<p>In the present thesis the density functional B3LYP has been used to study reactions of NO and O₂ in redox active enzymes.</p><p>Reduction of nitric oxide (NO) to nitrous oxide (N₂O) is an important part in the bacterial energy conservation (denitrification). The reduction of NO in three different bimetallic active sites leads to the formation of hyponitrous acid anhydride (N₂O₂^2-). The stability of this intermediate is crucial for the reaction rate. In the two diiron systems, respiratory and scavenging types of NOR, it is possible to cleave the N-O bond, forming N₂O, without any extra protons or electrons. In a heme-copper oxidase, on the other hand, both a proton and an electron are needed to form N₂O.</p><p>In addition to being an intermediate in the denitrification, NO is a toxic agent. Myoglobin in the oxy-form reacts with NO forming nitrate (NO₃ ^-) at a high rate, which should make this enzyme an efficient NO scavenger. Peroxynitrite (ONOO^-) is formed as a short-lived intermediate and isomerizes to nitrate through a radical reaction.</p><p>In the mechanism for pumping protons in cytochrome oxidase, thermodynamics, rather than structural changes, might guide protons to the heme propionate for further translocation.</p><p>The dioxygenation of arachidonic acid in prostaglandin endoperoxide H synthase forms the bicyclic prostaglandin G₂, through a cascade of radical reactions. The mechanism proposed by Hamberg and Samuelsson is energetically feasible.</p>

The capability to resolve the contributions from spectroscopically overlapping fluorophores has enabled significant breakthroughs in cellular imaging. However, commercial microscopes for this purpose use analog light detection with least squares curve-fitting analysis and improvements in sensitivity are needed. To this end, a microscope has been constructed with high throughput and single-photon detection capability. The fluorescence is separated through use of a prism spectrometer or a series of dichroic mirrors into four spectral bands and detected using four single-photon avalanche diode (SPAD) detectors, which provide high-quantum efficiency in the red spectral region. The detectors are connected to a time-correlated single photon counting module to provide sub-nanosecond temporal resolution for distinguishing fluorophores with different fluorescence lifetimes. Maximum-likelihood (ML) methods have been developed for analyzing the temporally and spectrally resolved photon count data from the SPADs to find the contributions from different fluorescent species and from background. Commercially available SPADs exhibit a count-rate dependent time shift in the impulse response function, and hence the instrument incorporates custom modified SPADs with improved timing stability. Nevertheless, there is still some time shift, and hence the ML-analysis has been extended to include this as an adjustable parameter for each individual SPAD. Monte Carlo simulations have also been developed to enable studies of the number of photons needed to resolve specific fluorophores.

In this thesis I have performed theoretical studies on the reaction dynamics in few-atom molecules. In particular, I have looked at reaction processes in which highly excited resonant states are involved. When highly excited states are formed, the dynamics becomes complicated and approximations normally used in chemical reaction studies are no longer applicable.To calculate the potential energy curve for some of these states as a function of internuclear distance, a combination of structure calculations and scattering calculations have to be performed, and the reaction dynamics on the potentials has been studied using both time-independent and time-dependent methods.The processes that have been studied and which are discussed in this thesis are ion-pair formation in electron recombination with H3+, dissociative recombination and ion-pair formation of HF+, mutual neutralization in H++F- collisions and dissociative recombination of BeH+. Isotope effects in these reactions have also been investigated. Our calculated cross sections are compared with experimentally measured cross sections for these reactions.

In the present thesis the density functional B3LYP has been used to study reactions of NO and O2 in redox active enzymes. Reduction of nitric oxide (NO) to nitrous oxide (N2O) is an important part in the bacterial energy conservation (denitrification). The reduction of NO in three different bimetallic active sites leads to the formation of hyponitrous acid anhydride (N2O22-). The stability of this intermediate is crucial for the reaction rate. In the two diiron systems, respiratory and scavenging types of NOR, it is possible to cleave the N-O bond, forming N2O, without any extra protons or electrons. In a heme-copper oxidase, on the other hand, both a proton and an electron are needed to form N2O. In addition to being an intermediate in the denitrification, NO is a toxic agent. Myoglobin in the oxy-form reacts with NO forming nitrate (NO3 -) at a high rate, which should make this enzyme an efficient NO scavenger. Peroxynitrite (ONOO-) is formed as a short-lived intermediate and isomerizes to nitrate through a radical reaction. In the mechanism for pumping protons in cytochrome oxidase, thermodynamics, rather than structural changes, might guide protons to the heme propionate for further translocation. The dioxygenation of arachidonic acid in prostaglandin endoperoxide H synthase forms the bicyclic prostaglandin G2, through a cascade of radical reactions. The mechanism proposed by Hamberg and Samuelsson is energetically feasible.

