Title: Study of protein structure and dynamics by means of optical spectroscopy Author: Tomáš Pazderka Institute: Institute of Physics of Charles University Supervisor: RNDr. Vladimír Kopecký, Ph.D., Institute of Physics of Charles University Abstract: The aim of this thesis is to improve understanding of protein structure and dynamics and extend experimental setup and data processing for such stud- ies. We focus on the extension of experimental feasability of vibrational optical activity (VOA). We have demonstrated a usability of intensity calibration in the field of Raman optical activity. Advantages for measurements on multiple instru- ments and/or using different configurations have been shown. A new instrumental setup has been developed for microsampling measurements of vibrational circular dichroism spectra with a spatial resolution of 1 mm. Using this technique, spatial inhomogeneities in a sample of protein fibrils have been observed. Model com- pounds for amide nonplanarity have been investigated utilizing several methods of optical spectroscopy and key spectral features for determination of amide non- planarity and the absolute configuration have been identified. A comprehensive set of Raman spectra of proteinogenic amino acids has been measured. Sample concentration dependencies and consequent...

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<p>  </p> <p>The next generation of nuclear reactor designs promise to provide clean, safe, and efficient energy to address our current climate crisis. But with these new technologies, nuclear fuel materials must be carefully designed and understood to meet these demands. Candidate oxide and metallic nuclear fuel materials being considered for use in these new reactor technologies, despite their potential, still have significant remaining materials challenges in understanding their long-term performance and integrity under extreme reactor conditions. As such these candidate fuels require extensive materials characterization to understand their long-term performance under reactor conditions. The objective of this study is to evaluate the microstructural evolution of candidate fuels U-50wt%Zr and ThO2 under the following contexts: 1) Investigation of phase stability in candidate metallic fuel U-50wt%Zr under thermal and irradiation treatment; 2) Investigate localized thermal properties of candidate oxide fuel ThO2 under irradiation through a novel correlative microscopy approach. </p> <p>The influence of thermal and irradiation treatment on phase stability in δ-U50wt%Zr was investigated through conventional APT-TEM methodology. U-Zr is a candidate metallic fuel for advanced fast reactor applications. However, there is still work remaining to better understand how these materials evolve under extreme reactor conditions, especially for the δU-50wt%Zr composition. Metallic fuels are susceptible to significant chemical redistribution under extreme conditions resulting in potential degradation of fuel properties and performance. In these experiments, U-50wt%Zr was subjected to thermal annealing and proton irradiation respectively. These treatments produced very different modulated structures in U-50wt%Zr, and the implications of such on phase stability in U-50wt%Zr will be discussed.</p> <p>Additionally, long-term nuclear reactor operation hinges upon efficient thermal transport in nuclear fuels. There is a critical need to understand localized thermal transport in these materials to enable intelligent design of high-performance fuels. A novel correlative atom probe tomography (APT)-transmission electron microscopy (TEM) approach was developed to investigate the influence of irradiation defects on localized thermal diffusivity in ThO2 upon proton irradiation, and implications of such results will be discussed. </p>

<p dir="ltr">The recent COVID-19 pandemic has emphasized the risk of respiratory infections leading to acute respiratory distress syndrome (ARDS). A significant factor contributing to poor ARDS outcomes is the impairment of lung surfactant due to infiltrating surface-active proteins and phospholipases during lung inflammation. Lung surfactant's vital role in stabilizing alveoli by reducing air-water interfacial tension becomes evident as its dysfunction severely compromises respiratory function. Although lung surfactant (LS) replacement therapy effectively addresses neonatal LS deficiencies, its efficacy in ARDS treatment for adults remains limited. The challenge lies in the chemical similarity between current animal-extracted surfactants and human lung surfactant which are both phospholipid-based. To address this issue, this dissertation outlines a transformative "polymer lung surfactant (PLS)" designed to overcome the limitations of conventional exogenous surfactants in treating ARDS.</p><p dir="ltr">Firstly, a formulation method, referred to as equilibration-nanoprecipitation (ENP), is established which achieves reproducibility, controls sizing, and limits dispersity of the PLS formulation consisting of block copolymer (BCP) kinetically "frozen" micelles/nanoparticles suspended in water. The method uses a two-step approach of 1) equilibrating the BCP nanoparticles in a water/co-solvent mixture and 2) removing co-solvent using dialysis against a large water reservoir. Comparison of ENP with a conventional solvent-exchange technique through experimental and computational analysis yields further insights into ENP's advantages.