Den ökande koldioxidhalten i atmosfären har lett till ett ökat intresse för användning av solljus, ett exempel är inom kemi. Att använda ljus i kemi kan leda till nya och intressanta kemiska reaktioner och kan tillämpas i användningsområden som exempelvis fotokatalys och fotovoltaik. Genom att kombinera de kraftfulla egenskaperna av ljus i kemi med den höga selektivitet som karaktäriserar proteiner kan intressanta och kraftfulla maskinerier erhållas, så kallade fotoaktiva proteiner. Att studera de fotoinducerade beteendena i fotoaktiva proteiner är däremot icke-trivialt eftersom många utmaningar uppstår från ett experimentellt och teoretiskt perspektiv. Denna uppsats fokuserar på det teoretiska perspektivet. Simulationer av beteenden hos fotoaktiva proteiner leder till utmaningar relaterade till den stora variationen av tids- och längdskalor involverade, där allt ifrån ultrasnabba och lokaliserade excitationsprocesser till storskaliga strukturförändringar som utspelar sig på större tidsskalor. Detta, tillsammans med det faktum att det inte finns en "svart låda" som vi kan använda för nya teoretiska studier motiverar ett försiktigt tillvägagångssätt för teoretiska studier av fotoaktiva proteiner. I detta projekt görs en teoretisk undersökning av två nyligen framställda fotosensibiliserande proteiner (PSP2 och PSP3). De skapades för att härma huvudprocesserna av fotosyntesen i plantor. Fotosensibiliserande proteinerna skiljer sig med en enda aminosyra (position 203), som är en aspartat i PSP2 och en tyrosin i PSP3. Även fast proteinerna är strukturellt lika så uppvisar de olika fotoinducerade beteenden. Målet med denna studie är att klargöra för de mekanistiska detaljerna bakom dessa olikheter. Som ett första steg i att teoretiskt studera PSP2 och PSP3 upprättar vi ett protokoll för teoretisk förberedelse av proteinerna. Detta protokoll används sedan för att teoretiskt undersöka fotofysiken i dessa två proteiner med hjälp av kvantmekaniska/ molekylär mekaniska simuleringar. Våra resultat ger en första ordningens kartläggning av de exciterade tillstånden i de två proteinerna. Vi erhåller en intressant laddningsöverföring tillstånd i PSP3 som involverar tyrosinen och proteinets kromofor, med en energi lägre än det tillstånd ansvarig för absorption av ljus. Denna laddningsöverföring saknas i PSP2 och kan därför vara anledningen till de olika fotoinducerade beteendena i proteinerna. Detta kräver dock fortsatta studier av de två systemen. / The increase of carbon dioxide levels in the atmosphere have resulted in an increasing interest in using solar light for different purposes, one being chemistry. The introduction of light in chemistry can drive new and exciting chemical reactions, finding applications in many fields such as photocatalysis and photovoltaics. Combining the aspects of light in chemistry together with the high selectivity that characterizes proteins make for interesting and powerful machineries, so-called photoactive proteins. However, studying the behaviors of photoactive proteins is a non-trivial task and many challenges arise from both an experimental and a theoretical point of view. This thesis takes a theoretical perspective. The challenges associated with simulating photoactive protein behavior originate from the wide range of time and length scales involved, ranging from ultrafast and localized excitation processes to large-scale structural changes occurring on longer timescales. This, together with the fact that there is no black box that we can use for novel theoretical studies of photoactive proteins motivates a careful approach for theoretical studies of photoactive proteins. In this project, we conduct a theoretical investigation of two photosensitizer proteins (PSP2 and PSP3), recently engineered to capture the essence of plant photosynthesis. The photosensitizer proteins differ by only one residue (position 203), which is an aspartate in PSP2 while a tyrosine in PSP3. Although structurally similar, the proteins demonstrate different photoinduced behaviors. This study aims to shed light on the mechanistic details underlying these differences. As a first step to study PSP2 and PSP3 computationally, we develop a computational protocol for protein preparation. The protocol is then used for a theoretical investigation of the photophysics of the two proteins using quantum mechanics/molecular mechanics simulations. Our results provide a first mapping of the electronic-state manifold of the two proteins. We find an intriguing charge-transfer state in PSP3, involving the tyrosine and the protein chromophore, located below bright state responsible for light absorption. This state is absent in PSP2 and could therefore be the reason for the different photoinduced behavior of the two proteins. However, this requires further studies of the two systems.

