For three decades, the ongoing HIV pandemic has taken the lives of tens of millions of people. Still, more tens of millions are fighting this incurable disease today. Current failures in combating this global problem are caused mainly by the virus's extreme ability of mutation, its very effective molecular shield which repels the immune system's attacks, and its immense variability. A breakthrough, achieved relatively recently, is the discovery of the so-called broadly neutralizing antibodies against HIV-1, which carry a very efficient and broad neutralizing response. So far, it's not known how to elucidate the production of these antibodies in the infected hosts to quell or altogether eliminate the virus. This work deals with experimental results, which led to both in vivo and in vitro proof-of-concept of the so-called protein mimetics, the ability to imitate viral surface epitopes, and therefore stimulate an efficient immune response carried by targeted broadly neutralizing antibodies. This effect is mediated by recombinant binding proteins, based on the Myomedin scaffold. This work describes the selection and characterization of these binding proteins mimicking the epitopes of one of the most effective broadly neutralizing antibodies, 10E8. It shows that the binding affinities of selected...

Antibiotic resistance is a global and accelerating matter. Over time, the bacteria have evolved several defense mechanisms against the antibiotics. One of the defense mechanisms is that the bacteria can produce enzymes with the ability to hydrolyze the characteristic b-lactam ring of the antibiotics. These enzymes are called b-lactamases. There are three different generations of antibiotics clinically available, and b-lactamases have co-evolved with the antibiotics over the generations. The third generation of antibiotics are called the carbapenems and b-lactamases which hydrolyze carbapenems are called carbapenemases. Carbapenemases are promiscuous, which means that they hydrolyze a variety of antibiotics. The b-lactamase IMI-1 is an imipenem-hydrolyzing enzyme and imipenem is a carbapenem, hence IMI-1 is a carbapenemase. In this project, IMI-1 was investigated in complex with the carbapenems imipenem, meropenem and biapenem using computational methods. More specifically, a homology model of IMI-1 was generated and the carbapenems were docked into the model. The system was then used for MD simulations where the important molecular interactions were identified, and the binding free energies were calculated using the LIE method. The results indicate that IMI-1 has flexible loops that enables an open and a closed conformation of IMI- 1. All three carbapenems were docked and simulated in both conformations of IMI-1. The results indicate that open and closed conformations confirms the promiscuity of carbapenemases since the flexibility enables various initial binding mechanisms. in other words, the hydrolysis may occur so quickly that the binding does not have much bearing of the activity of the enzyme. Furthermore, the calculated binding free energies indicate that IMI-1 is optimized for the catalytic process rather than the binding affinity. In conclusion, IMI-1 and similar systems requires further research using computational methods to counteract antibiotic resistance based on knowledge.

No description available.

The emergence of β-lactamase-mediated antibiotic resistance is one of the biggest threats in modern times. Combined with the discovery void of new forms of antibiotics, this sets the course toward a future where the efficacy of present-day health care will be jeopardized. To hinder the spread of β-lactamase-mediated antibiotic resistance, the development of the drug class β-lactamase inhibitors has been prioritized. The foremost candidate for development of this drug class, that has wide-spectrum inhibition of β-lactamases, is the clinically available avibactam of the diazabicyclooctane-scaffold (i.e., DBO-scaffold). However, the clinical applications of this inhibitor have been limited against one of the more rapidly spreading β-lactamases; OXA-48. In order to bolster the drug development of β-lactamase inhibitors of the DBO-scaffold, with good inhibitory activity toward OXA-48, DBO-ligands with different structure elements were analyzed for stability of the Michaelis Complex in the OXA-48 binding site using molecular dynamic simulations. The results indicate that elongation of the chain to the anionic group of the ligand combined with the addition of a methyl group to the DBO-ring was stabilizing for the productive position between the backbone hydrogens of Y211 and S70. The binding affinity was also estimated using the Linear Interaction Energy method, and an offset parameter of γ ≈ -19 kcal/mol was found and could represent the entropic differences of a flexible ligand-protein system. The results of this study may also indicate that the ligand stability of the Michaelis Complex is of minor consequence to the inhibition mechanism as a whole compared to the reaction rate.