In the thesis work we investigate four problems connected with dynamical processes in condensed medium, using different techniques of equilibrium and non-equilibrium statistical mechanics. Biology is rich in dynamical events ranging from processes involving single molecule [1] to collective phenomena [2]. In cell biology, translocation and transport processes of biological molecules constitute an important class of dynamical phenomena occurring in condensed phase. Examples include protein transport through membrane channels, gene transfer between bacteria, injection of DNA from virus head to the host cell, protein transport thorough the nuclear pores etc. We present a theoretical description of the problem of protein transport across the nuclear pore complex [3]. These nuclear pore complexes (NPCs) [4] are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. The first suggests that the plug is a reversible hydrogel while the other suggests that it is a polymer brush. In the thesis, we propose a model for the transport of a protein through the plug, which is treated as elastic continuum, which is general enough to cover both the models. The protein stretches the plug and creates a local deformation, which together with the protein is referred to as the bubble. The relevant coordinate describing the transport is the center of the bubble. We write down an expression for the energy of the system, which is used to analyze the motion. It shows that the bubble executes a random walk, within the gel. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. Further, on adopting the same kind of free energy for the brush too, one finds that though the energy cost for the entry of the particle is small but the diffusion coefficient is much lower and hence, explanation of the rapid diffusion of the particle across the nuclear pore complex is easier within the gel model. In chemical physics, processes occurring in condensed phases like liquid or solid often involve barrier crossing. Simplest possible description of rate for such barrier crossing phenomena is given by the transition state theory [5]. One can go one step further by introducing the effect of the environment by incorporating phenomenological friction as is done in Kramer’s theory [6]. The “method of reactive flux” [7, 8] in chemical physics allows one to calculate the time dependent rate constant for a process involving large barrier by expressing the rate as an ensemble average of an infinite number of trajectories starting at the barrier top and ending on the product side at a specified later time. We compute the time dependent transmission coefficient using this method for a structureless particle surmounting a one dimensional inverted parabolic barrier. The work shows an elegant way of combining the traditional system plus reservoir model [9] and the method of reactive flux [7] and the normal mode analysis approach by Pollak [10] to calculate the time dependent transmission coefficient [11]. As expected our formula for the time dependent rate constant becomes equal to the transition state rate constant when one takes the zero time limit. Similarly Kramers rate constant is obtained by taking infinite time limit. Finally we conclude by noting that the method of analyzing the coupled Hamiltonian, introduced by Pollak is very powerful and it enables us to obtain analytical expressions for the time dependent reaction rate in case of Ohmic dissipation, even in underdamped case. The theory of first passage time [12] is one of the most important topics of research in chemical physics. As a model problem we consider a particle executing Brownian motion in full phase space with an absorbing boundary condition at a point in the position space we derive a very general expression of the survival probability and the first passage time distribution, irrespective of the statistical nature of the dynamics. Also using the prescription adopted elsewhere [13] we define a bound to the actual survival probability and an approximate first passage time distribution which are expressed in terms of the position-position, velocity-velocity and position-velocity variances. Knowledge of these variances enables one to compute the survival probability and consequently the first passage distribution function. We compute both the quantities for gaussian Markovian process and also for non-Markovian dynamics. Our analysis shows that the survival probability decays exponentially at the long time, irrespective of the nature of the dynamics with an exponent equal to the transition state rate constant [14]. Although the field of equilibrium thermodynamics and equilibrium statistical mechanics are well explored, there existed almost no theory for systems arbitrarily far from equilibrium until the advent of fluctuation theorems (FTs)[15] in mid 90�s. In general, these fluctuation theorems have provided a general prescription on energy exchanges that take place between a system and its surroundings under general nonequilibrium conditions and explain how macroscopic irreversibility appears naturally in systems that obey time reversible microscopic dynamics. Based on a Hamiltonian description we present a rigorous derivation [16] of the transient state work fluctuation theorem and the Jarzynski equality [17] for a classical harmonic oscillator linearly coupled to a harmonic heat bath, which is dragged by an external agent. Coupling with the bath makes the dynamics dissipative. Since we do not assume anything about the spectral nature of the harmonic bath the derivation is valid for a general non-Ohmic bath.

