Untersuchung von Magnetostriktiven und Piezotronischen Mikrostrukturen und Materialien für biomagnetische Sensoren mittels Röntgenstrahlen

Detecting electric potential differences from the human physiology is an established technique in medical diagnosis, e.g., as electrocardiogram. It arises from a changing electrical polarization of living cells. Simultaneously, biomagnetism is induced and can be utilized for medical examinations, as well. Benefits in using magnetic signals are, no need for direct skin contact and an increased spatial resolution, e.g., for mapping brain activity, especially in combination with electrical examinations. But biomagnetic signals are very weak and, thus, highly sensitive devices are necessary. The development of small and easy to use biomagnetic sensors, with a sufficient sensitivity, is the goal of the Collaborative Research Centre 1261 - Magnetoelectric Sensors: From Composite Materials to Biomagnetic Diagnostics. This thesis was written as part of this collaboration, with the main focus on the investigation of crystalline structures and structure related properties of piezotronic and magnetostrictive materials by utilizing a selection of X-ray techniques, i.e., X-ray diffraction (XRD), X-ray reflectivity (XRR) and coherent X-ray diffraction imaging (CXDI). Piezotronics, realized by combining piezoelectricity and Schottky contacts in one structure, provides a promising path to enhance sensor sensitivity. A first study investigated the crystalline structure of three piezotronic ZnO rods, spatially resolved by scanning nano XRD and combined with electrical examinations of their Schottky contact properties. It is found that the crystalline quality has a clear impact on the electrical properties of the related Schottky contact, probably due to crystalline defects. A complementary transmission electron microscopy (TEM) and XRD study performed on hybride vapor phase epitaxy (HVPE) grown GaN showed a slight, photoelectrochemical etching related relaxion of strain originating from crystal growth. In a separate study, CXDI was utilized for three-dimensional visualization of strain in a gold coated ZnO rod, with spatial resolution below 30 nm. A distinct strain distribution was found inside the rod, denoted to depletion and screening effects occurring in bent piezotronic structures, and a high strain at the interface may be related to Schottky contact formation. This interface strain agrees with results obtained from TEM. A succeeding CXDI study was conducted on a ZnO rod coated with magnetostrictive FeCoSiB and the possibility for the investigation of the Schottky contacts electrical properties. It was found that FeCoSiB sputtered on ZnO results in an ohmic contact and that an external magnetic field causes a change of the electrical properties, probably due to a strain change, visualized by CXDI. In a fifth study, magnetostrictive FeCo/TiN multilayer structures were investigated by a combined TEM and XRD/XRR approach, showing a relaxation of the structure due to an annealing process and a cube-on-cube structure of the FeCo and TiN layers

