This thesis essentially deals with the development and numerical explorations of a few improved Monte Carlo filters for nonlinear dynamical systems with a view to estimating the associated states and parameters (i.e. the hidden states appearing in the system or process model) based on the available noisy partial observations. The hidden states are characterized, subject to modelling errors, by the weak solutions of the process model, which is typically in the form of a system of stochastic ordinary differential equations (SDEs). The unknown system parameters, when included as pseudo-states within the process model, are made to evolve as Wiener processes. The observations may also be modelled by a set of measurement SDEs or, when collected at discrete time instants, their temporally discretized maps. The proposed Monte Carlo filters aim at achieving robustness (i.e. insensitivity to variations in the noise parameters) and higher accuracy in the estimates whilst retaining the important feature of applicability to large dimensional nonlinear filtering problems. The thesis begins with a brief review of the literature in Chapter 1. The first development, reported in Chapter 2, is that of a nearly exact, semi-analytical, weak and explicit linearization scheme called Girsanov Corrected Linearization Method (GCLM) for nonlinear mechanical oscillators under additive stochastic excitations. At the heart of the linearization is a temporally localized rejection sampling strategy that, combined with a resampling scheme, enables selecting from and appropriately modifying an ensemble of locally linearized trajectories whilst weakly applying the Girsanov correction (the Radon- Nikodym derivative) for the linearization errors. Through their numeric implementations for a few workhorse nonlinear oscillators, the proposed variants of the scheme are shown to exhibit significantly higher numerical accuracy over a much larger range of the time step size than is possible with the local drift-linearization schemes on their own. The above scheme for linearization correction is exploited and extended in Chapter 3, wherein novel variations within a particle filtering algorithm are proposed to weakly correct for the linearization or integration errors that occur while numerically propagating the process dynamics. Specifically, the correction for linearization, provided by the likelihood or the Radon-Nikodym derivative, is incorporated in two steps. Once the likelihood, an exponential martingale, is split into a product of two factors, correction owing to the first factor is implemented via rejection sampling in the first step. The second factor, being directly computable, is accounted for via two schemes, one employing resampling and the other, a gain-weighted innovation term added to the drift field of the process SDE thereby overcoming excessive sample dispersion by resampling. The proposed strategies, employed as add-ons to existing particle filters, the bootstrap and auxiliary SIR filters in this work, are found to non-trivially improve the convergence and accuracy of the estimates and also yield reduced mean square errors of such estimates visà-vis those obtained through the parent filtering schemes. In Chapter 4, we explore the possibility of unscented transformation on Gaussian random variables, as employed within a scaled Gaussian sum stochastic filter, as a means of applying the nonlinear stochastic filtering theory to higher dimensional system identification problems. As an additional strategy to reconcile the evolving process dynamics with the observation history, the proposed filtering scheme also modifies the process model via the incorporation of gain-weighted innovation terms. The reported numerical work on the identification of dynamic models of dimension up to 100 is indicative of the potential of the proposed filter in realizing the stated aim of successfully treating relatively larger dimensional filtering problems. We propose in Chapter 5 an iterated gain-based particle filter that is consistent with the form of the nonlinear filtering (Kushner-Stratonovich) equation in our attempt to treat larger dimensional filtering problems with enhanced estimation accuracy. A crucial aspect of the proposed filtering set-up is that it retains the simplicity of implementation of the ensemble Kalman filter (EnKF). The numerical results obtained via EnKF-like simulations with or without a reduced-rank unscented transformation also indicate substantively improved filter convergence. The final contribution, reported in Chapter 6, is an iterative, gain-based filter bank incorporating an artificial diffusion parameter and may be viewed as an extension of the iterative filter in Chapter 5. While the filter bank helps in exploring the phase space of the state variables better, the iterative strategy based on the artificial diffusion parameter, which is lowered to zero over successive iterations, helps improve the mixing property of the associated iterative update kernels and these are aspects that gather importance for highly nonlinear filtering problems, including those involving significant initial mismatch of the process states and the measured ones. Numerical evidence of remarkably enhanced filter performance is exemplified by target tracking and structural health assessment applications. The thesis is finally wound up in Chapter 7 by summarizing these developments and briefly outlining the future research directions