There is currently a demand of mm‑wave on‑chip antennas to enable all kinds of new applications in several different areas. But the development requires, among other things, special equipment used during the measurement phase due to the small dimensions and the high frequencies. In this project a robotic measurement system, SAX (Single Arm eXtra), was designed and constructed at Micro and Nanosystems (MST) department at KTH Royal Institute of Technology (Sweden). The purpose of the SAX is to enable radiation pattern measurements of on‑chip antennas ( 140 GHz to 325 GHz ), whether the boresight is vertical or horizontal along with other requirements, by moving a converter with the measurement antenna around the antenna in question. Several alternative designs for the basic construction, both from other works and invented by the author, were analyzed based on the requirements for this project and other limitations. The chosen unique design, the SAX, is very compact and uses only one stepper motor. Several parts have been developed in this project to ensure the proper functionality of the SAX. That includes a main operator program, a motor input signal generating program, a motor input signal executing system, a security system, and a system for controlled rotation of the SAX. For the input signal to the motor two different algorithms to generate the time delays were developed and tested. They were adapted to make the motor manage the sweeps of an ever‑changing load with high inertia during acceleration and deceleration. One of them was developed to make the time delay array generation much more efficient albeit with larger approximation error. The SAX worked well and should be rather easy‑to‑use regarding the operation of the system, from the physical maneuvering to utilizing the sub‑systems to the running of the main operator program. It fulfilled the specific requirements by enable a cross pattern measurement from  -60° to +60°  both from above and from the side, adjustment of the radius between 15cm to 45cm , adjustment 10cm in height, to be rotated along the floor in steps of 1°, measurement steps of 1° with an accuracy of less than 0,5° (the largest error was measured to be ≤ 0,461°). However, some calibration work needs to be done before the optimal performance of the system is reached. As a verification of the operation of the system data from measurements of open‑ended waveguides was presented. / Det finns en efterfrågan på chipantenner för millimetervågor eftersom de kan möjliggöra allehanda produkter inom flera olika områden. Forskningen på dessa ställer dock bl.a. speciella krav på utrustning som används under testmätningsfasen p.g.a. de små dimensionerna och den höga frekvensen. I detta projekt har ett robotsystem, SAX (Single Arm eXtra), utformats och konstruerats på avdelningen för Mikro- och nanosystem på KTH. Syftet med SAX är att mäta högfrekventa chipantenner ( 140 GHz till 325 GHz ) genom att förflytta en frekvensomvandlare med tillhörande mätantenn i en cirkulär bana runt antennen ifråga, oavsett om den är riktad vertikalt eller horisontellt och givet andra kravspecifikationer. Flera designalternativ för den grundläggande konstruktionen, både från andras arbeten och framtagna av författaren själv, har analyserats utifrån kravspecifikation för detta projekt och andra begränsningar. Den valda unika designen, SAX, är väldigt kompakt och använder sig bara av en stegmotor. För att möjliggöra funktionen i den slutgiltiga produkten har flera delar tagits fram vilka inkluderar ett operatörsprogram, ett program för genererandet av motorstyrsignaler, ett program för motorstyrning, ett säkerhetssystem och ett rotationssystem för kontrollerad rotation av SAX. För genererandet av motorstyrsignaler i form av tidsfördröjda pulser framtogs två olika algoritmer. De ger anpassade accelerations- och retardationssignaler för att motorn ska klara av att förflytta en föränderlig last med stor tröghet. En av dessa framtogs med syfte att mycket effektivt generera pulstiderna om än med större approximationsfel. SAX fungerade tillfredsställande och torde vara ganska lättanvänd med tanke på vad systemet kräver av operatören, från att fysiskt manövrera systemet till att använda delsystemen till att använda operatörsprogrammet. Systemet uppfyllde de givna specifika kraven genom att möjliggöra mätningar i form av ett kryssmönster från -60° till +60°  både ovanifrån och från sidan, radiejustering från 15cm till 45cm , höjdjustering över 10cm , rotation över golvet i steg om 1° , mätningar i steg om 1° med en noggrannhet på 0,5° (den största avvikelsen uppmättes till ≤ 0,461°). Vidare kalibrering behöver dock utföras för att utnyttja den fulla potentialen hos konstruktionen. För att verifiera funktionsdugligheten för systemet presenterades data från mätningar gjorda på öppna vågledare.