Bio-sensing using toroidal microresonators & theoretical cavity optomechanics

In this thesis we report on two matters, (i) time-resolved single particle bio-sensing using a cavity enhanced refractive index sensor with unmatched sensitivity, and (ii) the theoretical analysis of parametric normal mode splitting in cavity optomechanics, as well as the quantum limit of a displacement transducer that relies on multiple cavity modes. It is the unifying element of these studies that they rely on a high-Q optical cavity transducer and amount to a precision measurement of an optical frequency. In the first part, we describe an experiment where a high-Q toroidal microcavity is used as a refractive index sensor for single particle studies. The resonator supports whispering gallery modes (WGM) that feature an evanescent fraction, probing the environment close to the toroid's surface. When a particle with a refractive index, different from its environment, enters the evanescent field of the WGM, the resonance frequency shifts. Here, we monitor the shift with a frequency resolution of df/f=7.7e-11 at a time resolution of 100µs , which constitutes a x10 improvement of the sensitivity and a x100 improvement in time resolution, compared to the state of the art. This unprecedented sensitivity is the key to real-time resolution of single lipid vesicles with 25nm radius adsorbing onto the surface. Moreover -- for the first time within one distinct measurement -- a record number of up to 200 identifiable events was recorded, which provides the foundation for a meaningful statistical analysis. Strikingly, the large number of recorded events and the high precision revealed a disagreement with the theoretical model for the single particle frequency shift. A correction factor that fully accounts for the polarizability of the particle, and thus corrects the deviation, was introduced and establishes a quantitative understanding of the binding events. Directed towards biological application, we introduce an elegant method to cover the resonator surface with a single lipid bilayer, which creates a universal, biomimetic interface for specific functionalization with lipid bound receptors or membrane proteins. Quantitative binding of streptavidin to biotinylated lipids is demonstrated. Moving beyond the detection limit, we provide evidence that the presence of single IgG proteins (that cannot be resolved individually) manifests in the frequency noise spectrum. The theoretical analysis of the thermo-refractive noise floor yields a fundamental limit of the sensors resolution. The second part of the thesis deals with the theoretical analysis of the coupling between an optical cavity mode and a mechanical mode of much lower frequency. Despite the vastly different resonance frequencies, a regime of strong coupling between the mechanics and the light field can be achieved, which manifests as a hybridization of the modes and as a mode splitting in the spectrum of the quadrature fluctuations. The regime is a precondition for coherent energy exchange between the mechanical oscillator and the light field. Experimental observation of optomechanical mode splitting was reported shortly after publication of our results [cf. Gröblacher et al., Nature 460, 724--727]. Dynamical backaction cooling of the mechanical mode can be achieved, when the optical mode is driven red-detuned from resonance. We use a perturbation and a covariance approach to calculate both, the power dependence of the mechanical occupation number and the influence of excess noise in the optical drive that is used for cooling. The result was one to one applied for data analysis in a seminal article on ground state cooling of a mechanical oscillator [cf. Teufel et al., Nature 475, 359--363]. In addition we investigate a setting, where multiple optical cavity modes are coupled to a single mechanical degree of freedom. Resonant build-up of the motional sidebands amplifies the mechanical displacement signal, such that the standard quantum limit for linear position detection can be reached at significantly lower input power.In dieser Dissertation werden zwei Themen behandelt. Im ersten Teil widmen wir uns experimentell der zeitaufgelösten Messung von Liposomen mit Hilfe eines Nahfeld-Brechungsindex-Sensors. Der zweite Teil handelt von der theoretischen Beschreibung des Regimes der starken Kopplung zwischen einem mechanischen Oszillator und dem Feld eines optischen Resonators. Des Weiteren erörtern wir ein Messschema, das es erlaubt eine mechanische Bewegung, mit Hilfe von