The purpose of this study is to observe what modifying the surface of cellulose nanofibrils may imply for their interactions with a surrounding saline aqueous solution. This will be studied by using GROMACS, a molecular dynamic simulation software. In particular, we will analyse the modified surfaces hydrophilicity compared to native nanocellulose. This will subsequently have an impact on the nanofibrils readiness to aggregate to one another and disperse in the solution. Specifically two types of surface modifications will be studied, sulfonation and carboxy- lation. The hydrophilicity of the surfaces will be determined by analysing the density profiles of the systems wherein the modified surfaces interacts with the aqueous solutions. Also, the energies from the interactions of the simulated systems will be studied. We concluded that both modifications increases the surfaces interactions with the sur- rounding solution. Modifying the surface of the cellulose nanofibril with sulfonate will increase the surfaces attraction towards water and may provide the best rate of dispersion in aqueous solutions and best prohibit aggregation. Carboxylation of the surface provides similar hydrophilic results as the sulfonation but not as prevalent.

Structure determination of proteins is vital for the understanding of their function. It often relies on techniques that use intense X-ray pulses to create diffraction patterns of protein crystals, which then contain information on the three-dimensional structure of the crystallised protein. An emerging technique called Single Particle Imaging (SPI) aims to make possible the structure determination without the need for crystallisation of the proteins, by taking diffraction patterns from many individual proteins. Translating the diffraction patterns to spatial geometry is a daunting task that requires sophisticated algorithms which are not always able to determine the structure because of fundamental uncertainties in the recovery process. To improve the structure determination process, one can try to rotate the protein to a known orientation using electric fields before the measurement takes place. However, as a result of how these experiments are performed, the proteins may have water around them during this orientation phase. Using molecular dynamics (MD) on ubiquitin, a small protein found in all eukaryotic cells, it is shown that a layer of water around a protein does not only help to achieve orientation faster (compared to an identical protein without this layer), the water also provides the protein with increased structural stability.

X-ray crystallography has been around for 100 years and remains the preferred technique for solving molecular structures today. However, its reliance on the production of sufficiently large crystals is limiting, considering that crystallization cannot be achieved for a vast range of biomolecules. A promising way of circumventing this problem is the method of serial femtosecond imaging of single-molecules or nanocrystals utilizing an X-ray free-electron laser. In such an approach, X-ray pulses brief enough to outrun radiation damage and intense enough to provide usable diffraction signals are employed. This way accurate snapshots can be collected one at a time, despite the sample molecule exploding immediately following the pulse due to extreme ionization. But as opposed to in conventional crystallography, the spatial orientation of the molecule at the time of X-ray exposure is generally unknown. Consequentially, assembling the snapshots to form a three-dimensional representation of the structure of interest is cumbersome, and normally tackled using algorithms to analyze the diffraction patterns. Here we explore the idea that the explosion data can provide useful insights regarding the orientation of ubiquitin, a eukaryotic regulatory protein. Through two series of molecular dynamics simulations totaling 588 unique explosions, we found that a majority of the carbon atoms prevalent in ubiquitin are directionally limited in their respective escape paths. As such we conclude it to be theoretically possible to orient a sample with known structure based on its explosion pattern. Working with an unknown sample, we suggest these discoveries could be applicable in tandem with X-ray diffraction data to optimize image assembly.

