Bio-nanotechnology is the use of biomolecules to control both the structure and property of nanomaterials. No biomolecule has been employed more often than DNA as exemplified in the numerous demonstrations of DNA-directed assembly of nanomaterials. DNA has been used to covalently functionalize and assemble soft nanoparticles (e.g. liposomes) and hard nanoparticles (e.g. gold and silica nanoparticles) into a variety of hierarchical nanostructures. The majority of previous work however has focused on the latter, i.e., the assembly of “hard” nanoparticles such as gold nanoparticles (AuNPs) as oppose to the assembly of soft materials. The primary focus of this thesis is to add to the growing field of DNA-directed assembly of soft materials owing to the promise of such materials in a variety of analytical and biomedical applications. The first class of soft materials considered are liposomes which interestingly can be deformed by relatively weak intermolecular forces. In addition, DNA anchored to its surface can readily diffuse laterally within the lipid bilayer while DNA attached to inorganic nanoparticles remain fixed in position. We systematically consider the effect of varying the liposome structure, size, charge, and fluidity on liposome assemblies, in chapter 2. In addition, the interesting properties of liposomes are highlighted by a side-by-side comparison to DNA-functionalized gold nanoparticles, offering fundamental insights into DNA-directed assembly. Furthermore, hybrid DNA-directed assemblies composed of both AuNPs and liposomes are described in Chapter 3. In particular, the photothermal effects of such DNA-coupled liposome and AuNP assemblies were modulated by controlling the distance between liposome and AuNP allowing such systems to have potential application in drug-delivery. In chapter 4, the utility of liposomes is demonstrated as we exploit the fluidity of its diffuse bilayer with split aptamer functionalization for the rapid and selective detection of metabolites. The second class of soft material of interest in this thesis are hydrogels, which are cross-linked hydrophilic polymers. Because hydrogels are swollen in water, they can be used to immobilize biomolecules such as DNA for a myriad of applications. In chapter 5, the preparation and characterization of DNA-functionalized polyacrylamide hydrogels are presented. The use of such a DNA-modified hydrogel for the simultaneous detection and removal of mercury from water is subsequently demonstrated.

We present a platform that allows homogeneous and heterogeneous 3-D soft materials to be continuously defined in a single step. Biopolymer solutions are introduced to a microfluidic device and radially distributed to feed to a common outlet at the device center. This forms concentric sheaths of complex fluids and upon crosslinking, a hydrogel tube at the exit. This approach allows for the controlled and continuous extrusion of tubes with tailored diameters of 500 μm to 1500 μm, wall thicknesses of 20 μm to 120 μm, and compositions, as well as predictable mechanical and chemical properties. Using the same platform, single and multi-walled hydrogel tubes with defined heterogeneities and patterns of discrete spots of secondary biopolymer materials can be continuously extruded. A tube-hosting device is presented which can independently perfuse and superfuse isolated tube segments, allowing precise microenvironmental control without cannulation for up to an hour.

We present a platform that allows homogeneous and heterogeneous 3-D soft materials to be continuously defined in a single step. Biopolymer solutions are introduced to a microfluidic device and radially distributed to feed to a common outlet at the device center. This forms concentric sheaths of complex fluids and upon crosslinking, a hydrogel tube at the exit. This approach allows for the controlled and continuous extrusion of tubes with tailored diameters of 500 μm to 1500 μm, wall thicknesses of 20 μm to 120 μm, and compositions, as well as predictable mechanical and chemical properties. Using the same platform, single and multi-walled hydrogel tubes with defined heterogeneities and patterns of discrete spots of secondary biopolymer materials can be continuously extruded. A tube-hosting device is presented which can independently perfuse and superfuse isolated tube segments, allowing precise microenvironmental control without cannulation for up to an hour.