mehreren optischen Resonatormoden genauer auszulesen. Die Gemeinsamkeit beider Arbeiten besteht darin, dass es sich jeweils um eine Präzisionsmessung einer optischen Frequenz handelt. Im experimentellen Teil benutzen wir Toroid-Mikroresonatoren mit extrem hoher optischer Güte als Biosensoren. Dabei handelt es sich um eine ringförmige Glasstruktur, entlang welcher Licht im Kreis geleitet wird. Dazu muss eine Resonanzbedingung erfüllt sein, die besagt, dass der (effektive) Umfang des Rings einem ganzzahligen Vielfachen der optischen Wellenlänge entspricht. Ein Teil des zirkulierenden Lichts ist als evaneszente Welle empfänglich für Brechungsindexänderungen nahe der Oberfläche des Resonators. Ein Partikel, dessen Brechungsindex sich von dem der Umgebung unterscheidet, induziert beim Eintritt in das evaneszente Feld eine Frequenzverschiebung der optischen Resonanz. Im Rahmen dieser Arbeit lösen wir relative Frequenzverschiebungen mit einer Genauigkeit von df/f=7.7e-11 und einer Zeitkonstante von 100µs auf. Dies stellt eine Verbesserung des derzeitigen Stands der Technik um einen Faktor x10 in der Frequenz und einen Faktor x100 in der Zeit dar. Diese bisher unerreichte Empfindlichkeit der Messmethode ist der Schlüssel zur Echtzeitdetektion einzelner Lipidvesikel mit einem Radius von 25nm . Zudem gelingt es uns innerhalb einer Messung, bis zu 200 Einzelteilchenereignisse aufzunehmen, welche die Basis für eine aussagekräftige Statistik liefern. Bemerkenswerterweise konnten wir Dank der außerordentlichen Präzision und der Vielzahl der Ereignisse eine Abweichung zur bis dato akzeptierten und angewandten Theorie feststellen. Wir ergänzen das Model um einen Korrekturfaktor, der die Polarisierbarkeit des Teilchens vollständig berücksichtigt und erlangen dadurch ein umfassendes und quantitatives Verständnis der Messergebnisse. Im Hinblick auf biologisch relevante Fragestellungen zeigen wir eine elegante Methode auf, die es erlaubt, den Resonator mit einer einzelnen Lipidmembran zu beschichten. Wir kreieren somit eine biomimetische Schnittstelle, welche das Grundgerüst für eine spezifische Funktionalisierung mit lipidgebundenen Rezeptoren, Antikörpern oder Membranproteinen darstellt. Des Weiteren zeigen wir, dass der Empfindlichkeit eine fundamentale Grenze durch thermische Brechungsindexfluktuationen gesetzt ist. Hierzu wird ein theoretisches Modell speziell für den relevanten niederfrequenten Bereich errechnet. Im zweiten Teil der Arbeit beschäftigen wir uns mit der theoretischen Beschreibung eines optischen Resonators, dessen Lichtfeld an eine mechanische Schwingung gekoppelt ist. Obwohl sich die Resonanzfrequenzen der Optik und der Mechanik typischerweise um mehrere Größenordnungen unterscheiden, existiert ein Regime der starken Kopplung, in dem die Fluktuationen des Lichts und die mechanischen Vibrationen hybridisieren. Dies offenbart sich zum Beispiel im Phasenspektrum, wo sich das ursprüngliche Maximum der Resonanz in zwei Maxima aufspaltet. Die starke Kopplung stellt die Grundlage für kohärenten Energie- und Informationsaustausch zwischen Licht und Mechanik dar und ist daher von besonderem technischen und wissenschaftlichen Interesse. Es ist anzumerken, dass die starke Kopplung und die einhergehende Aufspaltung der Resonanz bereits kurz nach Veröffentlichung unserer theoretischen Beschreibung im Experiment beobachtet wurde [vgl. Gröblacher et al., Nature 460, 724--727]. Wenn der optische Resonator (zur längeren Wellenlänge hin) verstimmt von der Resonanz angeregt wird, kann über dynamische Rückkopplung eine effektive Kühlung der mechanischen Schwingung erreicht werden. Wir berechnen die thermische Besetzungszahl der mechanischen Mode (und somit die Temperatur) mit Hilfe eines störungstheoretischen und eines Kovarianzansatzes. Dabei berücksichtigen wir sowohl ein klassisches Rauschen des optischen Feldes als auch den Einfluss der optomechanischen Kopplung auf die Grenztemperatur. Der hergeleitete Ausdruck für die finale Besetzungszahl wurde eins zu eins für die Datenanalyse in dem wegweisenden Artikel über das Kühlen eines mechanischen Oszillators in den Quantengrundzustand verwendet [vgl. Teufel et al., Nature 475, 359--363]. Abschließend betrachten wir ein Schema, bei dem die Lichtfelder mehrerer optischer Resonanzen an eine mechanischen Schwingung gekoppelt sind. Die resonante Verstärkung der Information über die mechanische Bewegung in den optischen Seitenbändern ermöglicht es, eine durch das Standard Quantenlimit begrenzte Empfindlichkeit bei signifikant niedriger Eingangsleistung zu erreichen

