Multifunctional proteins that undergo major structural changes to perform different functions are known as “Transformer Proteins”, which is a recently identified class of proteins. One such protein that shows a remarkable structural plasticity and has two distinct functions is the transcription antiterminator, RfaH. Depending on the interactions between its N-terminal domain and its C-terminal domain, the RfaH CTD exists as either an all-α-helix bundle or all-β-barrel structure. Another example of a transformer protein is the Ebola virus protein VP40 (eVP40), which exists in different conformations and oligomeric states (dimer, hexamer, and octamer), depending on the required function.I performed Molecular Dynamics (MD) computations to investigate the structural conversion of RfaH-CTD from its all-a to all-b form. I used various structural and statistical mechanics tools to identify important residues involved in controlling the conformational changes. In the full-length RfaH, the interdomain interactions were found to present the major barrier in the structural conversion of RfaH-CTD from all-a to all-b form. I mapped the energy landscape for the conformational changes by calculating the potential of mean force using the Adaptive Biasing Force and Jarzynski Equality methods. Similarly, the interdomain salt-bridges in the eVP40 protomer were found to play a critical role in domain association and plasma membrane (PM) assembly. This molecular dynamic simulation study is supported by virus like particle budding assays investigated by using live cell imaging that highlighted the important role of these saltbridges. I also investigated the plasma membrane association of the eVP40 dimer in various PM compositions and found that the eVP40 dimer readily associates with the PM containing POPS and PIP2 lipids. Also, the CTD helices were observed to be important in stabilizing the dimer-membrane complex. Coarse-grained MD simulations of the eVP40 hexamer and PM system revealed that the hexamer enhances the PIP2 lipid clustering at the lower leaflet of the PM. These results provide insight on the critical steps in the Ebola virus life cycle.

This thesis is divided into two parts; the first part presents results on the effect of the flow of fluids and electrochemical bias on single walled carbon nanotubes (SWNT). Issues pertaining to the entry of water into the cylindrical pores of the SWNT and its freezing dynamics have also been addressed in the first part of the thesis. The second part of the thesis deals with Raman scattering studies of iron perovskite namely CaFeO3 and La0.33Sr0.67FeO3 across their charge-disproportionation transition temperatures. PART 1 Chapter 1: Introduction This chapter presents an overview of the systems studied in this thesis, i.e., (i) SWNT and (ii) iron perovskite’s containing iron in Fe4+(d4) state, namely CaFeO3 and La0.33Sr0.67FeO3. It also contains an introduction to the two spectroscopic techniques used in the present thesis, namely Raman scattering and Nuclear Magnetic Resonance. A quantum mechanical picture of Raman scattering, in general, and resonance Raman scattering in particular along with a brief introduction to the apparatus used both for the micro Raman and the low temperature experiments is presented in this chapter. A general introduction to Nuclear Magnetic Resonance (NMR) is also given with an emphasis on various interactions leading to the broadening of the NMR absorption linewidths. Chapter 2: Carbon nanotube liquid flow sensors This chapter presents experimental results and theoretical understandings of the generation of electrical signals by flowing polar/ionic liquids over a mat of SWNT. We first present experimental findings that the flow of a variety of liquids on SWNT bundles induces an electrical signal (voltage/current) in the sample along the direction of the flow. The electrical response is found to be a logarithmic function of the flow speed over a wide range. The magnitude of the signal generated depends sensitively on the ionic conductivity and the polar nature of the liquid and weakly on the viscosity of the liquid. Furthermore its direction can be controlled by electrochemical biasing of the nanotubes. The ratio of the open circuit voltage to the short circuit current is found to be governed by the nanotube resistance. These experimental findings are inconsistent with the conventional idea of a streaming potential as the possible cause. Our measurements suggest that the dominant mechanism responsible for this highly sub-linear response should involve a direct forcing of the free charge carriers in the nanotubes by the fluctuating Coulombic field of the