Flies are a widely distributed pest insect that poses a significant threat to food security. Flight is essential for the dispersal of the adult flies to find new food sources and ideal breeding spots. The supply of metabolic fuel to power the flight muscles of insects is regulated by adipokinetic hormones (AKHs). The fruit fly, Drosophila melanogaster, the flesh fly, Sarcophaga crassipalpis, and the oriental fruit fly, Bactrocera dorsalis all have the same AKH that is present in the blowfly, Phormia terraenovae; this AKH has the code-name Phote-HrTH. Binding of the AKH to the extracellular binding site of a G protein-coupled receptor causes its activation. In this thesis, the structure of Phote-HrTH in SDS micelle solution was determined using NMR restrained molecular dynamics. The peptide was found to bind to the micelle and be reasonably rigid, with an S 2 order parameter of 0.96. The translated protein sequence of the AKH receptor from the fruit fly, Drosophila melanogaster, the flesh fly, Sarcophaga crassipalpis, and the oriental fruit fly, Bactrocera dorsalis were used to construct two models for each receptor: Drome-AKHR, Sarcr-AKHR, and Bacdo-AKHR. It is proposed that these two models represent the active and inactive state of the receptor. The models based on the crystal structure of the β-2 adrenergic receptor were found to bind Phote-HrTH with a predicted binding free energy of –107 kJ mol–1 for Drome-AKHR, –102 kJ mol–1 for Sarcr-AKHR and –102 kJ mol–1 for Bacdo-AKHR. Under molecular dynamics simulation, in a POPC membrane, the β-2AR receptor-like complexes transformed to rhodopsin-like. The identification and characterisation of the ligand-binding site of each receptor provide novel information on ligand-receptor interactions, which could lead to the development of species-specific control substances to use discriminately against these pest flies.

L’avancée des infrastructures informatiques a permis l’émergence de la modélisation moléculaire. À cet effet, une multitude de modèles mathématiques sont aujourd’hui disponibles pour simuler différents systèmes chimiques. À l’aide de la modélisation moléculaire, différents types d’interactions chimiques ont été observés. À partir des systèmes les plus simples permettant l’utilisation de modèles quantiques rigoureux, une série d’approximations a été considérée pour rendre envisageable la simulation de systèmes moléculaires de plus en plus complexes. En premier lieu, la théorie de la fonctionnelle de densité dépendante du temps a été utilisée pour simuler les énergies d’excitation de molécules photoactives. De manière similaire, la DFT indépendante du temps a permis la simulation du pont hydrogène intramoléculaire de structures analogues au 1,3,5-triazapentadiène et la rationalisation de la stabilité des états de transition. Par la suite, la dynamique moléculaire et la mécanique moléculaire ont permis de simuler les interactions d’un trimère d’acide cholique et d’un pyrène dans différents solvants. Cette même méthodologie a été utilisée pour simuler les interactions d’un rotaxane-parapluie à l’interface d’un système biphasique. Finalement, l’arrimage moléculaire et les fonctions de score ont été utilisés pour simuler les interactions intermoléculaires entre une protéine et des milliers de candidats moléculaires. Les résultats ont permis de mettre en place une stratégie de développement d’un nouvel inhibiteur enzymatique. / The evolution of computer systems has led to the emergence of molecular modeling. To this end, a variety of mathematical models are now available to simulate various chemical systems. Using molecular modeling, different types of chemical interactions were observed. From the simplest systems allowing the use of rigorous quantum models, a series of approximations were considered in order to make possible the simulation of increasingly complex molecular systems. First, time-dependent density fonctional theory has been used to simulate the excitation energies of photoactive molecules. Similarly, time-independent DFT has enabled the simulation of intramolecular hydrogen bonding in the 1,3,5-triazapentadiene system and the rationalization of the stability of the transition states. Subsequently, molecular dynamics and molecular mechanics were used to simulate the interactions of a trimer of cholic acid with a pyrene in different solvents. This methodology was then used to simulate the interactions of an umbrella-rotaxane at the interface of a biphasic system. Finally, molecular docking and the concept of scoring functions were used to simulate the intermolecular interactions between a protein molecule and thousands of potential ligands. The results were then used to create a strategy for the development of a new enzyme inhibitor.

