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Master of Science / Department of Chemistry / Takashi Ito / Solvent swelling of block copolymer microdomains plays an essential role in the improvement of microdomain alignment by solvent vapor annealing and in chemical separations using block copolymer monoliths. Here, investigation of the effects of solvent swelling on the molecular permeability and dimensions of cylindrical microdomains in polystyrene-block-poly(ethylene oxide) (PS-b-PEO) films is done by using single molecule tracking. These films are prepared by sandwiching benzene (with/without methanol) or THF (with/without methanol) solutions containing 5 nM sulforhodamine B (SRB) between two glass substrates. The PEO microdomains are aligned in the solution flow direction during the film preparation. The diffusional motions of individual SRB molecules are measured at different drying times to assess the microdomain radius and permeability. These parameters, on average, gradually decrease with an increase in drying time; however the trend differs slightly from one solvent system to another. A sharp decrease of microdomain radius is observed for benzene, benzene-methanol, THF and THF-methanol swollen films at initial drying condition (for example 2 days). In contrast, microdomain permeability does not decrease sharply; instead a gradual decreasing trend is seen for all solvent systems. In addition, mixing of a small amount of methanol (14% in PEO microdomains) either with benzene or with THF does not produce noticeable difference in the swelling of PEO microdoamins. Importantly, both benzene and THF offer similar microdomain swelling behavior at the same drying temperature, which is evident from the microdomain radius values, however THF shows comparatively larger microdomain permeability and better correlation between permeability and microdomain radius compared with benzene.

Master of Science / Department of Chemistry / Daniel A. Higgins / Single molecule tracking (SMT) measurements have been applied to the study of molecular mobility in sol-gel-derived silica gradient films in this thesis. Such gradient films have broad potential applications in controlled adhesion and transport of cells, vesicles and polymers; separation of complex chemical mixtures and in the development of new catalysts. Silica films were prepared by “infusion-withdrawal dip-coating”. In this method, a suitable substrate is slowly withdrawn from a silica sol of time varying composition. The deposition reservoir is initially filled with a sol derived from one silica precursor (tetramethoxysilane). A second sol, prepared from a different precursor (methyltrimethoxysilane), is then infused into the deposition reservoir, as the mixed sol is withdrawn. Films thus prepared were initially characterized by bulk fluorescence spectroscopy, infrared (IR) microscopy, contact angle goniometry, spectroscopic ellipsometry and surface profilometry. The fluorescence, IR and contact angle data all demonstrate the presence of a gradient in the methyl content of the silica film. The primary objective of the work performed under this thesis was to investigate the diffusion of Nile Red molecules in and on these films, as a function of position along the gradient, by SMT methods. Histograms of the mean-square displacement of the molecules depict the presence of at least two distinct populations: one incorporating fixed (entrapped or adsorbed) molecules and the other clearly reflecting the presence of mobile molecules. The latter population was observed to vary along the gradient dimension and also changed as the films aged over the course of five days. Molecular mobility is attributed to the presence of liquid-like silica oligomers in the films. Spatial variations in the observed mobility are tentatively assigned to variations in oligomer viscosity along the gradient. Film viscosity also changes as the polymerization of the oligomers continues during film aging.