La compréhension et le contrôle des interactions intermoléculaires est d'une importance fondamentale dans les domaines de la reconnaissance moléculaire et de l'ingénierie cristalline, ainsi que dans les systèmes biologiques. Parmi les contacts faibles les plus fréquents qui lient les molécules dans les solides organiques nous trouvons la liaison halogène, la liaison chalcogène, et la liaison hydrogène faible. Dans cette thèse, des études expérimentales et théoriques de densité de charge rhô(r) basées sur la méthodologie QTAIM ont été effectuées pour l'analyse des liaisons halogènes et chalcogènes, et pour leur comparaison avec les liaisons hydrogène faibles. Pour ce faire, nous avons réalisé l'affinement multipolaire de la densité électronique obtenue à partir de la diffraction des rayons-X sur monocristal, ainsi qu'à partir des calculs périodiques DFT. A l'issue de nos résultats, nous avons définie la nature de ces interactions faibles (électrophile-nucléophile) et caractérisé leur intensité et directionnalité. Basé sur la topologie de L(r) = ¬rhô delta inversé2 rhô(r), le descripteur électrostatique (delta(L/rhô)) nous a permis d'évaluer quantitativement l'interaction électrostatique entre les régions de concentration (CC) et de dilution (CD) de charge de la couche de valence des atomes. L'énergie d'interaction (Eint) a été décrite à partir de descripteurs topologiques de rhô(r). Nous nous sommes intéressés également à la formation de fragments structuraux récurrents, appelés synthons. Il a été prouvé que le synthon peut être créé non seulement par des groupements d'atomes similaires, mais aussi par des ensembles de sites CC et CD qui sont impliqués de façon similaire dans la formation de contact / Understanding and control of intermolecular interactions play a crucial role in molecular recognition, crystal engineering, and biological systems. Three very frequent weak contacts linking the molecules in organic solids are halogen, chalcogen, and weak hydrogen bondings. In this thesis, we perform experimental and theoretical charge density rho(r) studies based on the QTAIM methodology for analyzing halogen and chalcogen bonding, and for comparing them with weak hydrogen bonding, as derived from the high-resolution single crystal X-ray diffraction multipole-refined electron density and from density functional theory (DFT) calculations. Defining the nature of these weak interactions as electrophilic-nucleophilic, we particularly focus on their strength and directionality. Based on the topology of L(r) = ¬rho inverted delta2 rho(r), a proposed electrostatic descriptor (delta(L/rho)) permitted us to evaluate quantitatively the electrostatic intensity between charge concentration (CC) and charge depletion (CD) regions belonging to the valence shell of the interacting atoms. The interaction energy (Eint) was described from the topological properties of rho(r). The attention has been also paid to the formation of recurrent structural fragments, called synthons. By the developed approach, it is proved that the synthon arrangement can be created not only by groups of atoms, but also by sets of CC and CD sites similarly involved in the contact formation

Humic acids and humates are principal components of humic substances major organic constituents of soil, peat, coal and water around the world. I was involved in research into molecular dynamics simulations of interactions of quartz surfaces with aqueous solutions of ions and small organic molecules representing basic building blocks of larger biomolecules and functional groups of organic matter. We studied interactions of molecules with surfaces for a set of surface charge densities corresponding to the experimentally or environmentally relevant ranges of pH values employing molecular mechanics, molecular dynamics and ab initio techniques. Simulated quartz surfaces covered the range of surface charge densities 0.00, -0.03, -0.06 and -0.12 C-m-2, approximately corresponding to pH values 4.5, 7.5, 9.5 and 11. As model molecules, benzoic acid, phenol, o-salicylic acid and their conjugated bases were chosen. My task was to prepare topologies and parametric models of selected organic matter basic building blocks organic molecules. I focused on studying interactions of these molecules in an aqueous environment with mineral surface quartz. The aim was to process simulation results and analyse conformations of the adsorption complexes and their thermodynamic properties such as interaction energies, free energies and adsorption geometries.