</p><p dir="ltr">Next, various studies are highlighted which provide fundamental characterizations of the air-water surface behavior and physical properties of BCP nanoparticles in water. The air-water surface properties of block copolymers have been studied extensively when spread as free chains in organic solvent; however, little was previously known about air-water interfacial behavior of water-spread polymer nanoparticles. The studies address such topics as the effect of nanoparticle size, effect of nanoparticle core chemistry, and the effect of temperature on surface-mechanical behavior. Insights into nanoparticle molecular structure at the interface are provided through X-ray reflectivity and grazing incidence X-ray diffraction. The effect of temperature is further characterized by developing novel NMR and Langmuir trough methods to determine the physical state (glassy vs rubbery) of the core domain in the nanoconfined state at temperatures above and below physiologic temperature.</p><p dir="ltr">Lastly, <i>in vivo </i>studies are presented which demonstrate the detailed and promising proof-of-concept results on the efficacy of the PLS technology in mouse models of lung injury. The PLS therapy not only improves biomechanical function of the lung, but it also significantly lowers the extent of lung injury as shown by histological analysis and inflammatory marker measurements. An additional <i>in vivo </i>study is presented which highlights challenges in the delivery of the liquid PLS suspension to the lungs. The <i>in vivo </i>studies ultimately provide solid motivation for continued research into the development of the PLS therapy.</p><p dir="ltr">Given the promising potential of the PLS technology shown in the <i>in vivo</i> studies, the materials characterizations shared in this presentation offer valuable insights into the design of a novel PLS therapy. From these insights, key design parameters such as nanoparticle size characteristics, core chemistry, and core molecular weight can be chosen to produce the most desirable material properties. Overall, this dissertation furthers the progress of PLS therapeutic development and will hopefully ultimately contribute to improved health outcomes in patients suffering from ARDS.</p>

<p dir="ltr">Conducting polymers have garnered enormous attention due to their unique properties, including tunable chemical structure, high flexibility, solution processability, and biocompatibility. They hold promising applications in flexible electronics, renewable energies, sensing, and healthcare. Despite notable progress in conducting polymers over the past few decades, most of them still suffer from complicated synthesis routes, limited processability, low electrical conductivity, and poor ambient stability compared to their inorganic counterparts. Additionally, the susceptibility of conducting polymers to high temperatures makes them not applicable in real-life electronics. To address the challenges of developing high-performance and stable conducting polymers, we present two key approaches: dopant innovation for polymer-dopant interaction engineering and the discovery of new conjugated polymer hosts. From the perspective of dopant design, we first utilize cross-linkable chlorosilanes (C-Si) to design thermally and chemically stable conductive polymer composites. C-Si can form robust siloxane networks and simultaneously<i> </i>dope the host conjugated polymers. Besides, we have introduced a new class of dopants, namely aromatic ionic dopants (AIDs). The use of AIDs allows for the separation of doping and charge compensation, two processes involved in molecular doping, and therefore leads to highly efficient doping and thermally stable doped systems. We then provide insights into the design of novel conjugated polymer hosts. Remarkably, we have developed the first thermodynamically stable n-type conducting polymer, n-doped Poly (3,7-dihydrobenzo[1,2-b:4,5-b′]difuran-2,6-dione) (n-PBDF). n-PBDF is synthesized from a simple and scalable route, involving oxidative polymerization and reductive doping in one pot in the air. The n-PBDF ink is solution processable with excellent ink stability and the n-PBDF thin film is highly conductive, transparent, patternable, and robust. In addition, precise control over the doping levels of n-PBDF has been achieved through chemical doping and dedoping. By tuning the n-PBDF thin films between highly doped and dedoped states, the system shows controllable conductivity, optical properties, and energetics, thereby offering potential applications in a variety of organic electronics. Overall, this research advances the fundamental understanding of molecular doping and offers insights for the development of high-conductivity, stable conducting polymers with tunable properties for next-generation electronics.</p>

