Made available in DSpace on 2018-08-01T21:59:25Z (GMT). No. of bitstreams: 1 tese_11961_Dissertação Lucas Carvalho Trindade - PPGFis (2).pdf: 9990680 bytes, checksum: a02add814af0828b765718f180e67605 (MD5) Previous issue date: 2018-02-23 / Este trabalho descreve o desenvolvimento de uma simulação computacional, desenvolvida através do programa GROMACS. Mais especificamente, estudamos os resultados da simulação computacional referente a evolução do raio de giro da proteína Pectina Metilesterase (PME) do tomate em função da pressão aplicada, mantendo a temperatura fixa. Foi realizada uma descrição sobre os modelos físicos utilizados pelo programa. Também foi descrito, de forma suscinta, características sobre sistemas e estruturas dos aminoácidos e proteínas. As simulações computacionais consideraram uma temperatura de 26, 85oC e pressões aplicadas de 1 bar, 1 kbar, 3 kbar, 5 kbar, 7 kbar, 9 kbar e 10 kbar. As simulações trabalharam com um tempo de ação da pressão de até 100 pico segundos. Os resultados da simulação computacional indicaram uma redução não linear do raio de giro da enzima Pectina Metilesterase (PME) do tomate de acordo com o aumento da pressão aplicada, mantendo temperatura fixa.

The aim of this project is to develop superabsorbents from proteins in our case it is azygomycetes fungus, where the process of this fungus is studied experimentally in Universityof Borås. As a result of this experiment by-products of protein are produced and this project isabout the study to make use of such proteins as superabsorbing materials.The water absorbing capacity is computationally studied using Gibbs ensemble Monte Carlo(GEMC) simulations to determine the absorbing properties and to effectively improve theabsorbing capacity by using specific treatments, where this project focuses in using mesoscaleforce fields such as the MARTINI force field instead of atomistic force fields which wereused in studying the structure of the superabsorbents.For this purpose, the program code GEMMS is modified to make it read the desirable fileformats in order to perform the simulations. C++ is used here to code the program to read theGROMACS topology file (.top) for MARTINI force field instead of, as currently reading theatom type file (.atp) and the residue type file (.rtp) for the AMBER99 atomistic force field.

The possibility to orient a protein in space using an external electrical field was studied bymeans of molecular dynamics simulations. To model the possible conditions of an electrospray ionization (ESI) the protein Lysozyme in vacuum was considered under the influence ofdifferent field strengths. The simulations showed three distinct patterns: (1) the protein wasdenaturated when exposed to too strong electrical fields, above 1.5 V/nm; (2) the proteinoriented without being denaturated at field strengths between 0.5 V/nm and 1.5 V/nm (3) theprotein did not orient and did not denaturate if the strength of the field became to low, below0.5 V/nm. Our simulations show that the orientation of the protein in the fields correspondingto the second pattern takes place within time intervals from about 100 ps at 1.5 V/nm to about1 ns at 0.5 V/nm. We therefore predict, that there exists a window of field strengths, which issuitable for orientation of proteins in experimental studies without affecting their structure.The orientation of proteins potentially increases the amount of information that can beobtained from experiments such as single particle imaging. This study will therefore bebeneficial for the development of such modern techniques.

Model of nanoscale deformation mechanisms of cellular structures could render different results depending on the molecular dynamics (MD) simulator chosen. Also, the comparison of different MD simulators is typically an intricate task, requiring all configurations be converted appropriately with available parameter choices. This study aims to perform and compare MD simulations between two MD programs (GROMACS and LAMMPS), in which a phospholipid bilayer is deformed under different strain states. The two systems produced similar deformation behaviors and strain state effect on bilayer failure. However, GROMACS produced more pores at lower strains, lower stress, and higher damage values. Multiple setting options and algorithm variations have been considered as possible explanations for the differences. Overall, the study aids in the cross-check of parameter settings and simulation results in MD research, particularly on the mechanical damage of bilayer membranes. Besides, based on that, GROMACS and LAMMPS could be further exploited with better reproducibility.

