Les interactions protéine-protéine sont souvent contrôlées par de petits domaines protéiques qui régulent les chemins de signalisation au sein des cellules eucaryotes. Les domaines PDZ sont parmi les domaines les plus répandus et les plus étudiés. Ils reconnaissent spécifiquement les 4 à 10 acides aminés C-terminaux de leurs partenaires. Tiam1 est un facteur d'échange de GTP de la protéine Rac1 qui contrôle la migration et la prolifération cellulaire et dont le domaine PDZ lie les protéines Syndecan-1 (Sdc1), Caspr4 et Neurexine. Des petits peptides ou des molécules peptidomimétiques peuvent potentiellement inhiber ou moduler son activité et être utilisés à des fins thérapeutiques. Nous avons appliqué des approches de dessin computationnel de protéine (CPD) et de calcul d'énergie libre par simulations dynamique moléculaire (DM) pour comprendre et modifier sa spécificité. Le CPD utilise un modèle structural et une fonction d'énergie pour explorer l'espace des séquences et des structures et identifier des variants protéiques ou peptidiques stables et fonctionnels. Nous avons utilisé le programme de CPD Proteus, développé au laboratoire, pour redessiner entièrement le domaine PDZ de Tiam1. Les séquences générées sont similaires à celles des domaines PDZ naturels, avec des scores de similarité et de reconnaissance de pli comparables au programme Rosetta, un outil de CPD très utilisé. Des séquences contenant environ 60 positions mutées sur 90, ont été testées par simulations de DM et des mesures biophysiques. Quatre des cinq séquences testées expérimentalement (par nos collaborateurs) montrent un dépliement réversible autour de 50°C. Proteus a également déterminer correctement la spécificité de la liaison de quelques variants protéiques et peptidiques. Pour étudier plus finement la spécificité, nous avons paramétré un modèle d'énergie libre semi-empirique de Poisson-Boltzmann ayant la forme d'une énergie linéaire d'interaction, ou PB/LIE, appliqué à des conformations issues de simulations de DM en solvant explicite de complexes PDZ:peptide. Avec trois paramètres ajustables, le modèle reproduit correctement les affinités expérimentales de 41 variants, avec une erreur moyenne absolue de 0,4~kcal/mol, et donne des prédictions pour 10 nouveaux variants. Le modèle PB/LIE a ensuite comparé à la méthode non-empirique de calcul d'énergie libre par simulations alchimiques, qui n'a pas de paramètre ajustable et qui prédit correctement l'affinité de 12 complexes Tiam1:peptide. Ces outils et les résultats obtenus devraient nous permettre d'identifier des peptides inhibiteurs et auront d'importantes retombées pour l'ingénierie des interactions PDZ:peptide. / Small protein domains often direct protein-protein interactions and regulate eukaryotic signalling pathways. PDZ domains are among the most widespread and best-studied. They specifically recognize the 4-10 C-terminal amino acids of target proteins. Tiam1 is a Rac GTP exchange factor that helps control cellmigration and proliferation and whose PDZ domain binds the proteins syndecan-1 (Sdc1), Caspr4, and Neurexin. Short peptides and peptidomimetics can potentially inhibit or modulate its action and act as bioreagents or therapeutics. We used computational protein design (CPD) and molecular dynamics (MD) free energy simulations to understand and engineer its peptide specificity. CPD uses a structural model and an energy function to explore the space of sequences and structures and identify stable and functional protein or peptide variants. We used our in-house Proteus CPD package to completely redesign the Tiam1 PDZ domain. The designed sequences were similar to natural PDZ domains, with similarity and fold recognition scores comarable to the widely-used Rosetta CPD package. Selected sequences, containing around 60 mutated positions out of 90, were tested by microsecond MD simulations and biophysical experiments. Four of five sequences tested experimentally (by our collaborators) displayed reversible unfolding around 50°C. Proteus also accurately scored the binding specificity of several protein and peptide variants. As a more refined model for specificity, we parameterized a semi-empirical free energy model of the Poisson-Boltzmann Linear Interaction Energy or PB/LIE form, which scores conformations extracted from explicit solvent MD simulations of PDZ:peptide complexes. With three adjustable parameters, the model accurately reproduced the experimental binding affinities of 41 variants, with a mean unsigned error of just 0.4 kcal/mol, andgave predictions for 10 new variants. The PB/LIE model was tested further by comparing to non-empirical, alchemical, MD free energy simulations, which have no adjustable parameters and were found to give chemical accuracy for 12 Tiam1:peptide complexes. The tools and insights obtained should help discover new tight binding peptides or peptidomimetics and have broad implications for engineering PDZ:peptide interactions.