Doctor of Philosophy / Department of Chemistry / Daniel A. Higgins / This dissertation describes single-molecule tracking (SMT) studies for the quantitative characterization of one-dimensional (1D) solvent-filled surfactant-templated mesoporous silica (STMS) materials and other nanostructured materials, such as double-stranded DNA. SMT permits the simultaneous and quantitative assessment of the nanoscale and microscale morphologies and mass-transport properties of the materials with nanometer-scale spatial resolution. The efficiency and selectivity of catalytic reactions and chemical separations occurring in liquid-filled mesoporous materials are governed by the translational and orientational mobilities and surface interactions of the incorporated reagents and analytes. Polarization dependent SMT results demonstrate that the dye molecules used as probes of materials nanostructure are tightly confined within the one-dimensional (1D) pores of surfactant-templated mesoporous silica films. Spectroscopic single molecule tracking (sSMT) data reveal that the hydrophobic probe dyes are confined within nonpolar regions of the nanomaterials For this dissertation, surfactant templated mesoporous silica films were prepared by the spin coating of acid catalyzed tetramethoxysilane (TMOS)-based silica sols on glass substrates in the presence of Cetyltrimethylammonium bromide (CTAB). Cylindrical CTAB micelles formed during evaporation of the solvent acted as a structure directing template, forming nanometer-sized one-dimensional pores within the silica films. SMT experiments were performed using a wide-field fluorescence microscope that was sufficiently sensitive to allow detection of the fluorescence from individual dye molecules. A series of perylene diimide (PDI) dyes was employed for basic structural characterization of the silica materials. Single molecule fluorescence was recorded in the form of fluorescence videos. These videos revealed the presence of immobile dye molecules, along with those diffusing in one and two dimensions (1D and 2D). The 1D diffusing molecules provided basic evidence for the confinement mass transport of the dye molecules within the silica mesopores. Spectroscopic single molecule tracking (sSMT) studies served as an extension of basic SMT experiments and were employed to determine the location of the molecules. The polarity sensitive dye Nile Red (NR) was employed in these studies. It exhibits 1D diffusion, consistent with its confinement to the cylindrical pores, as was also the case for the PDI dyes. The sSMT data revealed that the majority of NR molecules were found in nonpolar environments having polarities similar to that of n-hexane. Single molecule emission polarization (SMEP) measurements were employed to explore the orientational confinement of the dyes. The results of these experiments demonstrated that the PDI and NR molecules diffuse with their long axes aligned parallel to the long axis of the pores. All of the dyes employed were found to be orientationally confined to ∼1 nm diameter pathways within the pores. The diffusion coefficient for the dyes was also shown to be ∼10^3 -fold smaller than in bulk solution. The results of the NR studies demonstrate that the dye molecules were confined to the hydrophobic cores of the micelles, and provide support for the conclusion that the PDI dyes are similarly confined. These studies afford an enhanced understanding of how nanostructuring of the pore-filling medium in solvent- and surfactant-filled mesoporous materials governs the mass transport and surface interactions of incorporated reagents and analytes. The dependence of molecular confinement on dye charge and structure was also explored in this dissertation. The confined translational and orientational motions of a series of four different PDI dyes diffusing along one dimension (1D) within individual cylindrical silica mesopores were investigated in these studies. Specifically, the motions of cationic and anionic PDI dyes were compared to those of two uncharged PDIs having different alkane tail lengths. All four dyes exhibited populations that were immobile, along with separate populations that diffused in either 1D or 2D. The anionic and cationic PDI dyes exhibited the largest and smallest populations, respectively, of immobile molecules, suggesting that electrostatic interactions between the charged dyes and the cationic surfactant head groups play a significant role in limiting molecular motion. The cationic and anionic PDI dyes also exhibit the largest populations of 2D diffusing molecules, suggesting they may more readily pass between the cylindrical micelles and through the silica pore walls. All four dyes also emit strongly polarized fluorescence as they move in 1D, indicating they are orientationally confined within the nanochannels. Nile Red dye was used to determine the dielectric constant, ε, of nonpolar microenvironments in double-stranded DNA (ds-DNA) single molecules both in aqueous buffer solution and when adsorbed on amine-modified chemical gradient surfaces. The value of ε within the DNA decreased with increasing buffer concentration. Values of ε ∼ 6.75 and ∼3.00 were obtained in 0.1 mM phosphate buffered saline (PBS) and in 10 mM PBS, respectively. Similar effects were observed upon adsorption to chemically graded amine-modified silica surfaces. Under 1 mM buffer, ε was measured to be ∼2.84 and ∼1.90 at the low amine (high silica), and high amine (low silica) ends of the gradient, respectively. An increase in the buffer concentration again led to a decrease in ε, but only at the low amine end. It is concluded that high buffer concentrations and binding to an amine surface cause condensation of the ds-DNA, forming less polar microenvironments within its structure. These results provide important knowledge of the factors governing the polarity of DNA microenvironments to which intercalators bind.