Recently, high-κ materials have become the focus of research and been extensively utilized as the gate dielectric layer in aggressive scaled complementary metal-oxide-semiconductor (CMOS) technology. Hafnium dioxide (HfO2) is the most promising high-κ material because of its excellent chemical, thermal, mechanical and dielectric properties and also possesses good thermodynamic stability and better band offsets with silicon. Hence, HfO2 has already been used as gate dielectric in modern CMOS devices. For future technologies, it is very difficult to scale the silicon transistor gate length, so it is a necessary requirement of replacing the channel material from silicon to some high mobility material. Two-dimensional layered materials such as graphene and molybdenum disulfide (MoS2) are potential candidates to replace silicon. Due to its planar structure and atomically thin nature, they suit well with the conventional MOSFET technology and are very stable mechanically as well as chemically. HfO2 plays a vital role as a gate dielectric, not only in silicon CMOS technology but also in future nano-electronic devices such as graphene/MoS2 based devices, since high-κ media is expected to screen the charged impurities located in the vicinity of channel material, which results in enhancement of carrier mobility. So, for sustenance and enhancement of new technology, extensive study of the functional materials and its processing is required. In the present work, optimization of HfO2 thin films for gate dielectric applications in Nano-electronic devices using electron beam evaporation is discussed. HfO2 thin films have been optimized in two different thickness regimes, (i) about 35 nm physical thicknesses for back gate oxide graphene/MoS2 transistors and (ii) about 5 nm physical thickness to get Equivalent Oxide Thickness (EOT) less than 1 nm for top gate applications. Optical, chemical, compositional, structural and electrical characterizations of these films have been done using Ellipsometry, X-ray Photoelectron Spectroscopy (XPS), Rutherford Back Scattering (RBS), X-ray Diffraction (XRD), Capacitance-Voltage and Current-Voltage characterization techniques. The amount of O2 flow rate, during evaporation is optimized for 35 nm thick HfO2 films, to achieve the best optical, chemical and electrical properties. It has been observed that with increasing oxygen flow rate, thickness of the films increased and refractive index decreased due to increase in porosity resulting from the scattering of the evaporant. The films deposited at low O2 flow rates (1 and 3 SCCM) show better optical and compositional properties. The effects of post deposition annealing (PDA) and post metallization annealing (PMA) in forming gas ambient (FGA) on the optical and electrical properties of the films have been analyzed. The film deposited at 3 SCCM O2 flow rate shows the best properties as measured on MOS capacitors. A high density film (ρ=8.2 gram/cm3, 85% of bulk density) with high dielectric constant of κ=19 and leakage current density of J=2.0×10-6 A/cm2 at -1 MV/cm has been achieved at optimized deposition conditions. Bilayer graphene on HfO2/Si substrate has been successfully identified and also transistor has been fabricated with HfO2 (35 nm) as a back gate. High transconductance compared to other back gated devices such as SiO2/Si and Al2O3/Si and high mobility have been achieved. The performance of back gated bilayer graphene transistors on HfO2 films deposited at two O2 flow rates of 3 SCCM and 20 SCCM has been evaluated. It is found that the device on the film deposited at 3 SCCM O2 flow rate shows better properties. This suggests that an optimum oxygen pressure is necessary to get good quality films for high performance devices. MoS2 layers on the optimized HfO2/Si substrate have been successfully identified and transistor has been fabricated with HfO2 (32 nm) as a back gate. The device is switching at lower voltages compared to SiO2 back gated devices with high ION/IOFF ratio (>106). The effect of film thickness on optical, structural, compositional and electrical properties for top gate applications has been studied. Also the effect of gate electrode material and its processing on electrical properties of MOS capacitors have been studied. EOT of 1.2 nm with leakage current density of 1×10-4 A/cm2 at -1V has been achieved.