Bio-nanotechnology is the use of biomolecules to control both the structure and property of nanomaterials. No biomolecule has been employed more often than DNA as exemplified in the numerous demonstrations of DNA-directed assembly of nanomaterials. DNA has been used to covalently functionalize and assemble soft nanoparticles (e.g. liposomes) and hard nanoparticles (e.g. gold and silica nanoparticles) into a variety of hierarchical nanostructures. The majority of previous work however has focused on the latter, i.e., the assembly of “hard” nanoparticles such as gold nanoparticles (AuNPs) as oppose to the assembly of soft materials. The primary focus of this thesis is to add to the growing field of DNA-directed assembly of soft materials owing to the promise of such materials in a variety of analytical and biomedical applications. The first class of soft materials considered are liposomes which interestingly can be deformed by relatively weak intermolecular forces. In addition, DNA anchored to its surface can readily diffuse laterally within the lipid bilayer while DNA attached to inorganic nanoparticles remain fixed in position. We systematically consider the effect of varying the liposome structure, size, charge, and fluidity on liposome assemblies, in chapter 2. In addition, the interesting properties of liposomes are highlighted by a side-by-side comparison to DNA-functionalized gold nanoparticles, offering fundamental insights into DNA-directed assembly. Furthermore, hybrid DNA-directed assemblies composed of both AuNPs and liposomes are described in Chapter 3. In particular, the photothermal effects of such DNA-coupled liposome and AuNP assemblies were modulated by controlling the distance between liposome and AuNP allowing such systems to have potential application in drug-delivery. In chapter 4, the utility of liposomes is demonstrated as we exploit the fluidity of its diffuse bilayer with split aptamer functionalization for the rapid and selective detection of metabolites. The second class of soft material of interest in this thesis are hydrogels, which are cross-linked hydrophilic polymers. Because hydrogels are swollen in water, they can be used to immobilize biomolecules such as DNA for a myriad of applications. In chapter 5, the preparation and characterization of DNA-functionalized polyacrylamide hydrogels are presented. The use of such a DNA-modified hydrogel for the simultaneous detection and removal of mercury from water is subsequently demonstrated.

Soft materials are ubiquitous in every aspect of our daily life. These materials composed of a wide range of subfields including surfactants, foams, emulsions, pastes, slurries, polymers, gels, and colloidal suspensions. In recent years, there has been a great interest focusing on the understanding of the macroscopic properties of various types of soft materials as a function of their microstructures. For example, the structure-property relationship of physically-associating triblock copolymer gels can be controlled by selecting different types of solvents and changing the temperature. In these systems, gelation occurs due to the significant changes in the solubility of one or more of the blocks with temperature compared to the other blocks. Therefore, changing the temperature can lead to the structural transitions and macroscopic properties. The other strategy that can be used to modify the macroscopic performance of polymer gels is through the incorporation of nanoparticles, such as graphene nanoplatelets and nanotubes. The addition of nanoparticles can also affect the mechanical properties of concentrated suspensions in which, understanding the structure/flow properties is vital for processing and manufacturing of a product. Despite significant advances in the field of soft materials, our understanding in linking the structure-property relationships of polymer gels and concentrated suspensions is incomplete. With this perspective, in this dissertation, shear-rheometry and scattering techniques were used to understand the structural changes of the self-assembled triblock copolymer gels over a wide length-scale and broad temperature-range. Graphene nanoplatelets have been incorporated into this system to investigate the self-assembly behavior and mechanical properties as a function of graphene concentration. On the other hand, in concentrated suspensions of functionalized nanoparticles in a low-molecular- weight polymeric media, the effect of nanoparticles on the rheological properties were investigated. The present work provides a better understanding of the nanoparticles’contributions on microstructure and mechanical behavior of soft materials.