Doctor of Philosophy / Department of Chemistry / Takashi Ito / This dissertation describes single-molecule tracking (SMT) measurements for the quantitative characterization of one-dimensional (1D) nanostructures in 200 nm-thick surfactant-templated mesoporous silica (STMS) and cylinder-forming polystyrene-poly(ethylene oxide) diblock copolymer (CF-PS-b-PEO) films with a μm-scale thickness. SMT is advantageous for the characterization of nanomaterials over conventional methods because it permits the simultaneous and quantitative assessment of the nanoscale and microscale morphologies, and mass-transport properties of the materials with a high nanometer-scale resolution under ambient conditions. It offers a unique means for the assessment and evaluation of the μm-scale nanostructure alignment in polymer films induced by vertical spin-coating (for STMS films), directional solution flow and solvent-vapor penetration (SVP) methods (both for CF-PS-b-PEO films), highly crucial for many potential technological applications using the materials. Through this work, we have identified suitable sample preparation conditions (e.g. solvent, temperature or solution flow rate) for obtaining highly-ordered mesoporous and microdomain structures over a long-range (> 5 μm). For the quantitative assessment of the 1D SMT data, orthogonal regression analysis was employed, providing assessment of the in-plane orientation and size of individual nanostructures with nanometer-scale precision. The analysis of the 1D trajectory data allowed the radius (ca. 11 nm) of cylindrical PEO microdomains to be estimated, yielding results consistent with the AFM results (ca. 14 nm). The distribution of the trajectory angles offered the estimation of the average orientation and order of the nanostructures in domains/grains for a μm-wide region of the polymer films, revealing the higher efficiency of SVP in the nanostructure alignment as compared to the spin coating and solution flow approaches. Systematic SMT measurements across the film depth and along lateral mm-scale distances afforded valuable insights into the shear- and solvent-evaporation-based alignment mechanisms induced by solution flow and SVP/spin coating approaches, respectively. Fluorescence recovery after photobleaching (FRAP) measurements in a SVP-aligned CF-PS-b-PEO film permitted the longer-range mass-transport properties to be probed, reflecting the effective continuity of the aligned cylindrical nanostructures over > 100 μm in length. In this dissertation, FRAP and more importantly SMT methods have provided a unique and useful means for the in-depth characterization of morphology and mass-transport characteristics in thin polymer films under ambient conditions, in confined spaces, and with a nanometer-scale resolution.

Doctor of Philosophy / Department of Chemistry / Daniel A. Higgins / This dissertation describes single-molecule tracking (SMT) studies for the quantitative characterization of one-dimensional (1D) nanostructures in surfactant-templated mesoporous silica monoliths prepared within microfluidic channels. Single molecule diffusion of fluorescent probe molecules within the cylindrical mesopores reflects microscopic morphologies and mass-transport properties of the materials with high temporal and spatial resolution. The pore organization and materials order are initially investigated as a function of sol aging prior to loading into the microfluidic channels. Mesopores in these materials are templated by Cetyltrimethylammonium bromide (CTAB). Wide-field fluorescence videos depict 1D motion of the dyes within the individual mesopores. Orthogonal regression analysis of these motions provides a measure of the mesopore orientation. Channels filled prior to gelation of the sol produce monoliths incorporating large monodomains with highly aligned mesopores. In contrast, channels filled close to or after gelation yield monoliths with misaligned pores that are also more disordered. Two-dimensional (2D) small angle X-ray scattering (SAXS) experiments support the results obtained by SMT. These studies help to identify conditions under which highly aligned mesoporous monoliths can be obtained and also demonstrate the utility of SMT for characterization of mesopore order. The non-ionic surfactant Pluronic F127 is also utilized as the structural-directing agent. The diffusive motions of PDI dyes that are uncharged, cationic and anionic are explored by SMT and fluorescence correlation spectroscopy (FCS). The SMT studies for the uncharged dye show development of 1D diffusion along the flow direction while charged dyes exhibit predominant isotropic diffusion, with each of these behaviors becoming more prevalent as a function of aging time after filling of the microfluidic channels. SMT studies from silica-free F127 gels suggest that partitioning plays a important role in governing the diffusion behavior of the PDI dyes within the surfactant-filled mesopores. FCS results exhibit similar mean diffusion coefficients for all three dyes that suggest these dyes diffuse through similar sample regions. These studies demonstrate that the silica pore walls in the mesoporous silica monoliths remain permeable after gelation and that partitioning of solute species to different regions within the pores plays an important role in restricting the dimensionality of their diffusive motion