liquid flowing past it. Two alternative understandings of the experimental findings are also presented in this chapter. The first mechanism invokes the idea of a “pulsating ratchet” whereby the charge carriers in the nanotubes experience an asymmetric spatial bias because of the shear-induced deformation of the ion-plus-polar atmosphere at the liquid-solid interface temporally modulated by the liquid flow. In addition, we also propose that experimental findings can be understood qualitatively in terms of three interrelated ideas: (a) Induced friction: The fluctuating charge density of the ions close to the nanotube couples coulombically to the charge carriers in the nanotube and, therefore, offers a friction to the motion of these charge carriers (in addition to the Ohmic friction intrinsic to the carbon nanotubes); (b) Flow-induced drag: In virtue of the above frictional coupling, an imposed liquid flow drags the charge carriers along through the nanotube; (c) Reduction of induced friction at high flow speeds: The space-time correlated Coulombic fluctuations, inherent to the liquid electrolyte, are advected by the liquid flow, and thus get Galilean boosted (Doppler shifted) as seen in the mean rest frame of the drifting carriers in the nanotube. This would cause a reduction of the frictional grip to the motion of the charge carriers in the nanotube with increasing flow speed resulting in a sublinear dependence of the charge drift-velocity (electrical response) on the liquid flow speed. With the above in mind, a quantitative derivation of these frictional effects, first from a heuristic argument, and then analytically from a Langevin-equation treatment have been presented. Chapter 3: Direct generation of voltage and current by gas flow over carbon nanotubes and semiconductors Having obtained experimental evidence of the generation of liquid flow induced electrical signals over single-walled carbon nanotubes, it was only natural to look for the same effect by flowing gases over nanotubes. We show here a direct generation of measurable voltages and currents when gas flows at modest speeds of a few meters per second over single-walled carbon nanotubes . Interestingly, unlike the previous effect (generation of voltages by flow of liquids over single-walled carbon nanotubes), this effect is not specific to single-walled carbon nanotubes and occurs for a wide variety of solids, including single and multi-walled carbon nanotubes, doped semiconductors and metals. Moreover, the gas flow induced signals depend quadratically on the gas flow velocities. This is in sharp contrast to the results obtained by flowing liquids over single-walled carbon nanotubes where the liquid flow generated signal was found to be logarithmically dependent on the flow velocities. In this chapter we provide evidence that the underlying mechanism for the gas flow generated electrical signal is an interplay of Bernoulli’s principle and the Seebeck effect: Pressure difference along streamlines gives rise to temperature difference across the sample which, in turn, produces the measured voltage. Chapter 4: Water at nanoscale confined in single-walled carbon nanotubes studied by NMR In this chapter, we seek experimental evidence of the occupancy of water in the cylindrical pores of the nanotubes. Proton NMR studies have been carried out as a function of temperature from 210 K to 300 K of water confined within SWNT. The NMR lineshape at and below the freezing point of bulk water is asymmetric which can be decomposed into a sum of two Lorentzians. The intensities of both the components decrease with lowering of temperature below 273 K, one component L1 vanishing below 242 K and the other component L2 below 217 K. Following the simulations of Koga et al. (Nature, 412, 802, 2001) showing that the radial density profile of confined water in SWNT has a distribution peak at the center which disappears below the freezing temperature, the L1 component is associated with the protons of the water molecules at the center and the L2 component is associated with protons of water molecules associated at a distance ~ 3Å away from the walls of the nanotubes. In this scenario the complete freezing of the water at ~ 212 K is preceded by the withdrawal of the water molecules from the center of the nanotubes. Chapter 5: Electrochemical tuning of band structure of single walled carbon nanotubes probed by in-situ resonance Raman scattering The work presented in this chapter is motivated by the experimental observation that SWNT have excellent actuating properties, i.e, porous sheets of carbon nanotubes were shown to suffer length changes when subjected to electrochemical