Chalcogenide glasses are highly nonlinear optical materials which can be used for fabricating active and passive photonic devices. This thesis work deals with the fabrication of buried, three dimensional, channel waveguides in chalcogenide glasses, using ultrafast laser inscription technique. The femtosecond laser pulses are focused into rare earth ions doped and undoped chalcogenide glasses, few hundred microns below from the surface to modify the physical properties such as refractive index, density, etc. These changes are made use in the fabrication of active and passive photonic waveguides which have applications in integrated optics. The first chapter provides an introduction to the fundamental aspects of femtosecond laser inscription, laser interaction with matter and chalcogenide glasses for photonic applications. The advantages and applications of chalcogenide glasses are also described. Motivation and overview of the present thesis work have been discussed at the end. The methods of chalcogenide glass preparation, waveguide fabrication and characterization of the glasses investigated are described in the second chapter. Also, the details of the experiments undertaken, namely, loss (passive insertion loss) and gain measurements (active) and nanoindentation studies are outlined. Chapter three presents a study on the effect of net fluence on waveguide formation. A heat diffusion model has been used to solve the waveguide cross-section. The waveguide formation in GeGaS chalcogenide glasses using the ultrafast laser, has been analyzed in the light of a finite element thermal diffusion model. The relation between the net fluence and waveguide cross section diameter has been verified using the experimentally measured properties and theoretically predicted values. Chapter four presents a study on waveguide fabrication on Er doped Chalcogenide glass. The active and passive characterization is done and the optimal waveguide fabrication parameters are given, along with gain properties for Er doped GeGaS glass. A C-band waveguide amplifier has been demonstrated on Chalcogenide glasses using ultrafast laser inscription technique. A study on the mechanical properties of the waveguide, undertaken using the nanoindentation technique, is presented in the fifth chapter. This work brings out the close relation between the change in mechanical properties such as elastic modulus and hardness of the material under the irradiation of ultrafast laser after the waveguide formation. Also, a threshold value of the modulus and hardness for characterizing the modes of the waveguide is suggested. Finally, the chapter six provides a summary of work undertaken and also discusses the future work to be carried out.

Currently conventional sources like coal, petroleum and natural gas meet the energy requirements of developing and undeveloped countries. Over a period of time there is high risk of these energy sources getting depleted. Hence an alternate source of energy i.e. renewable energy is the need of the hour. The advantages of renewable energy like higher sustainability, lesser maintenance, low cost of operation, and minimal impact on the environment make the role of renewable energy sources significant. Out of the various renewable energy sources like solar energy, wind energy, hydropower, biogas, tidal and geothermal, usage of solar energy is gradually increasing. Among various solar energy sources, Photovoltaics has dominated over the past two decades since it is free clean energy and availability of abundant sunlight on earth. Over the past few decades, thin film solar cells (TFSC) have gained considerable interest as an economically feasible alternative to conventional silicon (Si) photovoltaic devices. TFSCs have the potential to be as efficient as Si solar cells both in terms of conversion efficiency as well as cost. The advantages of TFSC are that they are easy to prepare, lesser thickness, requires lesser materials, light weight, low cost and opto-electronic properties can be tuned by varying the process parameters. The present study is focused on the fabrication of AgInS2/ZnS heterojunction thin film solar cell. AgInS2 absorber layer is deposited using both vacuum (sputtering/sulfurization) and non-vacuum (ultrasonic spray