Water aerosols affect the climate because they have an impact on the radiation balance and cloud formation. Water is present in all forms in the atmosphere (water, ice and steam), for example as rain and hail. Water aerosols play an important role in many biological and chemical processes in the atmosphere. The most common form of water in the atmosphere is water droplets or vapor which often come from oceans and lakes and these aerosols often contain organic compounds. It is therefore interesting to study if organic compounds, in this case glycerol, will reside on the surface or inside the water droplets. The investigations were performed by using theoretical studies, molecular dynamic simulations in GROMACS, and experimental investigations; X-ray photoelectron spectroscopy with a liquid jet. The experiments were performed at BESSY II, Berlin. The concentrations of glycerol were varied from 75:1; 8:1 to 4:1 (water: glycerol molecules). The results were that the experiments and simulations indicated that when theconcentration of glycerol increased the glycerol concentration at the surface of the waterdroplet increases until a monolayer of glycerol molecules was formed at the surface. When the monolayer was formed (or close to) less and less glycerol molecules were placed at thewater surface and more and more glycerol molecules were placed in the bulk of the waterdroplet. / Vattenaerosoler påverkar klimatet eftersom de har en inverkan på strålningsbalansen och molnbildningen. Vatten finns i alla former i atmosfären (vatten, is och ånga) som bland annat regn och hagel. Vatten aerosolerna spelar en viktig roll i många kemiska och biologiska processer i atmosfären. Den vanligaste formen av vatten i atmosfären är små vattendroppar eller ånga som ofta kommer från hav och sjöar och som ofta innehar organiska föreningar. Då vattenaerosoler påverkar klimatet och organiska föreningar är vanligt förekommande i vattendroppar är det intressant att undersöka om organiska föreningar, i detta fall glycerol, hamnar på ytan eller inuti vattnet. Undersökningarna har gjorts genom att använda teoretiska perspektiv, molekylärdynamiska simuleringar i GROMACS, samt experimentella undersökningar i form av röntgen fotoelektronspektroskopi med en vätskejet. Dessa experiment utfördes i BESSY II, Berlin. Koncentrationerna av glycerol varierades från75:1; 8:1 till 4:1 (vatten: glycerolmolekyler). Resultaten från experimenten och simuleringarna indikerade att när koncentrationen av glycerol ökade så ökade glycerolkoncentrationen på ytan av vattendroppen tills det bildades ett monolager av glycerolmolekyler på vattenytan. När monolagret hade bildats så placerades mindre och mindre glycerolmolekyler på vattenytan och fler och fler glycerolmolekyler placerades inne i vattendroppen.

Les travaux présentés dans ce manuscrit sont consacrés à l'étude de la diffusion du dioxyde de carbone dissous et de l'éthanol dans une solution hydroalcoolique modèle représentant le champagne. La première partie de ce travail aborde les différents formalismes de la diffusion moléculaire, ainsi que les méthodes théoriques et expérimentales utilisées pour rendre compte de ce phénomène de transport. Une attention particulière est apportée à la dynamique moléculaire en champ de forces classiques qui est utilisé dans ce travail avec le logiciel GROMACS. Cette méthode théorique procure un point de vue novateur dans la recherche sur le champagne et plus particulièrement sur le rôle de chaque espèce majoritaire dans la diffusion du CO2. La spectroscopie RMN, ainsi qu'une méthode expérimentale basée sur l'étude du taux de grossissement des bulles, ont également été utilisées. Dans la deuxième partie, les résultats théoriques et expérimentaux sont présentés et comparés entre eux afin de valider le protocole des simulations de dynamique moléculaire. Les viscosités de la solution modèle et du champagne, ainsi que les rayons hydrodynamiques du CO2 et de l'éthanol sont également étudiés. La dernière partie du manuscrit concerne le partenariat avec l'entreprise Bull et l'étude des performances du logiciel GROMACS. L'expertise des équipes de Bull, ainsi que les outils développés par l'entreprise, permettent d'étudier le passage à l'échelle (ou "scalabilité") et le comportement parallèle de GROMACS pour la modélisation du champagne. / The work presented in this manuscript is devoted to the study of the diffusion of dissolved carbon dioxide and ethanol in a hydroalcoholic solution model representing Champagne wines. The first part of this work deals with the different formalisms of molecular diffusion, as well as theoretical and experimental methods used to account for this phenomenon of transport. Particular attention is paid to the classical force field molecular dynamics that is used in this work with the GROMACS software. This theoretical approach provides a new perspective in research on champagne and particularly on the role of each of the main species in CO2 diffusion. NMR spectroscopy, and an experimental method based on the study of the bubbles growth rate, were also used. In the second part, the theoretical and experimental results are presented and compared with each other to validate the protocol of molecular dynamics simulations. The viscosities of the model solution and of the champagne, as well as the hydrodynamic radii of CO2 and ethanol, are also investigated. The last part of the manuscript focuses on the partnership with the Bull company and the study of the GROMACS software performance. The expertise of and the tools developed by the Bull company are used to study the scalability and the parallel behavior of GROMACS for modeling champagne.

Water is a fundamental part of life as we know it, and by that also a fundamental for biology, chemistry, and parts of physics. Understanding how water behaves and interacts is key in many fields of all these three branches of science. Numerical simulation using molecular dynamics can aid in building insight in the behavior and interactions of water. In this thesis molecular dynamics is used to simulate common rigid 3 point water models to see how well they replicate certain physical and chemical properties as functions of temperature. This is done with molecular dynamics program GROMACS which offers a complete set of tools to run simulations and analyze results. Everything has been automated to work with a python script and a file of input parameters. Most of the models follow the same trends and are valid within a limited temperature range. / Vatten är en av de fundamentala byggstenarna för liv, därmed är det även fundamentalt för biologi, kemi och delar av fysiken. Att förstå hur vatten beter sig och interagerar är en stor fråga inom dessa tre grenar av vetenskap. Med molekyldynamik går det att utföra numeriska simuleringar som kan användas som hjälpmedel för att bygga en djupare förståelse för riktigt vatten. I den här uppsatsen så har molekyldynamik använts till att simulera vanliga rigida 3 punkts parametiseringar av vatten för att se hur bra de kan replikera vissa egenskaper som funktioner av temperatur. Simuleringen är gjord med hjälp av molekyldynamik programet GROMACS som ger en fullständig uppsättning verktyg för att simulera och analysera molekylsystem. Alla simuleringar och analys är automatiserat med ett pythonprogram och en fil för parametrar. De allra flesta modeller följer liknande trender och är giltiga inom små temperaturintervall.