The swelling properties of Bentonite are highly affected by clay content and the clay-water interactions that arise from the ion distribution in the diffuse double layer formed near the charged montmorillonite (or smectite) surfaces. Existing continuum models describing the electric double layers, such as classical Poisson-Boltzmann and DLVO theory, ignore the ion-ion correlations, which are especially important for multivalent ions at high surface charge and ionic strength. To better understand the clay-water interactions, atomistic models were developed using both density functional theory of fluids (DFT) as well as classical molecular dynamics (MD) methods. In order to increase our understanding of water-saturated, swelling smectite clays, a DFT, technique was initially developed that allowed more accurate predictions of important thermodynamic properties of the diffuse double layers. This DFT approach was then extended to handle systems with mixtures of different sizes and charges. The extended DFT model was verified against experiments and Monte-Carlo simulations. One practical application was to predict the ion exchange equilibria in Bentonite clays, which have wide practical usage in different areas. Nevertheless, in the DFT work it was realized that DFT demands that the particles, ions in this case, which are described as hard spheres, realistically cannot be described as such at low water loadings, when ion specific hydration forces govern the electric double layer properties. To study how the deformation of the hydration shells of Ca2+ influences the properties of compacted smectite clays, MD simulations using the CLAYFF forcefield were employed in order to account for the deformation of the hydration shells. Comparisons of DFT and MD modeling then allowed to demonstrate under which conditions DFT modeling becomes increasingly inaccurate and when it still can give accurate results. / Under senare år har mycket forskning ägnats åt att förstå egenskaperna hos svällande leror som används för att skydda mot läckage av föroreningar från kontaminerade områden och från framtida slutförvar av radionuklider. Den fria svällningen förorsakas av de starka osmotiska krafter som uppstår när vatten tränger in mellan de tunna elektriskt negativt laddade lermineralskikten och löser de laddningskompenserande jonerna i det diffusa dubbelskiktet. I flera arbeten användandes av sk. kontinuum-teori har vattenmolekylens form, specifika orientering och bindning till katjonerna i de nanometerstora utrymmen mellan lerpartiklarna ej beaktats samt ej heller hur de hydratiserade jonerna orienteras på de atomärt ojämna ytorna. Detta möjliggörs dock genom modellering av de enskilda atomernas och jonernas interaktioner med molekyldynamik simuleringar, MD. I detta arbete har programmet Gromacs använts tillsammans med kraftfältet CLAYFF för att studera dessa fenomen i montmorillonitleror med natrium- och kalciumjoner. Simuleringarna visar att natrium bildar transienta innersfärkomplex vilka orienterar sig i bi-triangulära fördjupningar på ytan, ungefär 3.8 Å från mitt-planet mellan lerytorna. Denna orientering observeras ända upp till att avståndet mellan ytorna ökat till större än motsvarande fem lager vattenmolekyler mellan lerpartiklarnas ytor. Detta sker inte med kalcium, oberoende av avståndet mellan ytorna. Natriumjoner koordineras med fyra vattenmolekyler och en syreatom på leran vid ett lager vatten mellan ytorna och med fem till sex vattenmolekyler, ortogonalt orienterade med ökande mängd vatten mellan ytorna, och med en hydratiserad jon-radie av 3.1 Å. Kalcium koordinerar till sju vattenmolekyler vid ett vattenlager mellan ytorna, men ökar till åtta ortogonalt orienterade vattenmolekyler med en jonradie på 3.3 Å vid större avstånd. Generellt visas att när avståndet mellan lerytorna är mindre än ca 10 Å, deformeras de annars symmetriskt hydratiserade jonerna. En jämförelse mellan MD simuleringar och med klassisk täthetsfunktionalteori, DFT, visar att den senare inte kan beskriva hur yttersfärkomplexen samverkar med laddningarna bundna närmast ytan, dvs i Stern-lagret. / <p>QC 20170403</p>

Salt is a common substance of which the structure has been investigated in this study. Molecular dynamics simulations has been performed of a solution of Caesium Chloride in water for four different concentrations. Radial distribution functions show a change in the structure of oxygen-oxygen with increasing concentration, especially for the second solvent shell. Contributions of the ions increases the separation between the water molecules and a long range peak of approximately 0.9 nm appears for higher concentrations. The results can be compared with experimental results performed at Swedish University of Agricultural Sciences. These distances are much longer (around 3.4 Å) and shows signs of cluster formation.