Les mitochondries sont des organites dynamiques dont la morphologie dépend de l’équilibre fusion/fission de leurs membranes. Ce processus essentiel à la survie cellulaire est nommé dynamique mitochondriale et sa dérégulation est associée à des troubles neurologiques. Cependant les mécanismes précis régissant la dynamique mitochondriale ne sont pas élucidés. Cette thèse porte sur la protéine Fzo1p, une grande GTPase de la superfamille des Dynamin-related-Protein. C’est un élément clé impliqué dans la fusion mitochondriale de la membrane externe de la levure. Sa structure et sa dynamique ont été étudiées par modélisation et simulations de dynamiques moléculaires tout-atome dans une bicouche lipidique solvatée. Le modèle structural obtenu tient compte de données expérimentales, de template structuraux, et de modèles ab initio du domaine transmembranaire de Fzo1p. Ce modèle a été validé expérimentalement par mutagenèse dirigée. Des permutations de charges ont confirmé des ponts salins à longue distance prédits dans le modèle. En outre, des mutations ont montré que les domaines coiled-coil de Fzo1p, contrairement à sa partie N-terminale, sont indispensables à sa fonction. L’ensemble des résultats expérimentaux et in silico met en évidence l’implication des domaines charnières dans le changement conformationnel de Fzo1p, ainsi que des résidus critiques affectant sa stabilité. Les précisions atomiques obtenues sur l’interaction de Fzo1p avec le GDP permet de formuler des hypothèses sur le mécanisme moléculaire de la catalyse du GTP pour la fusion membranaire; voire à la compréhension de la dynamique mitochondriale. / Mitochondria are dynamic organelles whose morphology is determined by fusion and fission of their membranes. This essential process is known as mitochondrial dynamics. Defects in mitochondrial dynamics are associated with neurological disorders making the investigation of physiological relevance. However, the precise sequence of events that lead mitochondrial dynamics are still not well characterised. Fzo1p, a large GTPase of the Dynamin-Related Proteins superfamily, is a key component in mitochondrial outer membrane fusion in yeast. During this PhD project I built a model of the protein Fzo1p. The structure and dynamics of the model was investigated through molecular modelling and all-atom molecular dynamics simulation in a fully hydrated lipid bilayer environment. The Fzo1p structural model integrates information from several template structures, experimental knowledge, as well as ab initio models of the transmembrane segments. The model is validated experimentally through directed mutagenesis, for instance charge-swap mutations confirm predicted long-distance salt bridges. A series of mutants indicate that coiled-coil domains are required for protein function at variance with its N-terminal region. Overall, the experimental and in silico approaches pinpoint the hinge domains involved in the putative conformational change and identifies critical residues affecting protein stability. Finally, key Fzo1p-GDP interactions provide insights about the molecular mechanism of membrane fusion catalysis. The model provides insight on atomic level and proposes a structure that will be instructional to understanding mitochondrial membrane fusion.

In this research thermal properties enhancement of phase change material (PCM) using boron nitride nanomaterials such as nanoparticles and nanotubes is studied through experimental measurements, finite element method (FEM) through COMSOL 5.3 package and molecular dynamics simulations via equilibrium molecular dynamics simulation (EMD) with the Materials and Process Simulations (MAPS 4.3). This study includes two sections: thermal properties enhancement of inorganic salt hydrate (CaCl2∙6H2O) as the phase change material by mixing boron nitride nanoparticles (BNNPs), and thermal properties enhancement of organic phase change material (paraffin wax) as the phase change material via encapsulation into boron nitride nanotubes (BNNTs). The results of the proposed research will contribute to enhance the thermal transport properties of inorganic and organic phase change material applying nanotechnology for increasing energy efficiency of systems including electronic devices, vehicles in cold areas to overcome the cold start problem, thermal interface materials for efficient heat conduction and spacecraft in planetary missions for efficient thermal managements.