<p dir="ltr">Nanoparticles have seen immense development in the past several decades due to their intriguing physicochemical properties. The modern chemist is interested not only in methods of synthesizing nanoparticles with tunable properties but also in the chemistry that nanoparticles can drive. While several methods exist to synthesize nanoparticles, it is often advantageous to put nanoparticles on a variety of conductive substrates for multiple applications (such as energy storage and conversion). Despite enjoying over 200 years of development, the electrodeposition of nanoparticles suffers from a lack of control over nanoparticle size and morphology. Understanding that structure-function studies are imperative to understand the chemistry of nanoparticles, new methods are necessary to electrodeposit a variety of nanoparticles with control over macro-morphology but also microstructure. When a nanodroplet full of a metal salt precursor is incident on the electrode biased sufficiently negative to drive electroplating, nanoparticles form at a shocking rate (on the order of microseconds to milliseconds). We start with the general nuts-and-bolts of the experiment (nanodroplet formation and methods for electrodeposition). The deposition of new nanomaterials often requires one to develop new methods of measurement, and we detail new measurement tools for quantifying nanoparticle porosity and nanopore tortuosity within single nanodroplets. Owing to the small size of the nanodroplets and fast mass transfer, the use of nanodroplets also allows the electrodeposition of high entropy alloy nanoparticles at room temperature. Electrodeposition in aqueous nanodroplets can also be combined with stochastic electrochemistry for a variety of interesting studies. We detail the quantification of the growth kinetics of single nanoparticles in single aqueous nanodroplets. Nanodroplets can also be used as tiny reactors to trap only a few molecules, and the reactivity of those molecules can be electrochemically probed and evaluated with time. Overall, this burgeoning synthetic tool is providing unexpected avenues of tunability of metal nanoparticles on conductive substrates. Moreover, there is little understanding of how ion transfer can affect the fundamental of nanoparticle synthesis with nanodroplet-mediated electrodeposition. This thesis details different experiments performed to study the role of ion transfer during the nucleation and growth of nanoparticles.</p>

The mutation/deletion of the hereditary material in the cell nuclei is a chronic biochemical hazard; in fact, nuclear DNA faces tens of lesions from metabolic intermediates, hydrolytic reactions and external vectors a minute. The canonical lesions of DNA involve the DNA backbone as well as the nucleic bases and are mostly associated with reversible chemical modifications. However, the radiation field from beams of accelerated ions accounts for a dense streak of collisions and reactions with the DNA molecule, thereby achieving lethal clusters of elemental lesions. Double strand breaks (DSB), i.e., the cleft of the DNA backbone over both strands, are hazardous fractures of the chromatin fold associated with the radiation field, underlying cytotoxic outcomes and chromosomal aberrations. Eukaryotic cells, however, rejoin the fractured DNA moieties from DSB events via an apt enzymatic machinery, or the DDR. Prior to the deployment of enzymatic effectors, host enzyme sensors engage the DNA termini in reversible supramolecular assemblies, which requires that the fractured DNA moieties be fully exposed. The in silico assessments of the early layout of DNA lesions by radiations have defined DSBs as the closely associated modifications of the DNA backbone by means of “coarse” criteria, that is, within an arbitrary distance of the two clefts. However, the diverse DSB motifs, i.e. at a strand break distance of zero to several nucleotides, account for a different contact interface between the DNA termini, thus modulating the dynamics of the lesion sites. Moreover, it is reckoned that in the absence of excess external stimuli, far-distanced DSBs may not fracture the broken DNA moieties by thermal dissociation, within the characteristic timescales of the DDR activity. This thesis elaborate tackles the in silico assessment of the distribution of DSBs in a chromatin-like fold and the local mechanical strain enforced by blunt DSBs, by means of state-of-the-art Monte-Carlo track structure tools and classical molecular dynamics. We infer that i) a Poisson fit describes the spectrum of DSB motifs by the direct effect of accelerated hydrogen ions (H+) at a Bragg peak relevant energy range (500 keV - 5 MeV) and, notably, we observe a bias towards short-distanced, staggered DSBs; ii) the nucleosome fold, i.e. the elemental unit of the chromatin hierarchical framework, exerts an excess kinetic barrier on the disruption of DSBs, which is not observed in linear DNA, mediated by the contact interface between DNA and the core histone fold. In conclusion, we remark that in the absence of further data from in vitro and in vivo assessments, the (kinetic, thermodynamic) inferences about the thermal and mechanical resilience of broken DNA frameworks are as reliable as the force fields underneath; in fact, it is debated whether all-atom force fields and water models overestimate the force of the intermolecular contacts and over-stabilize the DNA double helix.