bias, with action observed up to 1 KHz. The fast response of the nanotube actuator rules out any mechanism related to the intercalation of ions as is applicable to the case of the polymer actuators. This chapter presents results of in-situ resonance Raman scattering of SWNT investigated under electrochemical biasing. The experimental results show that the intensity of the radial breathing mode varies significantly in a non-monotonic manner as a function of the cathodic bias voltage, but does not change appreciably under anodic bias. The tangential mode is, however, not affected. These results can be quantitatively understood in terms of the changes in the energy gaps between the one-dimensional van Hove singularities in the electron density of states arising possibly due to the alterations in the overlap integral of π-bonds between the p-orbitals of adjacent carbon atoms. This chapter also contains results from ab-initio restricted Hartree Fock calculations in a simplistic geometry where a nanotube is surrounded by two concentric rings of ions. The ab-initio calculation results suggest that the dominant contribution to the strain developed in the nanotubes originates from the electrostatic interactions between the ions and the delocalized π electrons as compared to the doping effects. PART 2 Chapter 6: Raman scattering in CaFeO3 and La0.33Sr0.67FeO3 across the charge disproportionation phase transition Temperature dependent micro-Raman studies of orthorhombic CaFeO3 and rhombohedral La0.33Sr0.67FeO3 were carried out with an aim to study the role of phonons in the formation of the charge disproportioned state (Fe4+ → Fe5++Fe3+) below the transition temperature (Tco) of 290 K and 200 K, respectively. Shell model lattice dynamics calculations were performed for CaFeO3 to assign the Raman modes and determine their vibrational pattern. Temperature dependence of the peak positions and peak widths of various modes for both the systems show distinct changes across their respective transition temperatures. In CaFeO3 the symmetric stretching mode at 707 cm−1 splits into two modes, 707 cm−1 and 684 cm−1 . Interestingly, the 707 (684) cm−1 mode appears only in HH(HV) polarization. In comparison, the Raman band at 704 cm−1 in La0.33Sr0.67FeO3 which has been assigned to the Raman forbidden symmetric stretching mode, disappears below Tco. In addition, two modes at 307 cm−1 and 380 cm−1 of La0.33Sr0.67FeO3 approach each other at Tco. Our experiments show that for both the systems, CaFeO3 and La0.33Sr0.67FeO3, the lattice distortion changes across Tco. Chapter 7: Summary and future outlook The last chapter summarizes our main findings reported in the thesis. It also contains possible future studies which are worth pursuing to add further insights in the issues addressed.

Fluorescent proteins are valuable tools as biochemical markers for studying cellular processes. Red fluorescent proteins (RFPs) are highly desirable for in vivo applications because they absorb and emit light in the red region of the spectrum where cellular autofluorescence is low. The naturally occurring fluorescent proteins with emission peaks in this region of the spectrum occur in dimeric or tetrameric forms. The development of mutant monomeric variants of RFPs has resulted in several novel FPs known as mFruits. Though oxygen is required for maturation of the chromophore, it is known that photobleaching of FPs is oxygen sensitive, and oxygen-free conditions result in improved photostabilities. Therefore, understanding oxygen diffusion pathways in FPs is important for both photostabilites and maturation of the chromophores. We used molecular dynamics calculations to investigate the protein barrel fluctuations in mCherry, which is one of the most useful monomeric mFruit variants, and its GFP homolog citrine. We employed implicit ligand sampling and locally enhanced sampling to determine oxygen pathways from the bulk solvent into the mCherry chromophore in the interior of the protein. The pathway contains several oxygen hosting pockets, which were identified by the amino acid residues that form the pocket. We calculated the free-energy of an oxygen molecule at points along the path. We also investigated an RFP variant known to be significantly less photostable than mCherry and find much easier oxygen access in this variant. We showed that oxygen pathways can be blocked or altered, and barrel fluctuations can be reduced by strategic amino acid substitutions. The results provide a better understanding of the mechanism of molecular oxygen access into the fully folded mCherry protein barrel and provide insight into the photobleaching process in these proteins.