abstract: The cell is a dense environment composes of proteins, nucleic acids, as well as other small molecules, which are constantly bombarding each other and interacting. These interactions and the diffusive motions are driven by internal thermal fluctuations. Upon collision, molecules can interact and form complexes. It is of interest to learn kinetic parameters such as reaction rates of one molecule converting to different species or two molecules colliding and form a new species as well as to learn diffusion coefficients. Several experimental measurements can probe diffusion coefficients at the single-molecule and bulk level. The target of this thesis is on single-molecule methods, which can assess diffusion coefficients at the individual molecular level. For instance, super resolution methods like stochastic optical reconstruction microscopy (STORM) and photo activated localization microscopy (PALM), have a high spatial resolution with the cost of lower temporal resolution. Also, there is a different group of methods, such as MINFLUX, multi-detector tracking, which can track a single molecule with high spatio-temporal resolution. The problem with these methods is that they are only applicable to very diluted samples since they need to ensure existence of a single molecule in the region of interest (ROI). In this thesis, the goal is to have the best of both worlds by achieving high spatio-temporal resolutions without being limited to a few molecules. To do so, one needs to refocus on fluorescence correlation spectroscopy (FCS) as a method that applies to both in vivo and in vitro systems with a high temporal resolution and relies on multiple molecules traversing a confocal volume for an extended period of time. The difficulty here is that the interpretation of the signal leads to different estimates for the kinetic parameters such as diffusion coefficients based on a different number of molecules we consider in the model. It is for this reason that the focus of this thesis is now on using Bayesian nonparametrics (BNPs) as a way to solve this model selection problem and extract kinetic parameters such as diffusion coefficients at the single-molecule level from a few photons, and thus with the highest temporal resolution as possible. / Dissertation/Thesis / Source code related to chapter 3 / Source code related to chapter 4 / Doctoral Dissertation Physics 2020

Spatial and temporal dynamics of polymer chains play critical roles in their rheological properties, which have a significant influence on polymer processing and fabrication of polymer-based (nano) materials. Many theoretical and experimental studies have aimed at understanding polymer dynamics at the molecular level that give rise to its bulk phase properties. While much progress has been made in the field over the past ~60 years, many aspects of polymers are still not understood, especially in complicated systems such as entangled fluids and polymers of different topologies. In addition, the physical properties of biological macromolecules, i.e. DNA, are expected to affect the spatial organization of chromosome in a cell, which has the potential impact on a broad epigenetics research. Here, we propose new methods for simultaneous visualization of diffusive motion and conformational dynamics of individual polymer chains, two most important factors that characterize polymer dynamics, based on a new single-molecule tracking technique, cumulative-area (CA) tracking method. We demonstrate the applicability of the CA tracking to the quantitative characterization of the motion and relaxation of individual topological polymer molecules under entangled conditions, which is possible only by using the newly-developed CA tracking, using fluorescently-labeled linear and cyclic dsDNA as model systems. We further extend the technique to multi-color CA tracking that allows for the direct visualization and characterization of motion and conformation of interacting molecules. We also develop a new imaging method based on recently developed 3D super-resolution fluorescence microscopy technique, which allows direct visualization of nanoscale motion and conformation of the single molecules that is not possible by any other methods. Using these techniques, we investigate spatial and temporal dynamics of polymers at the single-molecule level, with special emphasis on the effect of topological forms of the molecules and the confined geometry on their spatiotemporal dynamics. Our results demonstrate that the new methods developed in this thesis provide an experimental platform to address key questions in the entangled topological polymer dynamics. The research will provide a platform for developing new polymer-based materials and open the possibility of studying spatial organization of DNA in a confined geometry from physics point of view.