With the advent of the 5G technology standard for communication, it is esti-mated that around 50 billion devices around the world will be interconnectedunder this standard [1]. This has prompted the need to investigate new ma-terials, technologies and methods to conceal antennas for preserving the aes-thetic value of urban centers, and preventing these antenna systems from beingidentified or damaged. The aim of this thesis work was to identify possiblematerials and investigate methods for concealing Ericsson’s 5G mm-Wave Ad-vanced Antenna System(AAS) Radio Base Stations. A study of economicallyviable, commercially available materials for concealment, and methods to deter-mine their dielectric properties was done. A practical investigation of the effectsome available concealment materials on the RF performance of the mm-Wavebase station beams, was also performed. The results from the investigationsand measurements performed led to some useful conclusions and understand-ing about the various concealment material solutions. Overall, the investigatedconcealment materials were found to have two prominent effects:1. Reduction in EIRP (Equivalent Isotropic Radiated Power) of the basestation beams (attenuation).2. Distortion in the shape of the base station beams.The boresight beams for all the investigated cases were found to be attenu-ated(effect 1) by the concealments, but the steered beams were found to beboth attenuated in distorted(effect 2) by the concealments. In particular, con-cealments with a thin dielectric material mesh structure were found to have theleast effect on the base station beams. All other thicker(> λ0/2), compositeconcealments and even those with pure foam structures, were found to have anoticeable effect on the base station beams. In conclusion, thin dielectric mesh,films and paints could hence be of interest as concealment solutions for furtherinvestigations moving forward. / I och med införandet av 5G-tekniken för kommunikation bedöms det att cirka50 miljarder enheter runt om i världen kommer att vara uppkopplade via denna standard [1]. För att bevara det estetiska värdet av stadscentrum och förhindra att 5G-teknikens antenner identifieras eller skadas finns behov att undersöka nya material, tekniker och metoder för att dölja antenner. I detta examensarbete identifieras möjliga material samt undersöks metoder för att dölja Ericssons 5G mm-vågs Advanced Antenna System (AAS) radiobasstationer. Enstudie av ekonomiskt genomförbara, kommersiellt tillgängliga material för döljande och metoder för bestämning av dess dielektriska egenskaper gjordes. En empirisk undersökning av effekten av några tillgängliga maskeringsmaterial på RF-prestanda hos loberna från mm-vågsbasstationer utfördes också. Resultaten från de undersökningar och mätningar som utfördes ledde till några användbara slutsatser och förståelse för egenskaperna hos de olika maskeringsmaterialen. Sammantaget visade sig de undersökta maskeringsmaterialen ha två huvudsakliga effekter:1. Dämpning av EIRP (ekvivalent isotropisk utsrålad effekt) hos basstationsloberna.2. Distorsion av basstationslobernas form.De centrala basstationsloberna för alla undersökta fall visade sig dämpas (ef-fekt 1) av maskeringsmaterialen, men de utstyrda loberna befanns vara både dämpade och förvrängda (effekt 2) av maskeringsmaterialen. Maskeringsmaterial med en tunn dielektrisk nätstruktur visade sig ha den minsta effekten på basstationsloberna. Alla andra tjockare, sammansatta material och ävende med rena skumstrukturer visade sig ha en märkbar effekt på basstation-sloberna. Sammanfattningsvis kan därför tunna dielektriska nät, filmer (plastfolier) och färger vara av intresse som lösningar för vidare undersökningar.

xv Abstract The aim of this thesis is to investigate the accurate stabilization energy and binding free energy in various non-covalent complexes spanned from small organic molecules to biomolecules. Non-covalent interactions such as H-bonds, π...π stacking and halogen bonds are mainly responsible for understanding of most biological processes, such as small molecule interactions with surface, protein-ligand binding in the cell machinery, etc. In the thesis, different non-covalent complexes such as graphene…electron donor- acceptor complexes, DNA base pair interaction with silica surface, etc, were investigated. The reference stabilization energies were calculated at ab initio level, e.g., CCSD(T)/CBS method wherever possible. On the other hand, more approximated scaled MP2 method (MP2.5/CBS/6-31G*(0.25)) is taken as reference instead of CCSD(T)/CBS due to the size of the complexes. Further, the DFT and MM energies were also tested towards the reference one. The knowledge of non- covalent interaction is required for rationalizing of any association processes in nature which requires accurate description of the free energy change. The state-of- the-art molecular dynamics simulation in full atomic scale and biased metadynamics free energy method is used for binding free energy calculations. The well tempered...