The thesis describes the study of structure and dynamics of polymers in confined geometry. We study the finite size effect on the dynamics of non glassy and glassy polymers. Systematic measurement have been performed to address the issue of the possibility of entanglement and hence reptation dynamics of the polymer segments in confinement. The confinement effect on the glassy dynamics has been studied for Langmuir monolayers as well as for polymer nanoparticle hybrid systems. Slow and heterogeneous dynamics are the underlined observed behavior for dynamics in hybrid systems. The available theories explains the slowing down of the dynamics as the system is cooled from the liquid state in terms of increasing cooperative motion of the molecules. The size of the cooperative region is predicted to grow with reducing temperature. Experiments, theories and simulation in confined dimensions have been motivated to detect this length scale of the cooperatively rearranging region. The surface and interface effects on glass transition were studied using measurements based on modulated differential scanning calorimetry and small angle X ray scattering techniques. The dynamical heterogeneity in glassy polymers were studied using advanced X ray photon correlation spectroscopy techniques. Our studies presented in this thesis are also an small step to contribute to the existing experimental results on studying the surface, interface and finite size effects on the morphology and dynamics of confined systems. These effects were studied for, firstly ultra thin Langmuir monolayers and secondly polymer nanoparticle hybrid systems. In Chapter 1, we provide the theoretical background along with brief review of the literature for understanding the results presented in this thesis. The details of the experimental set up and their operating principle along with the details of the experimental conditions are provided in Chapter 2. In Chapter 3 we presents our experimental results on surface morphology and surface dynamics in ultra thin Langmuir monolayer of polymers. Chapter 4 and Chapter 5 discusses the result based on polymer nanoparticle hybrid systems. We provide the summary of our result and the future prospective of the work in Chapter 6. In appendix we have shown the complete derivation of the equation used in Chapter 3 for understanding the surface morphology of Langmuir monoalyers on water surface. Chapter 1 provides in detail the introduction to several aspects related with the dynamics of both glassy and non glassy polymers in confinement. It starts with brief introduction to structure and dynamics of polymers in bulk. In the next section we discuss the macroscopic viscoelastic behavior of materials followed by a very brief discussion on the common techniques used for such measurement. Further it discusses the theory and several available models present in literature to understand the dynamics of glass transition. This section is followed by discussion on surface and interface effects on structure and dynamics of such systems in confinement. Towards the end of this chapter we discuss the universal behavior of slow dynamic observed in soft glassy materials. Chapter 2 contains the details of the experimental techniques which has been used for the study. Brief introduction to basic principles of the measurements followed by details of the material and methods have been provided. The surface morphology and dynamics of Langmuir monolayer of polymers confined at air water interface, under compressive mechanical strain has been discussed in Chapter 3. The results presented for surface morphology are based on the studies using the combination of in situ grazing angle incidence small angle X ray scattering and ex situ atomic force microscopy measurements on monolayers transfered on silicon substrate. The issue of the presence of reptation motion in confinement has been addressed by performing systematic measurements as a function of surface concentration and molecular weight at fixed temperature. The glassy dynamical behavior has been studied on different glassy polymer layer as a function of surface concentration and temperature. In Chapter 4 we show the glass transition behavior of polymer nanoparticle (PMMA gold) hybrid system based on thermal measurements. This chapter discusses the role of the existence of a length scale in deciding the dynamics of the glass transition temperature of polymers. The confinement effect was tuned by the variation of the inter particle spacing between the nanoparticles in the polymer matrix. It also discusses the model to understand the observed behavior of the glass transition temperature in terms of the tunability of the polymer particle interface and the effect of the interface morphology on the dynamics of glass transition temperature. Chapter 5 is about the study of dynamics of polymer nanocomposites near glass transition as a function of temperature, wave vector and volume fraction of gold nanoparticles using X ray photon correlation spectroscopy. Based on our experimental results , we provide a phase diagram for dynamics in 2D space of temperature, wave vector and volume fraction for our PMMA gold nanoparticle hybrid samples. Chapter 6 contains the summary and the future perspective of the work presented.