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The present work demonstrates the application of molecular simulations (MD) in two different areas: proton transport in bulk water and estimation of the dipole moment of polar organic compounds. In both areas, relatively few successful and robust methodologies exist. In the first part, a new polarizable water model is developed for MD simulations of the proton transport process. The model was parametrized from a combination of quantum chemical calculations and experimental water properties. The model was implemented in MD simulation studies of liquid water at room temperature, as well as with excess protons. For pure water the model gave good agreement with experimental properties. The proton transport rate for a single excess proton also gave a good match with the experimental value. The water model was further extended to include chloride ions. At 0.2 M concentration the resulting density and structure agreed well with experiment, and the proton transport rate was found to be slightly reduced. The model was further extended to include multiple excess protons. For the second part of the project, an open source ab initio MD program, SIESTA, was used to perform simulations of several organic compounds which potentially have multiple stable conformations, to determine their average dipole moments. A series of methods was developed. The most robust method involved modifications to the SIESTA code and statistical analysis of the resulting configurations, in order to more accurately predict the average dipole moment. The resulting dipole moments were in good agreement with the experimental values for cases in which experimental values were reliable. Based on this study, a general method to estimate the average dipole moment of any compound is proposed.

Nowadays, increasing pressure from legislation and customer demands in the automotive industryare forcing manufacturers to produce greener vehicles with lower emissions and fuel consumption.As a result, electrified and hybrid vehicles are a growing popular alternative to traditional internalcombustion engines (ICE). The noise from an electric vehicle comes mainly from contact betweentyres and road, wind resistance and driveline. The noise emitted from the driveline is for the mostpart related to the gearbox. When developing a driveline, it is a factor of importance to estimatethe noise radiating from the gearbox to achieve an acceptable design.Gears are used extensively in the driveline of electric vehicles. As the gears are in mesh, a mainintrusive concern is known as gear whine noise. Gear whine noise is an undesired vibroacousticphenomenon and is likely to originate through the gear contacts and be transferred through themechanical components to the housing where the vibrations are converted into airborne andstructure-borne noise. The gear whine noise originates primarily from the excitation coming fromtransmission error (TE). Transmission error is defined as the difference between the ideal smoothtransfer of motion of a gear and what is in practice due to lack of smoothness.The main objective of this study is to simulate the vibrations generated by the gear whine noise inan electric powertrain line developed by AVL Vicura. The electric transmission used in this studyprovides only a fixed overall gear ratio, i.e. 9.59, under all operation conditions. It is assumed thatthe system is excited only by the transmission error and the mesh stiffness of the gear contacts. Inorder to perform NVH analysis under different operating conditions, a multibody dynamics modelaccording to the AVL Excite program has been developed. The dynamic simulations are thencompared with previous experimental measurements provided by AVL Vicura.Two validation criteria