The nuclear pore complex (NPC) is a proteinaceous gateway embedded in the nuclear envelope (NE) that regulates nucleocytoplasmic transport of molecules in eukaryotes. The NPC is formed by hundreds of proteins that are classified into approximately thirty different types of proteins called nucleoporin (Nup), each presents in multiples of eight copies. These nucleoporins are divided into two categories: the scaffold Nups forming the main structure of the NPC and the phenylalanine-glycine (FG) Nups that contain multiple repeats of intrinsically disordered and hydrophobic FG domains. These FG-Nups constitute the selective permeability barrier in the central channel of the NPC, which mediates the nuclear import of proteins into the nucleus, and the nuclear export of mRNA and pre-ribosomal subunits out of the nucleus. However, the precise copies of these Nups and their specific roles in the nucleocytoplasmic transport mechanism remain largely unknown. Moreover, the dysfunctional nuclear transport and the mutations of Nups have been closely associated with numerous human diseases, such as cancer, tumor and liver cirrhosis. We have developed and employed live-cell high-speed single-molecule microscopy to elucidate these critical questions remained in the nuclear transport and provide the fundamental knowledge for developing therapies. In this dissertation, I will present my major findings for the following three research projects: 1) determine the dynamic components of FG-Nups in native NPCs; 2) track the nucleocytoplasmic transport of transcription factor Smad proteins under ligand-activated conditions; and 3) elucidate the relationship between the nuclear export of mRNA and the presence and absence of specific Nups in live cells.Determination of the dynamic components for FG-Nups in native NPCs. Scaffold Nups have been intensively studied with electron microscopy to reveal their spatial positions and architecture in the past decades. However, the spatial organization of FG-Nups remains obscure due to the challenge of probing these disordered and dynamic polypeptides in live NPCs. By employing high-speed single-molecule microscopy and a live cell HaloTag labeling technique, I have mapped the spatial distribution for all eleven known mammalian FG-Nups within individual NPCs. Results show that all FG-Nups within NPCs are distinct in conformations and organized to form a ~300nm long hourglass shaped toroidal channel through the nuclear envelope. Exceptionally, the two remaining Nups (Nup98 and hCG1) almost extend through the entire NPC and largely overlap with all other FG-Nups in their spatial distributions. These results provide a complete map of FG-Nup organization within the NPC and also offer structural and functional insights into nucleocytoplasmic transport models. Tracking of the nucleocytoplasmic transport of Smad proteins under ligand-activated conditions. The inducement of transforming growth factor β1 (TGF-β1) was reported to cause the nuclear accumulation of Smad2/Smad4 heterocomplexes. However, the relationship between nuclear accumulation and the nucleocytoplasmic transport kinetics of Smad proteins in the presence of TGF-β1 remains obscure. By combining a high-speed single-molecule tracking microscopy technique (FRET), I tracked the entire TGF-β1-induced process of Smad2/Smad4 heterocomplex formation, as well as their transport through nuclear pore complex in live cells. The FRET results have revealed that in TGF-β1-treated cells, Smad2/Smad4 heterocomplexes formed in the cytoplasm, imported through the nuclear pore complexes as entireties, and finally dissociated in the nucleus. Moreover, it was found that basal-state Smad2 or Smad4 cannot accumulate in the nucleus without the presence of TGF-β1, mainly because both of them have an approximately twofold higher nuclear export efficiency compared to their nuclear import. Remarkably and reversely, heterocomplexes of Smad2/Smad4 induced by TGF-β1 can rapidly concentrate in the nucleus because of their almost fourfold higher nuclear import rate in comparison with their nuclear export rate. Thus, these single-molecule tracking data elucidate the basic