pyrolysis) techniques. ZnS window layer is prepared using thermal evaporation technique, detailed experimental investigation has been conducted and the results have been reported in this work. The thesis is divided into 6 chapters. Chapter 1 gives general introduction about solar cells and working principle of solar cell. It also discusses thin film solar cell technology and its advantages. Layers of thin film solar cell structure, Significance of each layers and possible materials to be used are emphasized. A detailed overview of the available literature on both AgInS2 absorber layer and ZnS window layer has been presented. Based on the literature review, objectives of the present work are defined. Chapter 2 explains the theory and experimental details of deposition techniques used for the growth of AgInS2 and ZnS films. Details of characterization techniques to study film properties are described in detail. Chapter 3 presents a systematic study of AgInS2 thin films deposited by sulfurization of sputtered Ag-In metallic precursors. Initially, AgInS2 films are deposited by varying the substrate temperature and properties of as-deposited films are characterized. Structural, morphological, electrical and optical properties of AgInS2 films are explained. From these studies, samples with better properties at particular substrate temperature are optimized. By fixing the substrate temperature, deposition time of silver is varied by keeping other deposition conditions same and the properties of films are discussed. It was observed that deposition time of silver doesn’t have much impact on structural properties of AgInS2 films. However, opto-electric properties of AgInS2 films are enhanced. Based on characterization studies, deposition time of silver is optimized. Deposition time of indium is varied by keeping substrate temperature and silver deposition to optimized value. The properties of as-deposited films are discussed. Based on the above studies, the optimized p type films have a band gap of 1.64 eV, carrier concentration of 1013 ions/cm3 and Resistivity of order 103 Ω-cm. Chapter 4 presents a systematic study of AgInS2 thin films deposited by ultrasonic spray pyrolysis. AgInS2 films are deposited by varying the substrate temperature and properties of as deposited films are characterized. Structural, morphological, electrical and optical properties of AgInS2 films are explained. From these studies, samples with better properties at particular substrate temperature are optimized. By fixing the substrate temperature, concentration of silver molarity in the precursor solution is varied by keeping other deposition conditions same and the properties of films are discussed. Structural, optical and electrical properties of AgInS2 films are enhanced with the increase in silver concentration. Based on characterization studies, concentration of silver is optimized. Similarly concentration of indium molarity in the precursor solution is varied and the properties of as-deposited films are discussed. Finally, sulfur molarity in the precursor solution is varied and properties of films are discussed. It was observed that increasing sulfur after certain limit does not have any effect on the properties of the films. Based on the above studies, this method resulted in the films with resistivity of 103 Ω-cm and band gap of 1.64 eV. These films showed a carrier concentration of 1013 ions/cm3. Chapter 5 describes the growth of ZnS films using thermal evaporation technique. Influence of thickness on the properties of ZnS films is explained. Samples with good crystallinity, high transmission, and wider gap are selected for device fabrication. This p type layer showed a band gap of 3.52 eV. Solar cells have been fabricated using the AgInS2 films developed by both sputtering and ultrasonic spray pyrolysis techniques. A maximum cell efficiency of 0.92 percent has been achieved for the cell with 0.950 µm thick sputtered AgInS2 layer and thermally evaporated 42 nm thick ZnS layer. In comparison, the ultrasonic spray pyrolysis deposited films gave an efficiency of 0.54 percent. These values are comparable to those mentioned in a couple of reports earlier. Chapter 6 summarizes the conclusions drawn from the present investigations and scope of future work is suggested.