Aggregate aus Molekülen, in denen die Moleküle über ihre elektronischen Übergangsdipole miteinander wechselwirken, finden wegen ihrer besonderen optischen und Energietransfer-Eigenschaften vielfach Anwendung in Natur, Technik, Biologie und Medizin. Beispiele sind die wechselwirkenden Farbstoffmoleküle, die in den Lichtsammelkomplexen Photosynthese betreibender Lebewesen Sonnenlicht absorbieren und die Energie als elektronische Anregung hocheffizient zu Reaktionszentren weiterleiten, oder Aggregate aus tausenden von organischen Farbstoffmolekülen in einem flüssigen Lösungsmittel. Die Wechselwirkung der Moleküle (Monomere) führt zu über mehrere Moleküle delokalisierten angeregten elektronischen Zuständen, die die Energietransfer-Dynamik und die Absorptionsspektren der Aggregate prägen. Die Lichtabsorption und der Energietransfer in molekularen Aggregaten werden oft stark von Vibrationen beeinflusst, sowohl von internen Vibrationsfreiheitsgraden der Monomere als auch von Vibrationen der Umgebung (z. B. das Proteingerüst in Lichtsammelkomplexen oder eine Flüssigkeitsumgebung), an die die elektronische Anregung koppelt. Da es schwierig ist, diese Vibrationen in die theoretische Beschreibung des Transfers und der Spektren einzubeziehen, ist ihr genauer Einfluss noch nicht gut verstanden. Um dieses Verständnis zu verbessern, entwickeln wir in dieser Arbeit neue Berechnungsmethoden und untersuchen damit die Auswirkungen der Vibrationen. Zuerst betrachten wir die diskreten internen Vibrationsfreiheitsgrade der Monomere. Dazu haben wir eine effiziente numerische Methode entwickelt, die es uns erlaubt, mehrere Freiheitsgrade pro Monomer explizit einzubeziehen und die volle Schrödinger-Gleichung zu lösen. Mit den Modellrechnungen können wir experimentelle Aggregat-Spektren der Helium-Nanotröpfchen-Isolation-Spektroskopie, mit der man die einzelnen Vibrationslinien der Monomere auflösen kann, zum ersten Mal quantitativ reproduzieren. In früheren theoretischen Behandlungen wurde oft nur ein einziger Vibrationsfreiheitsgrad pro Monomer berücksichtigt – nun zeigen wir, dass die Einbeziehung möglichst vieler Freiheitsgrade für eine realistische Beschreibung von Aggregat-Spektren wichtig ist. Um neben den internen Vibrationen auch den Einfluss der Umgebung beschreiben zu können, nutzen wir den Zugang offener Quantensysteme und nehmen an, dass die elektronische Anregung an ein strukturiertes Kontinuum von Vibrationsfreiheitsgraden koppelt. Erstmals wenden wir die sogenannte nicht-markovsche Quanten-Zustands-Diffusion auf die molekularen Aggregate an, wodurch wir mit Hilfe einer Näherung Spektren und Transfer mit einer sehr effizienten stochastischen Schrödinger-Gleichung berechnen können. So können wir Merkmale gemessener Aggregat-Spektren, wie das schmale J-Band und das breite strukturierte H-Band, in Abhängigkeit der Anzahl der Monomere und der Wechselwirkungsstärke zwischen den Monomeren beschreiben. Auch können wir den Übergang von kohärentem zu inkohärentem Transfer erfassen. Eine für den Transfer relevante Größe ist die Anzahl der kohärent gekoppelten Monomere im Aggregat. Diese schätzt man häufig aus der Verschmälerung des Aggregat-Spektrums ab. Wir finden jedoch für verschiedene Spektraldichten des Vibrationskontinuums sehr unterschiedliche Verschmälerungen des Aggregat-Spektrums, die wir analytisch erklären. So zeigen wir, dass die bisherige einfache Abschätzung der Anzahl der kohärent gekoppelten Monomere nicht gerechtfertigt ist, da die Verschmälerung stark vom angenommenen Modell abhängt.

<p>Co and Ni are two major elements in high temperature structural alloys that include superalloys for turbine engines and hard metals for cutting tools. The recent development of complex concentrated alloys (CCAs), loosely defined as alloys without a single principal element (e.g. CoNiFeMn), offers additional opportunities in designing new alloys through extensive composition and structure modifications. Within CCAs and Co- and Ni-based superalloys, solid-solution strengthening and stacking fault energy engineering are two of the most important strengthening mechanisms. While studied for decades, the potency and quantitative materials properties of these mechanisms remain elusive. </p> <p><br></p> <p>Solid-solution strengthening originates from stress field interactions between dislocations and solute of various species in the alloy. These stress fields can be engineered by composition modification in CCAs, and therefore a wide range of alloys with promising mechanical strength may be designed. This thesis initially reports on experimental and computational validation of newly developed theories for solid-solution strengthening in 3d transition metal (MnFeCoNi) alloys. The strengthening effects of Al, Ti, V, Cr, Cu and Mo as alloying elements are quantified by coupling the Labusch-type strengthening model and experimental measurements. With large atomic misfits with the base alloy, Al, Ti, Mo, and Cr present strong strengthening effects comparable to other Cantor alloys. </p> <p> </p> <p>Stacking fault energy engineering can enable novel deformation mechanisms and exceptional strength in face-centered cubic (FCC) materials such as austenitic TRIP/TWIP steels and CoNi-based superalloys exhibiting local phase transformation strengthening via Suzuki segregation. We employed first-principles calculations to investigate the Suzuki segregation and stacking fault energy of the FCC Co-Ni binary alloys at finite temperatures and concentrations. We quantitatively predicted the Co segregation in the innermost plane of the intrinsic stacking fault (ISF). We further quantified the decrease of stacking fault energy due to segregation.  </p> <p><br></p> <p>We further investigated the driving force of segregation and the origin of the segregation behaviors of 3d, 4d and 5d elements in the Co- and Ni-alloys. Using first-principles calculations, we calculated the ground-state solute-ISF interaction energies and revealed the trends across the periodic table. We discussed the relationships between the interaction energies and the local lattice distortions, charge density redistribution, density of states and local magnetization of the solutes. </p> <p><br></p> <p>Finally, this thesis reports on new methodologies to accelerate first-principles calculations utilizing active learning techniques, such as Bayesian optimization, to efficiently search for the ground-state energy line of the system with limited computational resources. Based on the expected improvement method, new acquisition strategies were developed and will be compared and presented. </p>