have been used to analyse the dynamic behaviour of the AVL Excite model:signal processing using the FFT method and comparison with the experimental measurements.The results from the AVL Excite model show that the FFT criterion is quite successful and allexcitation frequencies are properly observed in FFT plots. Nevertheless, when it comes to thesecond criterion, as long as not all dynamic parameters of the system such as damping or stiffnesscoefficients are provided with certainty in the model, it is too difficult to investigate the accuracy ofthe AVL Excite model.Another investigation is a numerical design study to analyses how the damping coefficientsinfluence the response. After reducing the damping parameters, the results show that the housingand bearings have the highest influence on the response. If more acceptable results are desired,future studies must be concentrated on these to obtain more acceptable damping values. / För närvarande tvingar ökat tryck från lagstiftning och kundkrav inom bilindustrin tillverkarna attproducera grönare fordon med lägre utsläpp och bränsleförbrukning. Som ett resultat ärelektrifierade och hybridfordon ett växande populärt alternativ till traditionellaförbränningsmotorer (ICE). Bullret från ett elfordon kommer främst från kontakten mellan däckoch väg, vindmotstånd och drivlinan. Bullret från drivlinan är i huvudsak relaterat till växellådan.Vid utveckling av en drivlina är det av betydelse att uppskatta bullret från växellådan för att uppnåen acceptabel design.Utväxlingar används i stor utsträckning i elfordons drivlina. Eftersom kugghjulen är i kontaktuppstår ett huvudproblem som är känt som ett vinande ljud från kugghjulskontakten.Kugghjulsljud är ett oönskat vibro-akustiskt fenomen och uppstår sannolikt på grund avkugghjulkontakterna och överförs via de mekaniska komponenterna till växellådshuset därvibrationerna omvandlas till luftburet och strukturburet ljud. Kugghjulsljudet härstammarhuvudsakligen från exciteringen som kommer från transmissionsfel (TE) i kugghjulskontakten.Överföringsfelet definieras som skillnaden mellan den ideala smidiga rörelseöverföringen hoskugghjulen och rörelsen som sker i verkligheten på grund av ojämnheter.Huvudsyftet med denna studie är att simulera vibrationerna som genereras avkugghjulskontakterna i en elektrisk drivlina utvecklad av AVL Vicura. Den elektriska drivlinan somanvänds i denna studie har endast ett fast utväxlingsförhållande, dvs 9,59, för alladriftsförhållanden. Det antas att systemet är exciterat endast av överföringsfelet och kugghjulensstyvhet i kuggkontakterna. För att kunna utföra NVH-analys under olika driftsförhållanden har enstelkroppsdynamikmodell utvecklats med hjälp av programmet AVL Excite. De dynamiskasimuleringarna jämförs sedan med tidigare experimentella mätningar som tillhandahålls av AVLVicura.Två valideringskriterier har använts för att analysera det dynamiska beteendet hos AVL Excitemodellen:signalbehandling med FFT-metoden och jämförelse med experimentella mätningar.Resultaten från AVL Excite-modellen visar att FFT-kriteriet är ganska framgångsrikt och allaexcitationsfrekvenser observeras korrekt i FFT-diagrammen. Men när det gäller det andra kriteriet,så länge som inte alla dynamiska parametrar i systemet, såsom dämpnings- ellerstyvhetskoefficienter, är tillförlitliga i modellen, är det för svårt att undersöka exaktheten hos AVLExcite-modellen.En annan undersökning som utförts är en numerisk designstudie för att analysera hurdämpningskoefficienterna påverkar responsen. Efter minskning av dämpningsparametrarna visarresultaten att växellådshus och lager har störst inflytande på resultatet. Om mer acceptabla resultatär önskvärda måste framtida studier koncentreras på dessa parametrar för att uppnå mer acceptabladämpningsvärden.

