehensive overview of the applications of the picosecond ultrasonics technique for the study of a single biological cell, the thickness of which can be from around 100 nm to a few µm. Measurement accuracy is high enough for imaging a single cell and for evaluating its local physical properties. To understand the detected data, an analytical model is developed. This model is used too for the inverse model resolution. The acoustic generation is simulated solving the coupled equations of heat diffusion and of acoustic wave propagation. Optical detection is then studied solving the Maxwell equations where both thermal and acoustic phenomena perturb optical index of the media. For experiments, a biocompatible sample holder, leakproof and thermocontrolled, is built. In the same way, the optical experimental setup is adapted to allow a two color probing of the ultrafast photo-acoustic response in a single cell. Finally, a microscope combining cell fluorescence visualisation and the picosecond ultrasonic laser setup is developed. It allows to localize precisely the cell sub-components and to probe them by the picosecond ultrasonics technique. The demonstration of the technique for the single cell imaging and the evaluation of its accuracy is performed on vegetal cells. Then, a quantitative measurement of the viscoelastic properties of single osteoblast cells (MC3T3-E1), adhering on a bone substitute material (Ti6Al4V), is performed. RGD peptide and BMP-2 proteins effects on the cell osteoblast viscoelastic properties are quantified. This work is performed with a tissue or bone substitute engineering research team.

Investigations of soft matter using ultrashort high intensity pulses have been made possible through the advent of X-ray free-electrons lasers. The last decade has seen the development of a new type of protein crystallography where femtosecond dynamics can be studied, and single particle imaging with atomic resolution is on the horizon. The pulses are so intense that any sample quickly turns into a plasma. This thesis studies the ultrafast transition from soft matter to warm dense matter, and the implications for structural determination of proteins.                    We use non-thermal plasma simulations to predict ultrafast structural and electron dynamics. Changes in atomic form factors due to the electronic state, and displacement as a function of temperature, are used to predict Bragg signal intensity in protein nanocrystals. The damage processes started by the pulse will gate the diffracted signal within the pulse duration, suggesting that long pulses are useful to study protein structure. This illustrates diffraction-before-destruction in crystallography. The effect from a varying temporal photon distribution within a pulse is also investigated. A well-defined initial front determines the quality of the diffracted signal. At lower intensities, the temporal shape of the X-ray pulse will affect the overall signal strength; at high intensities the signal level will be strongly dependent on the resolution. Water is routinely used to deliver biological samples into the X-ray beam. Structural dynamics in water exposed to intense X-rays were investigated with simulations and experiments. Using pulses of different duration, we found that non-thermal heating will affect the water structure on a time scale longer than 25 fs but shorter than 75 fs. Modeling suggests that a loss of long-range coordination of the solvation shells accounts for the observed decrease in scattering signal. The feasibility of using X-ray emission from plasma as an indicator for hits in serial diffraction experiments is studied. Specific line emission from sulfur at high X-ray energies is suitable for distinguishing spectral features from proteins, compared to emission from delivery liquids. We find that plasma emission continues long after the femtosecond pulse has ended, suggesting that spectrum-during-destruction could reveal information complementary to diffraction.