The purpose of this research project was to study the αᵧ phase in Alnico 6. Other phases were studies for comparison. Also the effect of an applied magnetic field on the formation of the αᵧ phase was investigated. Three single crystals of Alnico 6 were heat treated for one hour—one at 1250°C, one at 1000°C, and one at 800°C—and water-quenched. The microstructure of each sample was observed with the optical microscope, and X-ray diffraction patterns were taken to determine the crystal structure of the phases present. Several single crystal samples of Alnico 6 were heat treated at 1000°C and furnace-cooled. Some of the samples were heat treated and furnace-cooled in the presence of an applied magnetic field of about 5000Oe, and the others were heat treated and furnace-cooled without an applied magnetic field. Each set of samples were electrothinned, and the microstructure of the αᵧ and α₁ ₊ α₂ phases was studied using the electron microscope. Electron diffraction patterns and electron micrographs were taken from αᵧ regions and α₁ ₊ α₂ regions of each sample. By a combination of X-ray and electron diffraction, it was determined that the crystal structure of the α, α₁, α₂ and αᵧ phases is body-centered cubic, with a lattice parameter of 2.87 Å. Electron diffraction showed that the crystal structure of the combined α₁ ₊ α₂ phases is ordered body-centered cubic, and that the lattices of these two phases are coherent. Other investigators have found that only the α₁ phase is ordered in Alnico 5 and Alnico 8 and thus is believed be the case in Alnico 6 also. Electron diffraction showed the αᵧ phase to be ordered, with the degree of ordering less than that in the α₁ phase. Some difference was noted between the αᵧ phase formed with a magnetic field and that formed without a magnetic field. The αᵧ formed with a magnetic field showed twinning and some small lattice rotations, while stat formed without a field did not. The reason for this is not known.

In this thesis, we have employed two computational methods, molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) MD simulations with umbrella sampling (US), to gain insights into the molecular mechanism governing the molecular recognition and reactivity in several protein-ligand complexes. Three systems involving protein-ligand interactions are examined in this dissertation utilizing well-established computational methodologies and mathematical modeling. The three proteins studied here are acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1). These enzymes are known to interact with a variety of ligands. AChE dysfunction caused by organophosphorus (OP) chemicals is a severe hazard since AChE is a critical enzyme in neurotransmission. Oximes are chemical compounds that can reactivate inhibited AChE; hence in the development of better oximes, it is critical to understand the mechanism through which OPs block AChE. We have described the covalent inhibition mechanism between AChE and the OP insecticide phorate oxon and its more potent metabolites and established their free energy profiles using QM/MM MD-US for the first time. Our results suggest a concerted mechanism and provide insights into the challenges in reactivating phorate oxon inhibited AChE. Reactivating BChE is another therapeutic approach to detoxifying circulating OP molecules before reaching the target AChE. We explored the covalent modification of BChE with phorate oxon and its metabolites using hybrid quantum mechanics/molecular mechanics (QM/MM) umbrella sampling simulations (PM6/ff14SB) for the inhibition process. Our results reveal that the mechanism is distinct between the inhibitors. The PM6 methodology is a good predictor of these compounds' potency, which may efficiently help study OPs like phorate oxon with larger leaving groups. Finally, we investigated the interactions between Peptidyl-prolyl isomerase (PPIase), which consists of a peptidyl isomerase (PPIase) domain flexibly tethered to a smaller Trp-Trp (WW) protein-binding domain, and chimeric peptides based on the human histone H1.4 sequence (KATGAApTPKKSAKW), as well as the effects on inter-domain dynamics. Using explicit solvent MD simulations, simulated annealing, and native contact analysis, our modeling sugget that the residues in the N-terminal immediate to the pSer/Thr Pro site connect the PPIase and WW domains via a series of hydrogen bonds and native contacts.