Seven transmembrane (7-TM) G protein coupled receptors (GPCR) constitute the largest family of integral membrane proteins in eukaryotes with more than 1000 members and encoding more than 2% of the human genome. These proteins play a key role in the transmission and transduction of cellular signals responding to hormones, neurotransmitters, light and other agonists, regulating basic biological processes. Their natural abundance together with their localization in the cell membrane makes them suitable targets for therapeutic intervention. Consequently, GPCR are proteins with enormous pharmacologic interest, representing the targets of about 50% of the currently marketed drugs. The current limitations in the experimental techniques necessary for microscopic studies of the membrane as well as membrane proteins emerged the use of computational methods and specifically molecular dynamics simulations. The lead motif of this thesis is the study of GPCR by means of this technique, with the ultimate goal of developing a methodology that can be generalized to the study of most 7-TM as well as other membrane proteins. Since the bovine rhodopsin was the only protein of the GPCR family with a known threedimensional structure at an atomic level until very recently, most of the effort is centered in the study of this receptor as a model of GPCR.The scope of this thesis is twofold. On the one hand it addresses the study of the simulation conditions, including the procedure as well as the sampling box to get optimal results, and on the other, the biological implications of the structural and dynamical behavior observed in the simulations. Specifically, regarding the methodological aspects of the work, the bovine rhodopsin has been studied using different treatments of long-range electrostatic interactions and sampling conditions, as well as the effect of sampling the protein embedded in different one-component lipid bilayers. The binding of ions to lipid bilayers in the absence of the protein has also been investigated. Regarding the biological consequences of the analysis of the MD trajectories, it has been carefully addressed the binding site of retinal and its implications in the process of isomerization after photon uptake, the alteration a group of residues constituting the so-called electrostatic lock between helices TM3 and TM6 in rhodopsin putatively used as common activation mechanism of GPCR, and the structural effects caused by the dimerization based on a recent semi-empirical model. Finally, the specific binding of ions to bacteriorhodopsin has also been studied. The main conclusion of this thesis is provide support to molecular dynamics as technique capable to provide structural and dynamical informational about membranes and membrane proteins, not currently accessible from experimental methods). Moreover, the use of an explicit lipidic environment is crucial for the study the membrane protein dynamics as well as for the protein-protein and lipidprotein interactions.

Water plays a critical role in the function and structure of biological systems. Current techniques to study biologically relevant events that span many length and time scales are limited by the prohibitive computational cost of including accurate effects from the aqueous environment. The aim of this work is to expand the reach of current molecular dynamics techniques by reducing the computational cost for achieving an accurate description of water and its effects on biomolecular systems. This work builds from the assumption that the “local” effect of water (e.g. the local orientational preferences and hydrogen bonding) can be effectively modelled considering only the atomistic detail in a very limited region. A recent adaptive resolution simulation technique (AdResS) has been developed to practically apply this idea; in this work it will be extended to systems of simple hydrophobic solutes to determine a characteristic length for which thermodynamic, structural, and dynamic properties are preserved near the solute. This characteristic length can then be used for simulation of biomolecular systems, specifically those involving protein dynamics in water. Before this can be done, current coarse grain models must be adapted to couple with a coarse grain model of water. This thesis is organized in to five chapters. The first will give an overview of water, and the current methodologies used to simulate water in biological systems. The second chapter will describe the AdResS technique and its application to simple test systems. The third chapter will show that this method can be used to accurately describe hydrophobic solutes in water. The fourth chapter describes the use of coarse grain models as a starting point for targeted search with all-atom models. The final chapter will describe attempts to couple a coarse grain model of a protein with a single-site model for water, and it’s implications for future multi-resolution studies.

The method of dipole orientation of protein complexes using electric fields plays a key role in the development of single particle imaging, since it enables orientation of the protein in vacuum. In the orientation process the protein is exposed to an external electric field along which the dipole axis of the protein will eventually align. Earlier studies using molecular dynamics simulations have implemented a constant electric field to examine the dipole orientation process. However, when injected into the electric field the protein experiences a gradually increasing field strength converging to some terminal field strength rather than a constant electric field. In order to examine the effects of the time-dependant nature of the electric field, in comparison to a constant one, fields with different time dependances were implemented in molecular dynamics simulations in vacuum performed with GROMACS. Ubiquitin was chosen as a model protein. The results of the study show time-increasing fields tend to result in slower orientation, but preserve the structure of the protein better than for a constant field. It was also shown that after 10 ns electric field exposure, with terminal field strengths greater  or equal to 0.6Vnm^-1, there was no apparent difference of the average degree of orientation of proteins within the time-increasing fields and the constant one. However, for fields of greater or equal to 1.5Vnm^-1 the constant field tended to result in a larger change of the protein structure.