<p dir="ltr">DNA sequence design requires the ability to identify possible tertiary structural defects, secondary structure disruptions, and self-complimentary stretches that will disallow your complimentary strands to come together to form the desired duplex design. However, there is a need for those self-complimentary stretches, especially when designed with the intent for this to homo-oligomerize into the desired building block. With the programmability of nucleic acid hybridization, there is an expanding field wherein this specific, self-complimentary design feature can give new possibility of fine-tuning DNA self-assembly (Chapter 1) or overcome a previously thought limit of DNA ligation (Chapter 2).</p><p dir="ltr">The first chapter will closely look at the branched kissing loop interaction. This interaction was studied as a homo-polymerizable DNA building block that is topologically closed. As such, this paranemic motif has increased stability due to the Watson-Crick base pairing being “protected” by a 3-base adenine branch which close the loop of the sticky-end, meaning no free ends in the binding region. With this, herein we report that the intended higher-level structure could influence the lower-level building block formation. In DNA nanotechnology, this could mean the final higher-level structure would allow for fine-tuning as this would dictate the building blocks that fill in the defected parts of the higher-level structure.</p><p dir="ltr">The second chapter looks at the more finite than broad picture. Whilst the first chapter focusses on the impact the microscale has on the nanoscale through a homo-polymerizable design, the second chapter focusses on the ability to break barriers with homo-polymerizable design. In this chapter, we prove that with our splint strand design, when improved with a hairpin loop on the terminal ends, we can ligate DNA strands enzymatically as short as 16 nucleotides with an efficiency of 97% at high concentrations (100 uM). These hairpins allow for a stable, robust splint strand as they are a self-complimentary region which will maintain its shape throughout the process of joining together the 5’ and 3’ ends of the target strand.</p><p dir="ltr">Overall, this dissertation hopes to prove that homo-polymerizable DNA sequence designs are helping expand upon the DNA nanotechnology toolbox by introducing new possibilities for nanoscale design, as well as push past previously held boundaries through necessary added stability afforded by the self-complimentary strands.</p>

<p>Soft robotics is concerned with the modeling and designing of devices fabricated from materials with low Young’s moduli—much less than that of metal— that mimic the input/output operation and physical task utility of robotics.  The inherent compliance of soft robots lends these devices an adaptability and a capacity for human-machine interaction beyond that of conventional robotics. Multistable soft robotic grippers are a subset of the technology at the intersection of soft robotics and multistable structures. Multistable structures are continuum systems that exhibit more than one statically stable state, each associated with a strain energy minimum. The existence of these energetic minima allows the structures to adopt different stable configurations that can provide a reference point for open loop control schemes. Multistable soft robotics takes advantage of both the adaptability of soft robotics and the potential for simplified control of multistable structures.