L’avancée des infrastructures informatiques a permis l’émergence de la modélisation moléculaire. À cet effet, une multitude de modèles mathématiques sont aujourd’hui disponibles pour simuler différents systèmes chimiques. À l’aide de la modélisation moléculaire, différents types d’interactions chimiques ont été observés. À partir des systèmes les plus simples permettant l’utilisation de modèles quantiques rigoureux, une série d’approximations a été considérée pour rendre envisageable la simulation de systèmes moléculaires de plus en plus complexes. En premier lieu, la théorie de la fonctionnelle de densité dépendante du temps a été utilisée pour simuler les énergies d’excitation de molécules photoactives. De manière similaire, la DFT indépendante du temps a permis la simulation du pont hydrogène intramoléculaire de structures analogues au 1,3,5-triazapentadiène et la rationalisation de la stabilité des états de transition. Par la suite, la dynamique moléculaire et la mécanique moléculaire ont permis de simuler les interactions d’un trimère d’acide cholique et d’un pyrène dans différents solvants. Cette même méthodologie a été utilisée pour simuler les interactions d’un rotaxane-parapluie à l’interface d’un système biphasique. Finalement, l’arrimage moléculaire et les fonctions de score ont été utilisés pour simuler les interactions intermoléculaires entre une protéine et des milliers de candidats moléculaires. Les résultats ont permis de mettre en place une stratégie de développement d’un nouvel inhibiteur enzymatique. / The evolution of computer systems has led to the emergence of molecular modeling. To this end, a variety of mathematical models are now available to simulate various chemical systems. Using molecular modeling, different types of chemical interactions were observed. From the simplest systems allowing the use of rigorous quantum models, a series of approximations were considered in order to make possible the simulation of increasingly complex molecular systems. First, time-dependent density fonctional theory has been used to simulate the excitation energies of photoactive molecules. Similarly, time-independent DFT has enabled the simulation of intramolecular hydrogen bonding in the 1,3,5-triazapentadiene system and the rationalization of the stability of the transition states. Subsequently, molecular dynamics and molecular mechanics were used to simulate the interactions of a trimer of cholic acid with a pyrene in different solvents. This methodology was then used to simulate the interactions of an umbrella-rotaxane at the interface of a biphasic system. Finally, molecular docking and the concept of scoring functions were used to simulate the intermolecular interactions between a protein molecule and thousands of potential ligands. The results were then used to create a strategy for the development of a new enzyme inhibitor.

The very fundamental properties of biological membranes can be understood by studying their formation. This sets a good foundation for research related to how the membranes interact with organic molecules and ions; something of great value in the quest of explaining transport phenomena through cell membranes. It is furthermore of growing interest within the pharmacological research and contributes to the apprehension of life at the molecular level. In this thesis Molecular Dynamics has been used to simulate how evenly distributed phospholipids solvated in water leads to the formation of monolayers. An automation program has been written in Python for performing these simulations and is to be used as the foundation for performing simulations in further studies. The program was used to simulate model systems of high- and low concentrations of DPPC lipids. The DPPC lipid, like most other lipids, consist of a hydrophilic "head" part and two lipophilic "tails", which is the main cause of the lipids interacting in such a manner that forms membranes. The low concentration system was simulated for a total of 3 ns with all lipids having reached the surface at 1.5 ns, and the all lipids in the high concentration system had risen at 41 ns with a total simulation time of 43 ns. / De mest grundläggande egenskaperna hos cellmembran kan förstås genom att studera hur dessa bildas. Detta skapar en bra grund för forskning relaterad till hur membranen interagerar med organiska molekyler och joner; något av stort värde i bemödandet att förklara transportfenomen genom cellmembran. Dessutom är det av växande intresse inom den farmakologiska forskningen och bidrar till kunskapen om liv på den molekylära nivån. I denna avhandling har Molekylär Dynamik använts för att simulera hur jämnt fördelade fosfolipider lösta i vatten leder till bildandet av monoskiktade membran. Ett automatiseringsprogram har skrivits i Python för att utföra dessa simuleringar och ska komma att användas som grund för genomförandet av simuleringar i vidare studier. Programmet användes för att simulera modellsystem med höga och låga koncentrationer av DPPC lipider. DPPC lipiden, liksom de flesta andra lipider, består av en hydrofil ''huvud'' -del och två lipofila ''svansar'', vilket är den huvudsakliga orsaken till att lipiderna interagerar på ett sådant sätt som driver bildandet av ett membran. Lågkoncentrationssystemet simulerades i totalt 3 ns, varav 1,5 ns behövdes för att alla lipider skulle nå vattenytan. Alla lipider i högkoncentrationssystemet hade kommit upp till ytan efter 41 ns och för detta system utfördes simuleringen under en total tid på 43 ns.