The supramolecular modification of trans-resveratrol and related antioxidant molecules

The naturally occurring phytoalexin trans-Resveratrol (RES) is known to be a powerful antioxidant and is used as a nutraceutical. It is considered to be one of the factors contributing to the beneficial effects of red wine. The phenolic hydroxycinnamic acids caffeic acid (CAF), ferulic acid (FA), p-coumaric acid (PCA) and sinapic acid (SA) are found in a wide variety of plants and also have antioxidant activity. The acetophenone derivatives paeonol (2H4M) and vanillin (4H3M) display antioxidant, anti-inflammatory and antihypertensive activity. The use of these compounds as food fortifiers and nutraceuticals is limited as they exhibit adverse physical properties such as low aqueous solubility and low bioavailability. These properties may be improved by inclusion complex formation with cyclodextrins (CDs) and by cocrystallisation with generally regarded as safe (GRAS) coformers. A study of the CD complexation of RES, CAF, FA, PCA, SA, 2H4M and 4H3M was carried out both in solution and in the solid state. The solubility enhancement of the nutraceuticals by CD inclusion and by cocrystallisation was evaluated. The compounds hydrocaffeic acid (HCA), hydroferulic acid (FA), 2-hydroxy-5-methoxy acetophenone (2H5M) and 2-hydroxy-6-methoxy acetophenone (2H6M) have little or no known bioactivity but were included in the study as structural analogues for comparative purposes. Inclusion complexes were formed with the nutraceuticals and the native CDs (β- and γ-CD) by kneading and coprecipitation, as well as with methylated CDs by coprecipitation. The resulting inclusion complexes were characterised using powder X-ray diffraction (PXRD), ¹H nuclear magnetic resonance spectroscopy (¹H-NMR), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and hot stage microscopy (HSM). Single crystal X-ray diffraction was used to elucidate inclusion complex structures. Three novel RES inclusion complexes were formed with methylated CDs having common modes of inclusion and hydrogen bonding motifs. Inclusion complex formation with the methylated CDs also produced six new hydroxycinnamic acid complexes and five new hydroxyacetophenone complexes. While attempting to produce native CD inclusion complexes with the hydroxycinnamic acid compounds, crystals of SA were isolated, the structure of which had not been reported previously. The results of phase solubility studies revealed that, in general, CD inclusion complex formation improves the aqueous solubility of RES [randomly methylated CD (RAMEB) effecting a maximum increase of 63 times that of free RES] and hydroxycinnamic acids. The thermodynamic parameters and association constants for complexation between hydroxycinnamic acids and both β- and γ-CD were determined by isothermal titration calorimetry (ITC). For β-CD a 1:1 host-guest ratio was found with association constants in the range 246-774 M⁻¹. The interactions between the guests and β-CD were found to be enthalpy-driven, except for that of SA and β-CD which was entropy-driven. With γ-CD a 1:1 host to CAF ratio was found while PCA, FA and SA interact with γ-CD in a 2:1 molar ratio. The association constants were in the range 228-543 M⁻¹. The formation of 2:1 complexes in solution was found to be enthalpy-driven while that of 1:1 complexes was entropydriven. ¹H NMR spectroscopy was used to study the interaction of the acetophenone derivatives with β- and γ-CD in solution. Job plot analyses confirmed 1:1 host-guest complex ratios. The association constants spanned the range 145-336 M⁻¹. Similarly for γ-CD, complex stoichiometries were confirmed to be 1:1 with 2H6M and 4H3M with association constants 67 and 125 M⁻¹, respectively. Eight cocrystals were prepared with hydroxycinnamic acids and the GRAS compounds nicotinamide (NIC) and isonicotinamide (ISO) by coprecipitation, and were fully characterised. Single crystal X-ray diffraction confirmed the formation of cocrystals rather than salts. Analysis using ¹H NMR spectroscopy for quantitation revealed that the aqueous solubilities of FA and PCA were enhanced approximately ten-fold when tested in the form of their cocrystals with the coformer NIC