The goal of this thesis has been to find a means of i) designing an active square particle, and ii) continuously varying its degree of activity with the objective of understanding the effects of activity on the various phases of granular matter. The motivations, results and limitations of our methods of creating active particles are discussed in this thesis. The applicability of a stochastic model based on the Langevin equation in 2D as well as implications for future experiments are also discussed.

This thesis presents ultrafast photophysical measurements on a number of phosphorescent iridium complexes and establishes relationships between the relaxation rates and the vibrational properties of the material. When ultrafast luminescence is measured on the peak of the phosphorescence spectrum and on its red-side, 230 fs and 3 ps decay time constants were observed in all materials studied, and this was attributed to population redistribution amongst the three electronic substates of the lowest triplet metal-ligand charge transfer (MLCT) state. The observation of luminescence at higher values of energy embodied ultrafast dissipation of excess energy by intramolecular vibrational redistribution (IVR) and it was found that the dissipation channels and rate of IVR could be modified by chemical modification of the emitting molecule. This was tested in two ways. Firstly by adding electronically inactive dendrons to the core, an increase in the preference for dissipation of excess energy by IVR rather than by picosecond cooling to the solvent molecules was found, but this did not change the rate of IVR. The second method of testing was by fusing a phenyl moiety directly onto the ligand, this both increased the rate of IVR and also the preference for dissipation by it rather than by picosecond cooling. Fluorescence was recorded in an iridium complex for the first time and a decay time constant of 65 fs was found, thus allowing a direct observation of intersystem crossing (ISC) to be made. In a deep red emitting iridium complex internal conversion (IC) and ISC were observed and the factors controlling their time constants deduced. IC was found to occur by dissipation of excess energy by IVR. The rate of IC was found to be dependent on the amount of vibrational energy stored in the molecule, with IC fast (< 45 fs) when < 0.6 eV of energy is stored and slower (~ 70 fs) when the value is > 0.6 eV. The rate of ISC agreed with these findings, indicating that the very process of ISC may be thought of as closely analogous to that of IC given the strongly spin-mixed nature of the singlet and triplet MLCT states.

La présente étude examine et compare le comportement de deux nanocomposites à base de particules sphériques (SiO2 et TiO2) générées in situ au sein d'une matrice PDMS par le procédé sol-gel. La synthèse des réseaux PDMS-SiO2 et PDMS-TiO2 a été effectuée en utilisant plusieurs catalyseurs pour obtenir des morphologies différentes. Pour le suivi des réactions de synthèse et la détermination des taux de silice ou d'oxyde de titane, la pesée et la spectroscopie infrarouge ont été utilisées. La morphologie, l'état de dispersion, l'interaction polymère-charge, la dégradation thermique et les propriétés mécaniques ont été caractérisés et comparés au travers de plusieurs méthodes : 1) La spectroscopie IR à transmission pour la présence d'eau dans les nanocomposites ; 2) La MET et le SANS pour la dispersion et la morphologie ; 3) La DSC, la RMN du proton, la TSDC et le gonflement pour l'interaction polymère-charge ; 4) L'ATG pour la dégradation thermique ; 5) La Traction unixiale et la mesure dynamique pour les propriétés mécaniques. Des différences et des similitudes ont été observées entre les réseaux PDMS-SiO2 et PDMS-TiO2. Les deux types de réseaux aboutissent à un bon renforcement avec une amélioration des modules élastiques et des propriétés de rupture selon le catalyseur utilisé. Des différences apparaissent sur la forme des courbes de traction (avec un comportement plastique plus marqué sur les échantillons TiO2) et on note l'absence d'effet Payne pour les réseaux PDMS-SiO2 contrairement aux réseaux PDMS-TiO2. Les systèmes PDMS-SiO2 montrent une amélioration des propriétés thermiques par rapport au réseau non-chargé. De plus cette amélioration est liée aux conditions de synthèse et notamment à la nature du catalyseur. En effet, l'amélioration des propriétés thermiques est meilleure dans les échantillons catalysés avec le DEA. Pour les échantillons PDMS-TiO2, on a plutôt une dégradation des propriétés thermiques, les échantillons chargés de TiO2 se dégradant plus vite que le réseau non chargé et à plus faible température. Toutes les différences et similitudes observées ont pu être reliées à la nature de la charge, à la différence de morphologie (taille des particules, existence d'un réseau percolant de charge etc...) et à la qualité de l'interface PDMS-SiO2 ou PDMS-TiO2.