</p> <p>Achieving simplified control for soft robotics is a necessary milestone in creating functional and applied soft robots. </p> <p>This work presents a means for simple open-loop control of a multistable soft robotic gripper that is adaptable, controllable, and robust. The behavior is illustrated through a gripper geometry described by specific design parameters resulting in a near infinite design space. An analytical model based on lumped parameter springs is derived, allowing us to search the design space in a tractable fashion. Specifically, we predict the system’s stable states for any given design instance by searching for local minima in the energy landscape formed by a spring lattice representation of our device. The lattice is composed of linear, bistable, and torsional springs—each of which contributes to the energy landscape of the system. We validate our model against Finite Element simulations of our device, showing good agreement with the proposed model. The aptitude of the model sheds light on the fundamental mechanics of our soft robotic gripper topology, laying the foundation for efficient design optimization and simplified control of soft robots.</p>

Des pathologies telles que la myopathie et certains types de cancer, peuvent être causées par une mauvaise formation de l’enveloppe nucléaire (EN), processus se produisant lors de chaque division cellulaire mais aussi lors de la formation du pronoyau mâle. Un modèle in vitro, dérivé de gamètes d’oursins, a été utilisé afin d’étudier les différentes étapes de formation de l’EN et a permis de révéler plusieurs informations essentielles. Un des points critiques est que des membranes fortement enrichies en phosphoinositides polyphosphorylés (PPIs) sont essentielles à la formation de l’EN, notamment lors des étapes de fusion membranaire. Ces membranes proviennent du cytoplasme de l’ovocyte fécondé (MV1) et des noyaux de spermatozoïdes (NERs). Nous avons construit des modèles membranaires mimant les compositions lipidiques de ces membranes, puis étudié leur structure, leur dynamique ainsi que leur morphologie par spectroscopie de RMN des solides et microscopie électronique. Nous avons montré que les PPIs induisent une courbure membranaire positive, conduisant à la formation de petites vésicules ou de micelles allongées. Plus important encore, dans le modèle « MV1», les membranes sont très fluides. Le modèle « NERs » est constitué de membranes globalement ordonnées, semblables aux phases dites « liquides ordonnées » avec une modulation apportée par la PPIs. Nous avons également construit un modèle membranaire minant la composition lipidique des vésicules MV2, membranes non-enrichies en PPIs mais représentant 90 % des vésicules participant à la formation de l’EN. Ce modèle membranaire présente une dynamique intermédiaire à celle observée pour les modèles MV1 et NERs. Ces propriétés nouvelles ont permis de proposer un mécanisme décrivant le rôle des PPIs lors de la fusion membranaire conduisant à la formation de l’enveloppe nucléaire. / Diseases, such as myopathies and some types of cancer, can be caused by abnormal nuclear envelope (NE) assembly, a process that takes place at each cell division and during male pronuclear formation. A cell-free assay from sea urchin gametes, that mimics the in vivo male pronucleus formation, has been used to dissect the various stages of NE assembly. This in vitro assay has revealed several novel features. One of the critical aspects is that membranes highly enriched in polyphosphorylated phosphoinositides (PPIs), are essential for NE formation, especially during the stage of membrane fusion. Theses membranes are extracted from the cytoplasm of the fertilised oocyte (MV1) and sperm nuclei (NERs). We made model membranes with similar lipid composition to MV1 and NERs and studied their structure, dynamics and morphologies by solid-state NMR spectroscopy and electron microscopy. We show that PPIs have a positive membrane curvature, inducing small vesicles and elongated micelles. More importantly, we illustrate that “MV1-like” membranes are very fluid. “NERs-like” membranes are globally ordered and belong to the family of liquid ordered phases. We also evidenced that PPIs can counterbalance in part the ordering effect of cholesterol. Moreover we made model membranes with similar lipid composition to MV2, non-enriched in PPIs membranes which constitute 90% of the vesicles forming the NE. This model membrane shows an in-between dynamics compared to MV1 and NERs. We therefore propose a mechanism describing the role of PPIs during membrane fusion leading to nuclear membrane assembly.