Advanced instrumented stamps for micro transfer printing and novel application areas

Transfer printing refers to a set of techniques for deterministic assembly of functional micro/nano scale devices into two and three dimensional spatial arrangements. It provides a versatile route for realizing multifunctional heterogeneously integrated systems such as flexible electronics, biocompatible sensing and therapeutic devices, transparent and curved optoelectronic systems etc. Micro-transfer printing is an automated process that implements deterministic micro scale assembly using a molded viscoelastic stamp typically made out of PDMS. The process relies upon the control of adhesion and fracture at the interfaces between the stamp and the devices being assembled to pick up and release them. A widely exploited strategy to achieve variable adhesion from the stamp is to use the rate dependent effects of the viscoelastic stamp material. It is a very versatile process and has been used in the realization of many novel heterogeneously integrated systems. The process has been implemented industrially to assemble ultra-high concentration photovoltaic panels. This body of work presents the development of new stamp technologies to address the challenges associated with increasing parallelism and shortcomings associated with fixed geometry stamps. Starting from the concept of an active composite material with distributed sensing, actuation and compliance tuning, new stamp architectures are developed. These novel stamps replace the compliance of a bulk PDMS stamp with active functional structures with tunable stiffness; without effecting the ability of the stamps to be used for transfer printing. The new stamp architecture enables active monitoring and control of the micro transfer printing process. Using instrumentation to sense deflections/forces at each post allows detection, measurement and compensation of misalignments between the stamp and donor/receiving substrates. Furthermore this information is used to detect pick up and printing errors at individual posts, allowing for error handling to increase process robustness. Moreover the ability to selectively actuate allows to engage/disengage individual posts. This enables new transfer printing modes such as collect and place. Finally results of pilot experiments conducted to test the feasibility of using micro transfer printing in novel application areas are presented

Analysis of Strain Relaxation, Ion Beam Damage and Instrument Imperfections for Quantitative STEM Characterizations

It is illustrated that the preparation of thin specimens from bulk materials can have significant influence on the interpretability of (S)TEM data. The results of the presented measurements show that and the elastic strain relaxation in low dimensional structures alters the overall strain state of the material – and hence affects strain measurements – as well as the contrast of STEM measurements and is generally needed to be incorporated in comparative simulation studies that involve strained structures. Furthermore, the ion beam thinning process itself can introduce – even with relatively low energies – a serious alteration of the surface which can affect the contrast of STEM measurements. Hence, the correlation to thickness measurements is complicated due to the distinct difference in scattering behaviour between (partially) amorphized surface layers in comparison with crystalline material. Although parts of these effects cannot be avoided the inclusion of amorphous pseudo-oxide layers in simulations has been shown to provide reasonable agreement with the experimental data. Furthermore, the impact of a finite electron source with limited coherence has been investigated. It can be shown that a reproduction of experimental contrast by simulation can only be achieved by the inclusion of an additional focus spread as well as a lateral point spread due to partial spatial coherence. Finally, the previous results are combined to reconstruct the three-dimensional shape of several antiphase domains within gallium phosphide grown on silicon-(001). At first the concept was demonstrated for a simple but highly strained interface and second for large structures with thousands of atomic columns. It is shown that although the contrast mechanism for annular dark-field imaging is in principle straight forward and mathematically simple, the details of atomic resolution microscopy are still very challenging. Realistic assumptions about the specimen properties and the electron optics have been shown to be of great relevance for data evaluation. It is clear that the research should be extended to the regime of low angular dark-field imaging where strain and inelastic scattering play a even more relevant role. Furthermore, it is of great importance to investigate the aforementioned practical aspects of damage layers and optical imperfections for other advanced imaging techniques like diffraction imaging. In addition, it is worth investigating in how far through focus depth section can be utilized to increase the reliability of structure restoration along the transmission direction. It is expected that the improvement of accuracy and robustness of atomic counting techniques will greatly increase the power of a (S)TEM by providing simultaneously lateral and depth information about arrangement and composition. Furthermore, it is clear that the role of high performance simulations will have an even more important role in the future