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The relationship between protein structure, motions, and catalytic activity is an evolving perspective in enzymology. An interactive approach, where experimental and theoretical studies examine the same catalytic mechanism, is instrumental in addressing this issue. We combine various techniques, including steady state and pre-steady state kinetics, temperature dependence of kinetic isotope effects (KIEs), site-directed mutagenesis, X-ray crystallography, and quantum mechanics/molecular mechanics (QM/MM) calculations, to study the catalytic mechanisms of thymidylate synthase (TSase). Since TSase catalyzes the last step of the sole intracellular de novo synthesis of thymidylate (i.e. the DNA base T), it is a common target for antibiotic and anticancer drugs. The proposed catalytic mechanism for TSase comprises a series of bond cleavages and formations including activation of two C-H bonds: a rate-limiting C-H→C hydride transfer and a faster C-H→O proton transfer. This provides an excellent model system to examine the structural and dynamic effects of the enzyme on different C-H cleavage steps in the same catalyzed reaction. Our experiments found that the KIE on the hydride transfer is temperature independent while the KIE on the proton transfer is temperature dependent, implying the protein environment is better organized for H-tunneling in the former. Our QM/MM calculations revealed that the hydride transfer has a transition state (TS) that is invariable with temperature while the proton transfer has multiple subsets of TS structures, which corroborates with our experimental results. The calculations also suggest that collective protein motions rearrange the network of H-bonds to accompany structural changes in the ligands during and between chemical transformations. These computational results not only illustrate functionalities of specific protein residues that reconcile many previous experimental observations, but also provide guidance for future experiments to verify the proposed mechanisms. In addition, we conducted experiments to examine the importance of long-range interactions in TSase-catalyzed reaction, using both kinetic and structural analysis. Those experiments found that a remote mutation affects the hydride transfer by disrupting concerted protein motions, and Mg2+ binds to the surface of TSase and affects the hydride transfer at the interior active site. Both our experiments and computations have exposed interesting features of ecTSase that can potentially provide new targets for antibiotic drugs targeting DNA biosynthesis. The relationship between protein structure, motions, and catalytic activity learned from this project may have general implications to the question of how enzymes work.

Le projet de cette thèse était l'évaluation du processus de réactivation et l'étude du site actif de l'AChE inhibée par un agent neurotoxique par des méthode computationnelles. L'objectif était de guider le design rationnel de nouveau réactivateurs. Une étude initiale avec un modèle QM tronqué a indiqué la nécessité de modéliser l'environnement enzymatique pour compenser la charge du Glu334. Elle a aussi confirmé le rôle du trou oxyanionique dans la stabilisation des états de transition de la réactivation. Des simulations QM/MM de la réactivation par le réactivateur classique 2-PAM, ainsi que par deux réactivateurs au coeur aromatique non chargé ont été effectuées. Il a été démontré que le Glu202, un résidu à proximité de la triade catalytique de l'AChE, doit être protoné pour que la réactivation ait lieu. Ces simulations ont aussi montré que le réactivateur peut être déprotoné dans le site actif de l'AChE par His447. Les réactivateurs au coeur aromatique non chargé sont plus nucléophiles que la 2-PAM et l'un d'entre eux est plus aisément déprotoné dans le site actif. Nos résultats indiquent que la capacité d'un réactivateur à être facilement déprotoné est plus importante que sa nucléophilie. Enfin, un mécanisme de migration de protons a été identifié par des calculs QM/MM et EVB. Il implique deux glutamates derrière le site actif, Glu450 et Glu452. La possibilité que ces deux protons soient temporairement protonés et donc impliqués dans une migration de protons a été confirmé par des calculs CpHMD. La migration de proton passe par la N-protonation d'une liaison amide, ce qui constitue un nouveau mécanisme. / The project of this PhD was to investigate the reactivation process and the active site of nerve agent inhibited AChE by computational methodologies to gain insight about the rational design of new reactivators. An initial truncated QM model study provided some insight in the necessary compensation of Glu334 by the enzyme. It also confirmed the role of the oxyanionic hole in the stabilization of the transition state of the reactivation. QM/MM simulations of the reactivation with classical reactivator 2-PAM, as well as two non-pyridinium reactivators, were performed. It was shown that Glu202, a residue near the catalytic triad of AChE, needs to be protonated for the reactivation to occur. Those simulations also showed that the reactivator can be deprotonated in the active site of AChE by His447. Non-pyridinium reactivator were found to have a greater nucleophilicity than 2-PAM and, for one of them, to be easily deprotonated in the active site. Our results indicate that the capacity of a reactivator to be deprotonated in the active site of the enzyme is more important than its nucleophilicity. Finally, a proton relay mechanism was identified through QM/MM and EVB simulations. It involves two glutamate residues, Glu450 and Glu452, positioned behind the active site. The potential for these two residues to be transiently protonated and thus involved in a proton relay was confirmed by CpHMD simulations. This proton relay mechanism relies on the N-protonation of an amide which is a novel mechanism.