Indiana University-Purdue University Indianapolis (IUPUI) / Protein malfunction can cause human diseases, which makes the protein a target in the process of drug discovery. In-depth knowledge of how protein functions can widely contribute to the understanding of the mechanism of these diseases. Protein functions are determined by protein structures and their dynamic properties. Protein dynamics refers to the constant physical movement of atoms in a protein, which may result in the transition between different conformational states of the protein. These conformational transitions are critically important for the proteins to function. Understanding protein dynamics can help to understand and interfere with the conformational states and transitions, and thus with the function of the protein. If we can understand the mechanism of conformational transition of protein, we can design molecules to regulate this process and regulate the protein functions for new drug discovery. Protein Dynamics can be simulated by Molecular Dynamics (MD) Simulations. The MD simulation data generated are spatial-temporal and therefore very high dimensional. To analyze the data, distinguishing various atomic interactions within a protein by interpreting their 3D coordinate values plays a significant role. Since the data is humongous, the essential step is to find ways to interpret the data by generating more efficient algorithms to reduce the dimensionality and developing user-friendly visualization tools to find patterns and trends, which are not usually attainable by traditional methods of data process. The typical allosteric long-range nature of the interactions that lead to large conformational transition, pin-pointing the underlying forces and pathways responsible for the global conformational transition at atomic level is very challenging. To address the problems, Various analytical techniques are performed on the simulation data to better understand the mechanism of protein dynamics at atomic level by developing a new program called Probing Long-distance interactions by Tapping into Paired-Distances (PLITIP), which contains a set of new tools based on analysis of paired distances to remove the interference of the translation and rotation of the protein itself and therefore can capture the absolute changes within the protein. Firstly, we developed a tool called Decomposition of Paired Distances (DPD). This tool generates a distance matrix of all paired residues from our simulation data. This paired distance matrix therefore is not subjected to the interference of the translation or rotation of the protein and can capture the absolute changes within the protein. This matrix is then decomposed by DPD using Principal Component Analysis (PCA) to reduce dimensionality and to capture the largest structural variation. To showcase how DPD works, two protein systems, HIV-1 protease and 14-3-3 σ, that both have tremendous structural changes and conformational transitions as displayed by their MD simulation trajectories. The largest structural variation and conformational transition were captured by the first principal component in both cases. In addition, structural clustering and ranking of representative frames by their PC1 values revealed the long-distance nature of the conformational transition and locked the key candidate regions that might be responsible for the large conformational transitions. Secondly, to facilitate further analysis of identification of the long-distance path, a tool called Pearson Coefficient Spiral (PCP) that generates and visualizes Pearson Coefficient to measure the linear correlation between any two sets of residue pairs is developed. PCP allows users to fix one residue pair and examine the correlation of its change with other residue pairs. Thirdly, a set of visualization tools that generate paired atomic distances for the shortlisted candidate residue and captured significant interactions among them were developed. The first tool is the Residue Interaction Network Graph for Paired Atomic Distances (NG-PAD), which not only generates paired atomic distances for the shortlisted candidate residues, but also display significant interactions by a Network Graph for convenient visualization. Second, the Chord Diagram for Interaction Mapping (CD-IP) was developed to map the interactions to protein secondary structural elements and to further narrow down important interactions. Third, a Distance Plotting for Direct Comparison (DP-DC), which plots any two paired distances at user’s choice, either at residue or atomic level, to facilitate identification of similar or opposite pattern change of distances along the simulation time. All the above tools of PLITIP enabled us to identify critical residues contributing to the large conformational transitions in both HIV-1 protease and 14-3-3σ proteins. Beside the above major project, a side project of developing tools to study protein pseudo-symmetry is also reported. It has been proposed that symmetry provides protein stability, opportunities for allosteric regulation, and even functionality. This tool helps us to answer the questions of why there is a deviation from perfect symmetry in protein and how to quantify it.

First, the effect of transition metal oxide (e.g., V2O5, Co2O3, etc.) on the physical properties (e.g., density, glass transition temperature (Tg), optical properties and mechanical properties) and chemical durability of a simplified borosilicate nuclear waste glass was investigated. Adding V2O5 in borosilicate nuclear waste glasses decreases the Tg, while increasing the fracture toughness and chemical durability, which benefit the future formulation of nuclear waste glasses. Second, structural study of ZrO2/SiO2 substitution in silicate/borosilicate glasses was systematically conducted by molecular dynamics (MD) simulation and the quantitative structure-property relationships (QSPR) analysis to correlate structural features with measured properties. Third, for bioactive glass formulation, mixed-network former effect of B2O3 and SiO2 on the structure, as well as the physical properties and bioactivity were studied by both experiments and MD simulation. B2O3/SiO2 substitution of 45S5 and 55S5 bioactive glasses increases the glass network connectivity, correlating well with the reduction of bioactivity tested in vitro. Lastly, the effect of optical dopants on the optimum analytical performance on atom probe tomography (APT) analysis of borosilicate glasses was explored. It was found that optical doping could be an effective way to improve data quality for APT analysis with a green laser assisted system, while laser spot size is found to be critical for optimum performance. The combined experimental and simulation approach adopted in this dissertation led to a deeper understanding of complex borosilicate glass structures and structural origins of various properties.