RUPEE: A Big Data Approach to Indexing and Searching Protein Structures

Title from PDF of title page viewed July 7, 2021Yugyung LeeVitaIncludes bibliographical references (pages 149-158)Thesis (Ph.D.)--School of Computing and Engineering and Department of Mathematics and Statistics. University of Missouri--Kansas City, 2021Given the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. Despite their maturity, existing protein structure searches either compromise the quality of results to obtain faster response times or suffer from longer response times to provide better quality results. Existing protein structure searches that focus on faster response times often use sequence clustering or depend on other simplifying assumptions not based on structure alone. In the case of sequence clustering, strong structure similarities are often hidden behind cluster representatives. Existing protein structure searches that focus on better quality results often perform full pairwise protein structure alignments with the query structure against every available structure in the searched database, which can take as long as a full day to complete. The poor response times of these protein structure searches prevent the easy and efficient exploration of relationships between protein structures, which is the norm in other areas of inquiry. To address these trade-offs between faster response times and quality results, we have developed RUPEE, a fast and accurate purely geometric protein structure search combining a novel approach to encoding sequences of torsion angles with established techniques from information retrieval and big data. RUPEE can compare the query structure to every available structure in the searched database with fast response times. To accomplish this, first, we introduce a new polar plot of torsion angles to help identify separable regions of torsion angles and derive a simple encoding of torsion angles based on the identified regions. Then, we introduce a heuristic to encode sequences of torsion angles called Run Position Encoding to increase the specificity of our encoding within regular secondary structures, alpha-helices and beta-strands. Once we have a linear encoding of protein structures based on their torsion angles, we use min-hashing and locality sensitive hashing, established techniques from information retrieval and big data, to compare the query structure to every available structure in the searched database with fast response times. Moreover, because RUPEE is a purely geometric protein structure search, it does not depend on protein sequences. RUPEE also does not depend on other simplifying assumptions not based on structure alone. As such, RUPEE can be used effectively to search on protein structures with low sequence and structure similarity to known structures, such as predicted structures that results from protein structure prediction algorithms. Comparing our results to the mTM-align, SSM, CATHEDRAL, and VAST protein structure searches, RUPEE has set a new bar for protein structure searches. RUPEE produces better quality results than the best available protein structure searches and does so with the fastest response times.Introduction -- Encoding Torsion Angles -- Indexing Protein Structures -- Searching Protein Structures -- Results and Evaluation -- Using RUPEE -- Conclusion -- Appendix A. Benchmarks of Known Protein Structures -- Appendix B. Benchmarks of Protein Structure Prediction

Optical Response in Planar Heterostructures: From Artificial Magnetism to Angstrom-Scale Metamaterials