<div>The interactions of femtosecond lasers with gold targets were investigated with a numerical method combining molecular dynamics (MD) and the two-temperature model (TTM). Previous works using MD-TTM method did not consider all the thermodynamic parameters and the interatomic potential dependent of the electron temperature simultaneously. Therefore, we developed a LAMMPS function to achieve this. To accurately capture the physics behind the interactions, we also included the electron blast force from free electron pressure and the modified Fourier law with steep electron temperature gradient in our model. For bulk materials, a stress non-reflecting and heat conducting boundary is added between the atomistic and the continuum parts. The modified boundary force in our study greatly reduces the reflectivity of the atomistic-continuum boundary compared with its original form. Our model is the first to consider all these factors simultaneously and manage to predict four femtosecond laser ablation phenomena observed in the experiments. </div><div><br></div><div>In this dissertation, the thermodynamic parameters in the two-temperature model were extensively explored. We considered three different approaches to calculate these parameters: namely interpolation, <i>ab initio</i> calculation, and analytical expression. We found that simple interpolation between solid state and plasma state could lead to high level of inaccuracy, especially for electron thermal conductivity. Therefore, <i>ab initio</i> calculation and analytical expression were used for the calculation of the thermodynamic parameters in more advanced studies. The effects of electron thermal conductivity and electron-phonon coupling factor on electron and lattice temperatures were analyzed.</div><div><br></div><div>Our studies considered electron temperature dependent (ETD) and electron temperature independent (ETI) interatomic potentials. The ETI interatomic potential is easier to implement and therefore it is used in our phase change study to investigate the effects of target thickness on melting. Homogeneous melting occurred for thin films, while melting can be observed through the movement of the solid-liquid interface in thick or bulk materials. However, the ETI potential overestimated the bond strength at high temperatures. Therefore, ablation process was studied with the ETD potential. Three ablation mechanisms were found in our simulations at different laser fluences. Short nonthermal ablation was only observed at the ablation threshold. With increasing laser fluence, spallation was then seen. In high laser fluence regime, phase explosion occurred on the surface and coexisted with spallation.</div><div><br></div><div>Lastly, we researched on the effects of the delay time between two femtosecond laser pulses. Various delay times did not have much influence on melting depth. In low laser fluence regime, with increasing delay time, the target went through nonthermal ablation, to spallation and to no ablation. In high laser fluence regime, longer delay time encouraged phase explosion while suppressed spallation.</div>

<p>  We utilize thermoreflectance (TR) thermal imaging to experimentally study heat transport and reliability of micro to nano-scale devices. TR imaging provides 2D thermal maps with sub-micron spatial resolution. Fast thermal transients down to 50 ns resolution can be captured. In addition, finite element modeling is carried out to better understand the underlying physics of the experiment. We describe four main applications; 1) Development of a full-field thermoreflectance imaging setup with a variable optical (laser) heating source as a general characterization tool. We demonstrate the setup’s sensitivity to extract anisotropic<br> thermal conductivity of thin flms and evaluate its sensitivity for detecting buried (below the surface) defects in 3D integrated circuits. This method provides a low-cost noncontact alternative to destructive defect localization methods. It also doesn’t require any special sample<br> preparations. 2) Physics of localized electromigration-failures in metallic interconnects is investigated. One can distinguish two separate mechanisms responsible for electromigration depending on the current density and temperature gradient. 3) Thermal transport in silicon near sub-micron electrical heaters is studied. Quasiballistic and hydrodynamic (fluid-like) behavior is observed at room temperature for different device sizes and geometries. 4) Temperature-dependent thermoreflectance coefcient of phase-change materials is characterized. We focus on tungsten (W) doped VO₂ (W_0.02V_0.98O₂) compound, which experiences an insulator-to-metal transition (IMT) at ≈33 °C. Strong TR-signal non-linearity is observed at the IMT temperature. This non-linearity is used to localize the phase-change boundary with resolutions down to ≈0.2 µm. TR full-feld imaging enables a simple and fast characterization complementing near-feld microscopy techniques. <br>  </p>