Occupational exposure limits are generally decreasing and traditional samplers used for quantifying occupational exposures have numerous limitations: cost, disposability, detection of low concentrations, and some even fail to match international inhalable sampling conventions. A low cost, high-flow (10 L min-1) inhalable prototype sampler was developed from the 37-mm cassette and tested in previous studies. These studies called for additional field testing as an area and personal sampler. The sampler was paired with the IOM (2 L min-1), a traditional inhalable air sampler, and deployed in metal working facilities. The samplers were compared to determine whether the prototype matched the IOM and whether the new sampler could improve the sensitivity for detecting lower concentrations of metals. The following processes were sampled: welding, grinding, soldering, pouring, sawing, tending and shooting guns. A total of 21 out of 28 paired samples had detectable metals out of 15 possible metals. There were seven out of eight personal samples and 14 out of 20 area samples with detectable metal concentrations. The average sample time was seven hours, but ranged from 4.2 – 8.3 hours. The most common metals that were detected on 10 or more samples were iron, manganese, zinc, copper, and lead. Metal concentrations collected by the two samplers were not statistically different for the aggregate metal concentrations collected (p = 0.67), metals collected by sample type, personal or area (p = 0.52) or by particle “sizes,” small or large (p = 0.40), collected from the processes. While the samplers were not statistically different, linear regression equations to assess the sampler relationships showed that there were significant differences between the two samplers. Over the total metal concentrations collected, the prototype collected about 71% of what the IOM collected. By sample type, the prototype performed better during area sampling as opposed to personal sampling and by particle size, the prototype performed better in the collection of smaller, heat generated particles, as opposed to larger, mechanically generated particles. Though minor differences were found between concentrations detected on the prototype and IOM, it was determined that in general, these differences were negligible in their interpretation and comparison to occupational exposure limits. Plots also indicated that the prototype sampler performs well at sampling low concentrations of metals, however, only a small amount of metals were detected on the prototype that were not found on the IOM, therefore, the improvement of sensitivity was not assessed. High-flow sampling was hindered by the ability of air sampling pumps to maintain the required operation flow rate of 10 L min-1 for the duration of a work shift. Additional field studies are needed to determine whether the sensitivity for detecting lower concentrations of metals can be improved.

Protein pK(a)s and metalloprotein reduction potentials are studied with computational methodologies based on an ab initio quantum mechanics (QM) description of the protein and a linearized Poisson-Boltzmann Equation (LPBE) description of the solvent. The practical applicability of the QM/LPBE method is extended to proteins by using a QM description of the ionizable residue and a molecular mechanics (MM) description of the rest of the protein. This QM/MM/LPBE method is used to predict the pKa of Lys55 in the serine protease inhibitor turkey ovomucoid third domain (OMTKY3) and the prediction of 11.0 is in good agreement with the experimental value of 11.1. This is the first time a protein pKa value has been predicted with QM/MM methods. The QM/LPBE method is used to predict and interpret the pKa values of the five carboxyl residues (Asp7, Glu10, Glu19, Asp27, and Glu43) in OMTKY3. All the predicted pKa values are within 0.5 pH units of experiment, with a root mean square deviation of 0.31 pH units. We find that the decreased pKa values observed for some of the residues are primarily due to hydrogen bonds to the carboxyl oxygens. Hydrophobic effects are also shown to be important in raising the pKa. Interactions with charged residues are shown to have relatively little effect on the carboxyl pKa values in this protein, in general agreement with experiment. The relative Cu2+/Cu+ reduction potentials of six type-1 copper sites (cucumber stellacyanin, P. aeruginosa azurin, poplar plastocyanin, C. cinereus laccase, T. ferrooxidans rusticyanin and human ceruloplasmin), which lie in a reduction potential range from 260 mV to over 1000 mV, have been studied with the QM/LPBE method. For the first time, the range and relative orderings of the reduction potentials are reproduced well compared to experimental values. The study suggests that the main interactions determing the relative reduction potentials of blue copper sites are located within 6 Å of the Cu atoms. Further analysis suggests that the reduction potential differences of type-1 copper sites are caused by axial ligand interactions, hydrogen bonding to the S(Cys), and protein constraints on the inner sphere ligand orientations.

Ces dernières années, les méthodes hybrides QM/MM combinant la mécanique quantique (QM) et la mécanique moléculaire (MM) se sont revélées des méthodes de choix pour l'étude de systèmes chimiques et biochimiques contenant plus d'une centaine d'atomes. Nous avons mis en évidence les apports et difficultés liés à leur utilisation à travers des systèmes variés: modélisation de ligands phosphines, réactivité d'une protéine de type acide phosphatase pourpre, modélisation de l'interaction protéine-ligand.