The idea of expanding the range of properties of natural substances with artificial matter was introduced by V. G. Veselago in 1967. Since then, the field of metamaterials has dramatically advanced. Man-made structures can now exhibit a plethora of extraordinary electromagnetic properties, such as negative refraction, optical magnetism, and super-resolution imaging. Typical metamaterial motifs include split ring resonators, dielectric and plasmonic particles, fishnet and wire arrays. The principle of operation of these elements is now well-understood, and they are being exploited for practical applications on a global scale, ranging from telecommunications to sensing and biomedicine, in the radio frequency and terahertz domains. Accessing and controlling optical and near-infrared phenomena requires scaling down the dimensions of meta- materials to the nanometer regime, pushing the limits of state-of-the-art nano- lithography and requiring structurally less complex geometries. Hence, within the last decade, research in metamaterials has revisited a simpler, lithography- free structure, particularly planar arrangements of alternating metal and dielectric layers, termed hyperbolic metamaterials. Such media are readily realizable with well-established thin-film deposition techniques. They support a rich canvas of properties ranging from surface plasmonic propagation to negative refraction, and they can enhance the photoluminescence properties of quantum emitters at any frequency range. Here, we introduce a computational approach that allows tailoring the dielectric and magnetic effective properties of planar metamaterials. Previously, planar hyperbolic metamaterials have been considered non-magnetic. In contrast, we show theoretically and experimentally that planar arrangements com- posed of non-magnetic constituents can be engineered to exhibit a non-trivial magnetic response. This realization simplifies the structural requirements for tailoring optical magnetism up to very high frequencies. It also provides access to previously unexplored phenomena, for example artificially magnetic plasmons, for which we perform an analysis on the basis of available materials for achieving polarization-insensitive surface wave propagation. By combining the concept of metamaterials’ homogenization with previous transfer matrix approaches, we develop a general computational method for surface waves calculations that is free of previous assumptions, for example infinite or purely periodic media. Furthermore, we theoretically demonstrate that hyperbolic metamaterials can be dynamically tunable via carrier injection through external bias, using transparent conductive oxides and graphene, at visible and infrared frequencies, respectively. Lastly, we demonstrate that planar graphene-based van der Waals heterostructures behave effectively as supermetals, exhibiting reflective properties that surpass the reflectivity of gold and silver that are currently considered the state-of-the-art materials for mirroring applications in space applications. The (meta)materials we introduce exhibit an order-of-magnitude lower mass density, making them suitable candidates for future light-sail technologies intended for space exploration.</p

Femtosecond Coherent Vibrational Dynamics of Anabaena Sensory Rhodopsin

The photo-induced isomerization of retinal protonated Schiff base (RPSB) inside the protein pocket is one of the fastest (<ps) and most stereo-selective photochemical reactions in nature. The ground state structure of the RPSB and its surrounding protein constructions are thought to be the two most crucial factors to drive this reaction. The investigation of each factor individually was the main goal of this thesis. Anabaena Sensory Rhodopsin (ASR), a recently discovered microbial retinal protein, serves as an ideal system for this study as it binds two structural isomers (all-trans: AT and 13-cis: 13C) of the RPSB within the same protein constructions in its photocycle. In the present work, the photo-induced dynamics of the RPSB in ASR has been explored with the help of time resolved coherent vibrational spectroscopic methods, which monitor the photo-induced sub-ps structural changes of the RPSB. These studies have helped to shed light on the intricate relationship between electronic and vibrational dynamics of the RPSB. In the first half of this thesis, a comparative study showed both electronic and vibrational dynamics are widely distinct for the AT and 13C isomers of the RPSB in ASR. In particular, the 13C isomer exhibited more than five folds faster dynamics than the AT isomer. One possible molecular origin behind this dynamical difference was found by comparing the ground state Raman spectra of the two isomers. It depicted an increase in the amplitude of hydrogen-out-of-plane (HOOP) modes for the 13C isomer, which is usually considered to be an evidence of distortion in the ground state structure for the retinal system. The ground state pre-distortion has been reported as a potential element for the acceleration of the isomerization reaction for the 13C isomer, in analogy with the cis isomers of visual rhodopsin and bacteriorhodopsin. The second half of this work explored the role of the part of protein helix inside the retinal pocket as well as that far away from the pocket. In particular, the replacement of the amino acid residues in vicinity of the RPSB by point mutation caused an acceleration of the reaction rate for the AT isomer, but it had only a minor effect for the 13C isomer of the RPSB. Furthermore, the truncation of the part of the protein, embedded into the cytoplasmic region, affected the formation of the primary photoproduct. All these experimental results lead to two major conclusions of this thesis: (i) the protein constructions govern the retinal isomerization dynamics and (ii) the same protein cage exerts differential interactions on two structural isomers of the RPSB