This thesis discusses the development of MANGO, a tool created to model normal-conducting magnets which were installed in the 1970s in the experimental areas at CERN, and store their analysis. MANGO formulates an answer to two problems faced by the physicists of the Beam Department when they model a beam line: first, how to produce new magnetic field maps and, second, how to easily access existing ones? It contains a multi-use package that offers an automated process to produce magnetic field maps from finite-element models of magnets. In addition, the package can visualise the field density or the flux lines of a magnet, and can benchmark a model and automatically store the solutions in a database, while tailoring its content to the level of expertise in electromagnetism and finite-elements modelling of the users. To development of the tool starts by modelling the different types of the normal-conducting magnets using two-dimensional finite element modelling (Opera-2D). After the successful development of one finite element model, it is benchmarked to justify its use in the creation of magnetic field maps. To address the second challenge and avoid any duplication of work, MANGO integrates a Git repository with submodules, where the finite-element models, the magnetic field maps and the documentation are stored. / I detta examensarbete diskuteras utvecklingen av MANGO, ett verktyg som skapats för att modellera normalkonduktiva elektromagneter, som installerades på 1970-talet i CERN:s experimentområden, och lagra deras analys. Mer specifikt formulerar MANGO ett svar på två problem som fysiker vid Beam Department står inför när de modellerar en partikelstrållinje. Hur skapar man nya magnetfältskartor och, hur får man enkelt tillgång till nuvarande magnetfältskartor? Det innehåller ett programbibliotek med flera användningsområden, som skapar nya magnetfältskartor från nuvarande magnetmodeller, som skapas av programbibliotek självt. Med den programbibliotek kan man visualisera en magnets fältdensitet eller flödeslinjer, benchmarka modellen och automatiskt lagra magnetlösningar och numeriska simuleringar i databasen, utöver att modellera magneter, och samtidigt ge möjlghet för anpassning av innehållet till användarens kunskapsnivå och färdigheter. För att utveckla MANGO börjar författaren med att modellera de olika typerna av normalkonduktiva elektromagneter med hjälp av tvådimensionell finit elementmodellering (Opera-2D). Efter den framgångsrika utvecklingen av en finit elementmodell, fortsätter författaren med benchmarking av modell för att motivera dess användning inom skapandet av magnetfältskartor. För att besvara det andra problemet integrerar MANGO ett Git-databas där finita elementmodellerna, magnetfältskartorna och dokumentationen lagras, för att undvika dubbelarbete. Git databas har undermoduler för att kunna skapa olika åtkomster per användarnivå.

In recent years great advances in the field of biomedical engineering and organic electronics have been achieved. One promising application would be the regulation of blood glucose concentration in type 2 diabetes patients. This application would eliminate medication and would improve the standard of life. To achieve this goal a system is needed which receives information about the glucose concentration and reacts upon it. This output reaction could then be used to stimulate the body's own glucose regulation mechanisms. This thesis combined a glucose sensor with an artificial neuron to take the first step towards such a system. Two different artificial neurons, the Axon-Hillock neuron and the astable multivibrator, were characterized and examined upon their usability. The Axon-Hillock, build with organic electrochemical transistors, revealed that it could be applied for both regulating high and low blood glucose concentrations. The astable multivibrator, build with silicon-based transistors, was not as functional as the Axon-Hillock neuron but with more development it could become as good. The placement of the glucose sensor in the astable multivibrator circuit is essential parameter to consider. The results demonstrate that the examined system is functional and could become a part of a larger closed-loop system. Future tests on an animal model may demonstrate its viability as a treatment for type 2 diabetes.