molecular mechanism to understand nuclear transport and accumulation of Smad protein. Elucidation of the relationship between the nuclear export of mRNA and the presence and absence of specific Nups in live cells. In addition to explore the dynamic organization of NPC, in vivo characterization of the exact copy number and the specific function of each nucleoporin in the nuclear pore complex (NPC) remains desirable and challenging. Using live-cell high-speed super-resolution single-molecule microscopy, we first quantify the native copies of nuclear basket FG-Nups (Nup153, Nup50 and Tpr). Second, with same imaging technique and the auxin-inducible degradation strategies, I track the nuclear export of mRNA through native NPCs in absence of these FG-Nups. I found that these FG-Nups proteins possess the stoichiometric ratio of 1:1:1 and play distinct roles in the nuclear export of mRNAs in live cells. Tpr’s absence in the NPC dominantly reduces nuclear mRNA’s probability of entering the NPC for export. Complete depletion of Nup153 causes mRNA’s successful nuclear export efficiency dropped approximately four folds. Remarkably, the relationship between mRNA’s successful export efficiency and the copy number of Nup153 is not linear but instead follows a sigmoid function, in which mRNA can gain its maximum successful export efficiency as Nup153 increased from zero to around half of their full copies in the NPC. Lastly, the absence of Tpr or Nup153 also alters mRNA’s export routes through the NPC, but the removal of only Nup50 has almost no impact upon mRNA export route and kinetics. / Biology

Polymer flooding is one of the most used chemical methods for enhanced oil recovery(EOR). However, laboratory studies and field applications of polymer injections often encounter polymer-induced clogging due to polymer transport and entrapment, leading to permeability reduction and diminished recovery performance. In this work, we focus on understanding polymer flow behavior using microfluidics devices and fluorescence microscopy. Microfluidic devices were designed to mimic and replicate the pore-network structures of oil-bearing conventional reservoir rocks. We present various flow experiments to study polymer transport and the underlying mechanisms of polymer retention in porous media. We assess the polymer-induced clogging of partially hydrolyzed polyacrylamides - HPAMs, using tracers. Afterward, we use a commercially available fluorescent polymer with microfluidics and single-molecule microscopy to give insights into individual molecule dynamics. Furthermore, we perform numerical simulations to replicate and extend the experimental work. As these experiments were conducted using commercially fluorescent polymer of low molecular weight and due to limitations of tracers to track polymers, we extended this work to investigate the transport of HPAMs, which is the most used polymer for EOR, at molecule-scale. However, existent methods in the literature are not suitable for fluorescently labeling ultra-high molecule weight polymers. Therefore, we present a novel method for synthesis of dye-labeled polymers that successfully tagged the HPAMS. Finally, we assessed the conformation and flow dynamics of the fluorescently labeled HPAM molecules. The findings highlight a limitation in some polymer screening workflows in the industry that suggest selecting the candidate polymers based solely on their molecular size and the size distribution of the rock pore-throats. Moreover, we present, for the first time, direct visualization of the three main mechanisms underlying polymer retention in porous media. We bring the first molecular evidence of polymer pore-clogging and permeability reduction reversibility, which sheds light on the controversy in the literature. In addition, we propose a new method for fluorescent labeling water-soluble ultra-high molecular weight polyacrylamides-based polymers that preserves their viscosifying properties. The method can be extended to any polymers containing carboxyl groups or groups that can be functionalized into carboxyls, and therefore, the applicability covers any fields that employ polymers.