<div>Organic mixed ion-electron conducting (OMIEC) polymers are capable of transporting both electrons and ions. This unique functionality underpins many emerging applications, including biosensors, electrochemical transistors, and batteries. The fundamental operating principles and structure-function relationships of OMIECs are still being investigated. Computational tools such as coarse-grained molecular dynamics (CGMD), which use simpler representations than in atomistic modeling, are ideal to study OMIECs, as they can explore the slow dynamics and large length scale features of polymers. Nevertheless, methods development is still required for CGMD simulations to accurately describe OMIECs.</div><div><br></div><div>In this thesis, two CGMD simulation approaches have been adopted. One is a so-called "top-down" approach to develop a generic model of OMIECs. Top-down models are phenomenological but capable of exploring a broad space of materials variables, including backbone anisotropy, persistence length, side-chain density, and hydrophilicity. This newly developed model was used to interrogate the effect of side-chain polarity and patterning on OMIEC physics. These studies reproduce experimentally observed polymer swelling while for the first time clarifying several molecular factors affecting charge transport, including the role of trap sites, polaron delocalization, electrolyte percolation, and suggesting side-chain patterning as a potential tool to improve OMIEC performance.</div><div><br></div><div>The second strategy pursued in this thesis is bottom-up CGMD modeling of specific atomistic systems. The bottom-up approach enables CGMD simulations to be quantitatively related to specific materials; yet, the sources of error and methods for addressing them have yet to be systematically established. To address this gap, we have studied the effect of the CG mapping operator, an important CG variable, on the fidelity of atomistic and CGMD simulations. A major observation from this study is that prevailing CGMD methods are underdetermined with respect to atomistic training data. In a separate study, we have proposed a hybrid machine-learning and physics-based CGMD framework that utilizes information from multiple sources and improves on the accuracy of ML-only bottom-up CGMD approaches. </div>

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18117号 / 理博第3995号 / 新制||理||1576(附属図書館) / 30975 / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 高田 彰二, 教授 大野 睦人, 准教授 土井 知子 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Yes / Inhaled nanoparticles (NPs) are experienced by the first biological barrier inside the alveolus known as lung surfactant (LS), a surface tension reducing agent, consisting of phospholipids and proteins in the form of the monolayer at the air-water interface. The monolayer surface tension is continuously regulated by the alveolus compression and expansion and protects the alveoli from collapsing. Inhaled NPs can reach deep into the lungs and interfere with the biophysical properties of the lung components. The interaction mechanisms of bare gold nanoparticles (AuNPs) with the LS monolayer and the consequences of the interactions on lung function are not well understood. Coarse-grained molecular dynamics simulations were carried out to elucidate the interactions of AuNPs with simplified LS monolayers at the nanoscale. It was observed that the interactions of AuNPs and LS components deform the monolayer structure, change the biophysical properties of LS and create pores in the monolayer, which all interfere with the normal lungs function. The results also indicate that AuNP concentrations >0.1 mol% (of AuNPs/lipids) hinder the lowering of the LS surface tension, a prerequisite of the normal breathing process. Overall, these findings could help to identify the possible consequences of airborne NPs inhalation and their contribution to the potential development of various lung diseases. / University of Technology Sydney (UTS) FEIT Research Scholarship, UTS IRS (S.I.H.), 2018 Blue Sky scheme–Suvash Saha (Activity 2232368), N.S.G is supported by the Vice-Chancellor fellowship funded by QUT.

Single-molecule spectroscopy has provided a means to uncover pathways and heterogeneities that were previously hidden beneath the ensemble average. Such heterogeneity, however, is often obscured by the artifacts of experimental noise and the occurrence of undesired processes within the experimental medium. This has subsequently caused in the need for new analytical methodologies. It is particularly important that objectivity be maintained in the development of new analytical methodology so that bias is not introduced and the results improperly characterized. The research presented herein identifies two such sources of experimental uncertainty, and constructs objective approaches to reduce their effects in the experimental results. The first, photoblinking, arises from the occupation of dark electronic states within the probe molecule, resulting in experimental data that is distorted by its contribution. A method based in Bayesian inference is developed, and is found to nearly eliminate photoblinks from the experimental data while minimally affecting the remaining data and maintaining objectivity. The second source of uncertainty is electronic shot-noise, which arises as a result of Poissonian photon collection. A method based in wavelet decomposition is constructed and applied to simulated and experimental data. It is iii found that, while making only one assumption, that photon collection is indeed a Poisson process, up to 75% of the shot-noise contribution may be removed from the experimental signal by the wavelet-based procedure. Lastly, in an effort to connect model-based approaches such as molecular dynamics simulation to model-free approaches that rely solely on the experimental data, a coarse-grained molecular model of a molecular ionic fluorophore diffusing within an electrostatically charged polymer brush is constructed and characterized. It is found that, while the characteristics of the coarse-grained simulation compare well with atomistic simulations, the model is lacking in its representation of the electrostatically-driven behavior of the experimental system.