This thesis explores and evaluates the temperature measuring capabilities of a phase-sensitive optical time-domain reflectometer (φ-OTDR), which exploits Rayleigh backscattering in normal single mode optical fibers. The device is constructed and its setup explained, and a protocol for making temperature measurements with it is developed. Performance tests are made and the device is shown to achieve fully distributed temperature measurements on fibers hundreds of meters in length with a spatial resolution of 1 m and a temperature resolution of 0.1 K. In addition, the capabilities of the device to measure normal strain in the measurement fiber are tested using the same approach, albeit with less success. The device is capable of very precise measurements, making it very sensitive to the environmental conditions around the measuring fiber but also susceptible to disturbances. Some discussion is had on how to avoid or deal with these disturbances. Furthermore, the technique is shown to be able to run in conjunction with other φ-OTDR measurement techniques from the same device simultaneously. / Det här examensarbetet utforskar och utvärderar förmågorna att mäta temperatur hos en fas-känslig optisk tidsdomän-reflektometer (φ-OTDR), som utnyttjar bakåtriktad Rayleigh-spridning i vanliga optiska singelmodfibrer. Anordningen konstrueras och dess komponentstruktur förklaras, och ett protokoll tas fram för att utföra mätningar med den. Prestandatester utförs och anordningen visas kapabel att göra fullt distribuerade temperaturmätningar längs hundratals meter långa fibrer, med en rymdsupplösning på 1 m och en temperaturupplösning på 0.1 K. Dessutom testas förmågan att mäta normaltöjning hos testfibern med samma metod, dock med mindre framgång. Anordningen är väldigt känslig för förhållandena i omgivningen runt mätningsfibern, vilket gör den kapabel till mätningar med mycket hög precision, men också mottaglig för störningar. Lite diskussion hålls kring hur dessa störningar kan undvikas eller hanteras. Vidare visas att mätningstekniken kan köras samtidigt som andra φ-OTDR-baserade tekniker från samma anordning.

Ligand-gated ion channels play an important role in electrochemical signal transduction across diverse organisms, yet their structural and functional intricacies are not fully understood. Particularly lacking is the knowledge of their response to variations in pH, an aspect necessary for understanding their physiological relevance and potential therapeutic targeting in neurological diseases. In this thesis project, I have investigated the mechanistic response of sTeLIC, a recently reported prokaryotic member of the pentameric ligand-gated ion channel family, to different environmental conditions. Using molecular dynamics simulations, a total of 16 different environmental conditions have been explored including variations in pH (neutral and alkaline), the presence and absence of calcium, and the inclusion of an electric field acting as an external driving force on charged atoms. The results reveal a comprehensive pH-sensing and gating mechanism involving key residues, notably E106 (on the β6 strand) and E160 (on loop F), and their local microenvironments. Additionally, an inhibitory mechanism for calcium is proposed, with E160 playing an important role. The simulations including an electric field has provided support for a non-conventional ion pathway through the pore. Collectively, these results offer insights into a mechanistic framework that may extend to other physiologically relevant systems, providing a foundation for further investigations and potential future therapeutic intervention. / pLGICs har en viktig roll i det elektrokemiska signalsystemet i många organismer, men detaljerna i deras struktur och framför allt funktion är fortfarande inte helt klargjorda. Särskilt är detaljerna kring deras reaktion på ändringar i pH-värde relativt okända, vilket är en viktig del i att förstå kanalernas fysiologiska roll och för att potentiellt hitta läkemedel mot neurologiska sjukdomar där dessa är inblandade. I det här arbetet har jag undersökt hur sTeLIC, som är ett nyligen publicerat bakteriellt protein i familjen pLGICs, reagerar på olika ändringar i miljön. Jag har använt molekyldynamiksimuleringar för att unders öka 16 olika miljöer med två olika pH-värden (neutralt och alkaliskt), med eller utan kalcium samt med eller utan en extern drivkraft över membranet i form av ett elektrisk fält. Arbetet har resulterat i en föreslagen mekanism förhur sTeLIC känner av pH och hur öppningen av kanalen går till. Denna mekanism involverar aminosyrorna E106, som finns på β6-strängen, och E160, som finns på F-loopen, samt deras omgivning. Dessutom har en modulatorisk mekanism föreslagits för en kalciuminhiberande effekt på sTeLIC som också involverar E160. Simuleringarna med en drivkraft över membranet har gett stöd för en ny väg för joner genom kanalen. Tillsammans ger dessa resultat insikt i en mekanism som eventuellt kan appliceras p ̊a andra system. Detta har lagt grunden för fortsatt undersökning som potentiellt kan leda till framtida läkemedelsutveckling inom området.