Cette étude porte sur la réticulation du caoutchouc naturel époxydé (ENR) par les acides dicarboxyliques, via les sites époxy. La réaction de réticulation de ces élastomères fonctionnalisés, contenant 10 à 50 % en moles de sites époxy réactifs, a été suivie par rhéologie à 180°C. Les matériaux obtenus ont été caractérisés par des expériences de traction, par analyse mécanique dynamique et pas DSC. L'étude de mélanges binaires d'ENR et d'acide dodécanedioïque a montré que les propriétés mécaniques sont optimales pour un certain ratio d'agent réticulant, mais qu'elles sont limitées par le long traitement thermique nécessaire pour réticuler le matériau (3 heures). L'ajout de 1,2-diméthylimidazole (DMI) a permis d'augmenter considérablement l'efficacité de la réaction (plateau atteint en seulement 20 minutes). Une quantité équimolaire d'accélérateur et de fonctions carboxyliques est nécessaire pour optimiser la cinétique et les propriétés des matériaux à la rupture. Ceci est associé à la formation d'un dicarboxylate d'imidazolium, soluble dans la matrice élastomère. Le rôle de cet intermédiaire a été mis en valeur par des expériences de RMN du solide, couplées à de la RMN en solution sur un polyisoprène liquide époxydé. Ces expériences de RMN ont également confirmé que les ponts du réseau étaient des liaisons esters, et ont permis d'établir la régiosélectivité de la réaction. L'ajout de charges et d'antioxydants a permis de développer un matériau industriel. Des expériences de fatigue et de vieillissement sur ces systèmes chargés montrent que les performances des réseaux ester se comparent favorablement à celles des réseaux obtenus par vulcanisation classique au soufre ou au peroxyde.

Nous décrivons un procédé de coacervation original et polyvalent qui permet d'encapsuler des substances hydrophobes dans l'eau avec un contrôle précis des propriétés de la dispersion finale. Le composé hydrophobe est d'abord émulsionné dans une solution aqueuse d'un polyélectrolyte amphiphile à squelette hydrophobe de type " alkali-swellable ". Un changement des conditions physicochimiques (pH, force ionique) provoque alors la précipitation du polymère à la surface des gouttelettes hydrophobes. Notre travail s'organise suivant trois directions complémentaires. Tout d'abord, nous nous attachons à comprendre la microstructure des solutions de polymères, d'où découlent en partie leurs propriétés interfaciales. Pour cela, nous développons une méthode originale de détection d'agrégats hydrophobes qui exploite le solvatochromisme du Rouge du Nil. Puis, nous analysons les propriétés rhéologiques linéaires et non linéaires des solutions de copolymères -viscosité, forces normales, fracturation aux grandes déformations- en relation avec la composition des chaînes et les caractéristiques physicochimiques des solutions. Enfin nous posons les bases d'un modèle d'émulsification dans des phases continues viscoélastiques. Ce cadre conceptuel permet de relier l'architecture et la composition des copolymères amphiphiles utilisés à leurs propriétés rhéologiques en solution et aux caractéristiques de la dispersion obtenue à la fin du procédé. Il est ainsi possible de définir à priori les conditions optimales qui permettront d'encapsuler à façon une large gamme de substances hydrophobes.