Density functional theory (DFT) calculations of polyethylene (PE) HVDC cable insulation have been performed for systems containing four different chemical impurities: acetophenone, cumene, $\alpha$-methyl styrene and $\alpha$-cumyl alcohol. Systems were generated by molecular dynamics (MD) equilibration at four different temperatures relevant for cable insulation applications: 277 K, 293 K, 343 K and 363 K. With the goal of gaining better measure of variations in hole and electron traps energies, four initial configurations were also stochastically generated at each temperature, which yielded four different final configurations after equilibration. The counterpoise correction scheme was implemented for DFT calculations, by distributing ghost atoms thought any empty pockets of space in between the PE chains. The PBE functional was selected for DFT simulations. The resulting band gaps were in agreement with those of earlier GGA-based studies, and thus lower by 3 eV than empirical band gaps. For all impurities, the first HOMO state and the first two LUMO states were generally located on the impurity molecule, forming one hole trap and two electron traps, but certain configurations generated increased electron trap numbers, or eliminated hole traps. No dependence could be derived between temperature and trap depth for either electron or hole traps. Mean electron trap energies were largely in agreement with results from earlier studies, they were deepest for acetophenone, and they varied by as much as 0.6 eV between different configurations. Hole traps are universally shallow and vary by up to 0.7 eV between configurations, and are similar in depth for all impurities. Results suggest that electron trap depths correlate with the presence of molecular features such as oxygen atoms and conjugated double bonds. The dependence of trap depth on the spatial configuration of the impurity molecule suggests that results could be improved by more precise quantum mechanical treatment of the dynamics of the impurity. / Täthetsfunktionalteori (DFT) har använts för beräkningar av isolering till HVDC kablar som består av polyeten innehållande fyra olika kemiska orenheter: acetofenon, kumen, alfa-metylstyren och alfa-kumylalkohol. System att studera genererades genom molekylärdynamisk ekvilibrering vid fyra olika temperaturer relevanta för tillämning till kabelisolering: 277 K, 293 K, 343 K och 363 K. För att få ett mått på de variationer som existerar i energierna på hål- och elektronfällor genererades stokastiskt fyra initialkonfigurationer vid varje temperatur, vilket fyra olika konfigurationer efter relaxering. Motviktskorrigering implementerades för DFT-beräkningar, genom att fördela "spökatomer" i de tomrum som bildas mellan PE-kedjorna i den amorfa fasen. PBE-funktionalen användes för DFT-simuleringar. De resulterande bandgapen stämde överens med tidigare GGA-baserade studier, och var därmed runt 3 eV smalare än empiriskt uppmätta bandgap. För alla orenheter var det första HOMO-tillståndet och de två första LUMO-tillstånden i allmänhet placerade på orenheten, vilket resulterade i en hålfälla och två elektronfällor, men vissa konfigurationer gav upphov till fler elektronfällor, eller eliminerade hålfällorna. Inget samband kunde härledas mellan temperaturen och djupet på fällorna för vare sig elektron- eller hålfällor. Medelvärdet på elektronfällornas energier överensstämde till stor del med resultat från tidigare studier, energierna var högst för acetofenon, och de varierade med så mycket som 0,6 eV mellan olika konfigurationer. Hålfällorna var genomgående grunda, varierade med upp till 0,7 eV mellan olika konfigurationer, och hade likartat djup för alla orenheter. Resultaten indikerar att variationerna elektronfällornas medeldjup uppstår på grund av orenheternas olika molekylära uppbyggnad: förekomst av syreatomer och konjugerade dubbelbindningar i orenheterna leder till djupare elektronfällor. Det faktum att djupet på elektron- och hålfällor varierar mellan olika rumsliga konfigurationer av av orenheten och polyetenstrukturen ger en antydan om att resultaten kan komma att förbättras om dynamiken hos orenheten simuleras med mer exakta kvantmekanisk metoder.