This thesis deals with the use of electric fields for evaluation and control of chemical systems. An electric field can result in the flow of charge across an interface between a metal and a solution, by means of chemical reactions. This interplay between electricity and chemistry, i.e. electrochemistry, is a field of crucial importance both within research and industry. Applications based on electrochemical principles encompass such diverse areas as batteries and fuel cells, pH electrodes, and the glucose monitor used by people suffering from diabetes.A major part of the present work concerns the use of static electric fields in solutions containing a non-contacted metal surface. In such a setup it is possible to control the extent of electrochemical reactions at different positions on the metal. This allows the formation and evaluation of various types of gradients on electrodes, via indirectly induced electrochemical reactions. This approach is a new and simple way of forming for instance molecular gradients on conducting surfaces. These are very advantageous in biomimetic research, because a gradient contains a huge amount of discrete combinations of for example two molecules. The basis for the technique is the use of bipolar electrochemistry. Briefly, a surface can become a bipolar electrode (an electrode that acts as both anode and cathode) when the electric field in the solution exceeds a certain threshold value, thereby inducing redox reactions at both ends. In our experiments, the driving force for these reactions will vary along the electrode surface. Since the result of an electrochemical reaction can be the deposition or removal of material from an electrode, bipolar electrochemistry can be used to create gradients of that material on a surface. In order to gain a deeper understanding of these processes, the potential and current density distributions at bipolar electrodes were investigated with different methods. Especially the use of imaging techniques was important for the visualization and analysis of the gradients. Using this knowledge, the formation of more complex gradients was facilitated, and the results were further compared to simulations based on simple conductivity models. These simulations also provided us with means to predict the behavior of new and interesting setup geometries for pattering applications.The other major part is more application driven and deals with the use of alternating electric fields for chemical analysis, a technique known as electrochemical impedance spectroscopy (EIS). In this work, EIS has been applied for the analysis of engine oils and industrial cutting fluids. Emphasis was placed on practical aspects of the measurement procedure, and on the evaluation of the results using statistical methods. It was for example shown that it was possible to simultaneously determine the amount of different contaminants in low conducting solutions. Generally, EIS is used to measure the impedance of a solution or a solid, often as a function of the frequency of the alternating electric field. The impedance of a system is closely correlated to its complex dielectric constant, and EIS can therefor be used to examine many chemical and physical processes. It is further well suited for characterizing low conducting media with little or no redox-active species. The evaluation of impedance data is often a quite complex task, which is why we have made use of statistical methods that drastically reduce the effort and quickly reveal significant intrinsic parameters.