Nuclear magnetic resonance (NMR) spectroscopy was used to determine the structure of transmembrane (TM) segment IX of the Na+/H+ exchanger isoform 1 (NHE1) in dodecylphosphocholine micelles. Studying isolated TM segments in this fashion constitutes a well-established "divide and conquer" approach to the study of membrane proteins, which are often extremely difficult to produce, purify, and reconstitute in full-length polytopic form. A similar approach was combined with NMR spin relaxation experiments to determine the peptide backbone flexibility of NHE1 TM VII. The combined NMR structural and dynamics studies are consistent with an important role for TM segment flexibility in the function of NHE1, a protein involved in apoptosis and myocardial disease. The study of the rhomboid protease system is also described from two perspectives: 1) I attempted to produce several TM constructs of the substrate spitz or a related construct and the production and purification are described in detail; and 2) I present coarse-grained molecular dynamics simulation results for the E. coli rhomboid ecGlpG and a spitz TM construct. Spitz appears to preferentially associate with rhomboid near TMs 1 and 3 rather than the proposed substrate gate at TM 5. The two proteins primarily interact at the termini of helices rather than within the hydrocarbon core of the bilayer. Finally, I present a detailed analysis of coarse-grained molecular dynamics simulations of the fibroblast growth factor receptor 3 TM domain dimerization. Specifically, algorithms are described for analyzing critical features of wild-type and G380R mutant constructs. The G380R mutation is the cause of achondroplasia, the most common form of human dwarfism. The results suggest that the proximity of a residue to the dimer interface may impact the severity of the mutant phenotype. Strikingly, heterodimer and mutant homodimer constructs exhibit a secondary dimer interface which may explain the increased signaling activity previously reported for the G380R mutation--the helices may rotate with the introduction of G380R. The unifying theme of this work is the 'study of membrane proteins' using complementary techniques from structural biology and computational biochemistry.

The overall objective of this PhD thesis research is to understand and control phase separation in mixed perfluorinated fatty acid-phospholipid surfactant systems that have applications as pulmonary surfactant (PS) mixtures, with an ultimate view of controlling film composition, morphology and mechanical properties. In this context the interaction between perfluorooctadecanoic acid (C18F), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), the major component of native PS extract, and 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG) has been explored in Langmuir monolayers and Langmuir–Blodgett (LB) films using a combination of atomic force microscopy (AFM), fluorescence microscopy (FM) and Brewster angle microscopy (BAM) measurements. Thermodynamic and morphological studies of binary and ternary mixed films made of C18F, DPPC and DPPG indicated that both the phospholipids and C18F were miscible over a wide range of compositions. The mixed phospholipid-C18F films contained multimolecular aggregates that were highly enriched in the phospholipids. Furthermore, it was found that the magnitude of the DPPC-C18F interaction could be modulated by altering the concentration of sodium ions in the underlying subphase. Using a highly simplified lung mimic fluid (pH 7.4, 150mM NaCl), DPPC and C18F became fully immiscible. Moreover, the performance characteristics of the mixed films demonstrated the usefulness of C18F as an additive for PS formulations. The effectiveness of a PS protein mimicking peptide was evaluated against DPPC to allow comparison with previous measurements of DPPC-C18F mixed system. The mixing thermodynamics of the peptide and DPPC in Langmuir monolayer implied a repulsive interaction between the film components. The hysteresis response of the mixed monolayer films indicated that the lipid-protein mixture improved the re-spreading of DPPC films. Moreover, molecular-level organization of the mixed films explored by both FM and BAM confirmed the formation of liquid-expanded DPPC domains in the presence of minute amount of the peptide. In order to obtain a thorough understanding of the effect of the deposition process and surfactant tail polarities on the interfacial behavior of perfluorocarbon-hydrocarbon mixed monolayer films, both BAM and AFM measurements of arachidic acid (C20) with perfluorotetradecanoic acid (C14F) and palmitic acid (C16) with C18F mixed monolayer were performed. These measurements revealed that film morphology was minimally perturbed upon its deposition onto solid substrates. Coarse grained molecular dynamics (MD) simulations of films comprised of DPPC molecules with tails of various polarities suggested that the phase separation between the monolayer components could be controlled by varying surfactant tail polarities.