Fluctuations in protein structure are vital to function. This contrasts the dominating structure-function paradigm, which connects the well-defined three-dimensional protein structure to its function. However, catalysis is observed in disordered enzymes, which lack a defined structure. Disordered proteins are involved in molecular recognition events as well. The aim of this Thesis is to describe the structural changes occuring in protein structure and to investigate the mechanism of molecular recognition. Protein architecture is classified in a hierarchical manner, that is, it is categorized into primary, secondary, and tertiary levels. One of the major questions in biology today is how proteins fold into a defined three-dimensional structure. Some protein folding models, like the framework model, suggest that the secondary structure, like α-helices, is formed before the tertiary structure. This Thesis raises two questions: First, are structural fluctuations that occur in the protein related to the folding of the protein structure? Second, is the hierarchic classification of the protein architecture useful to describe said structural fluctuations? Kinetic studies of protein folding show that important dynamical processes of the folding occur on the microsecond timescale, which is why time-resolved fluorescence spectroscopy was chosen as the principal method for studying structural fluctuations in the peptides. Time-resolved fluorescence spectroscopy offers a number of experimental advantages and is useful for characterizing typical structural elements of the peptides on the sub-microsecond timescale. By observing the fluorescence lifetime distribution of the fluorescent probe, which is a part of the hydrophobic core of a four-helix bundle, it is shown that the hydrophobic core changes hydration state, from a completely dehydrated to a partly hydrated hydrophobic core. These fluctuations are related to the tertiary structure of the four-helix bundle and constitute structural transitions between the completely folded four-helix bundle and the molten globule version. Equilibrium unfolding of the four-helix bundle, using chemical denaturants or increased temperature, shows that the tertiary structure unfolds before the secondary structure, via the molten globule state, which suggests a hierarchic folding mechanism of the four-helix bundle. Fluctuations of a 12 amino acid long helical segment, without tertiary structure, involve a conformational search of different helical organizations of the backbone. Binding and recognition of a helix-loop-helix to carbonic anhydrase occurs through a partly folded intermediate before the final tertiary and bimolecular structure is formed between the two biomolecules. This confirms the latest established theory of recognition that the binding and the folding processes are coupled for the binding molecules.

La possibilité d'effectuer des dépôts par voie électrochimique est utilisée dans l'industrie notamment dans les procédés de revêtements métalliques. Cette méthode de réduction des ions est connue depuis longtemps et apparaît encore comme un outil prometteur de synthèse de nouveaux micro- ou nano-matériaux ayant une structure et une morphologie contrôlées. Dans ce contexte, nous avons étudié la croissance de films d'or au niveau de l'interface air/liquide d'une solution aqueuse d'ions tétrachloroaurates (AuCl4-). Ces dépôts métalliques sont obtenus par confinement des processus d'électrodéposition ou de cémentation dans cette zone de la solution. Pour cela, nous avons mis à profit une interaction électrostatique entre les anions métalliques en solution et un film monomoléculaire d'un tensioactif chargé positivement (le diméthyldioctadécylammonium). L'étude des processus électrochimiques a mis en évidence l'existence de deux potentiels de réduction des ions métalliques. L'un est associé à un processus de croissance "bidimensionnelle" le long de l'interface air/liquide. Il est directement lié à la présence de la monocouche. L'autre correspond au processus ayant lieu classiquement en solution: il conduit à un épaississement des dépôts. Nous avons alors montré qu'il est possible de contrôler le mode de croissance des films d'or entre propagation "bidimensionnelle" et épaississement tridimensionnel. De plus, la synthèse des dépôts par cémentation nous a permis de mettre en évidence l'influence de la pression de surface ainsi que de l'ajout d'ions chlorure sur la croissance des dépôts métalliques. Cet ajout de chlorure permet en particulier la formation de dépôts à l'aspect dendritique.

Dans cette thèse, nous étudions le comportement à longue distance des membranes polymérisées en utilisant une approche de groupe de renormalization non-perturbative (NPRG). Après une présentation du NPRG, nous introduisons les membranes. Dans notre travail, nous nous concentrons sur différents types de membranes polymérisées: homogène, anisotrope et avec du désordre gelé́. De plus, nous avons aussi étudié les points de Lifshitz dans les systèmes magnétiques. Nos résultats, aussi bien pour les membranes que pour Lifshitz, se comparent bien aux résultats perturbatifs dans les différents cas limites: couplages faibles, basse température et large-d (ou large-n pour Lifshitz). Mais, en utilisant le NPRG, nous pouvons aller au de-là̀ de ces cas limites et atteindre les cas qui sont physiquement intéressants. La question de l'ordre de la transition entre la phase froissé et la phase plate dans les membranes homogènes est depuis longtemps sans une réponse définitive. Malgré̀ que nos résultats ne permettent pas encore de lever cette question, ils semblent indiquer que la transition est du premier ordre en accord avec des simulations récentes. Une propriété́ importante des membranes polymérisées est l'existence d'une phase plate à basse température avec un comportement non-trivial. Cette phase décrit correctement le comportement du graphène malgré̀ que les dégrées de liberté́ électroniques ne soient pas pris en compte