Coarse-grained (CG) molecular dynamics (MD) simulations have seen a wide range of applications from biomolecules, polymers to graphene and metals. In CG MD simulations, atomistic groups are represented by beads, which reduces the degrees of freedom in the systems and allows larger timesteps. Thus, large time and length scales could be achieved in CG MD simulations with inexpensive computational cost. The representative example of large time- and length-scale phenomena is the conformation transitions of single polymer chains as well as polymer chains in their architectures, self-assembly of biomaterials, etc. Polymers exist in many aspects of our life, for example, plastic packages, automobile parts, and even medical devices. However, the large chemical and structural diversity of polymers poses a challenge to the existing CG MD models due to their limited accuracy and transferabilities. In this regard, this dissertation has developed CG models of polymers on the basis of accurate and transferable hydrocarbon models, which are important components of the polymer backbone. CG hydrocarbon models were created with 2:1 and 3:1 mapping schemes and their force-field (FF) parameters were optimized by using particle swarm optimization (PSO). The newly developed CG hydrocarbon models could reproduce their experimental properties including density, enthalpy of vaporization, surface tension and self-diffusion coefficients very well. The cross interaction parameters between CG hydrocarbon and water models were also optimized by the PSO to repeat the experimental properties of Gibbs free energies and interfacial tensions. With the hydrocarbon models as the backbone, poly(acrylic acid) (PAA) and polystyrene (PS) models were constructed. Their side chains were represented by one COOH (carboxylic acid) and three BZ beads, respectively. Before testing the PAA and PS models, their monomer models, propionic acid and ethylbenzene, were created and validated, to confirm that the cross interactions between hydrocarbon and COOH beads, and between hydrocarbon and BZ beads could be accurately predicted by the Lorentz-Berthelot (LB) combining rules. Then the experimental properties, density of polymers at 300 K and glass transition temperatures, and the conformations of their all-atom models in solvent mixtures of water and dimethylformamide (DMF) were reproduced by the CG models. The CG PAA and PS models were further used to build the bottlebrush copolymers of PAA-PS and to predict the structures of PAA-PA in different compositions of binary solvents water/DMF. Although CG models are useful in understanding the phenomena at large time- or length- scales, atomistic information is lost. Backmapping is usually involved in reconstructing atomistic models from their CG models. Here, four machine learning (ML) algorithms, artificial neural networks (ANN), k-nearest neighbor (kNN), gaussian process regression (GPR), and random forest (RF) were developed to improve the accuracy of the backmapped all-atom structures. These optimized four ML models showed R2 scores of more than 0.99 when testing the backmapping against four representative molecules: furan, benzene, naphthalene, graphene. / Doctor of Philosophy / Polymers have a wide range of applications from packaging, foams, coating to pipes, tanks and even medical devices and biosensors. To improve the properties of these materials it is important to understand their structure and features responsible for controlling their properties at the molecular-level. Molecular dynamic (MD) simulations are a powerful tool to study their structures and properties at microscopic level. However, studying the molecular-level conformations of polymers and their architectures usually requires large time- or length-scales, which is challenging for the all-atom MD simulations because of the high computational cost. Coarse-grained (CG) MD simulations can be used to study these soft-materials as they represent atomistic groups with beads, enabling the reduction of the system sizes drastically, and allowing the use of large timesteps in MD simulations. In MD simulations, force-fields (FF) that describe the intramolecular and intermolecular interactions determine the performance of simulations. Here, we firstly optimized the FF parameters for hydrocarbons. With the optimized CG hydrocarbon models, two representative CG polymer models, poly(acrylic acid) (PAA) and polystyrene (PS) were built by using hydrocarbons as the backbones of polymers. Furthermore, the PAA and PS chains were grafted on a linear hydrocarbon backbone to form a bottlebrush copolymer. Although CG MD models are useful in studying the complex process of polymers, the atomic detailed information is lost. To reconstruct accurate atomistic structures, backmapping by using machine learning (ML) algorithms was performed. The performance of the ML models was better than that of the existing backmapping packages built in Visual Molecular Dynamics (VMD).

Soft materials and compliant structures often undergo significant deformation without failure, a unique feature making them distinct from classical rigid materials. These substantial deformations provide a means for faster or more energy efficient deformations, which can be achieved by taking advantage of elastic instabilities. We intend to utilize structural instabilities to generate advanced functionality within soft materials. In particular, we use the buckling of thin, flexible plates to control or enhance the flow of fluid in a micro channel. The buckling deformation is created or altered via two different stimuli, first a mechanical strain and then an electrical signal. We investigate the behavior of each system under different conditions experimentally, numerically, or theoretically. We also show that the coupled interaction between fluid and the soft film plays a critical role in the shape of deformation and consequently in the functionality of the mechanism. We first embed a buckled thin film in a fluid channel within a soft device. By applying a mechanical strain to the device, we show both experimentally and numerically that the height of the buckled film changes accordingly as does the flow rate. We then offer an analytical solution by extending the classical lubrication theory to higher-order terms as a means to more accurately describe the flow in a channel with a buckled thin film, and in general, the flow in channels with any constrictions provided the Reynolds number is low. Next, we use an electrical signal to make a confined dielectric film undergo out-of-plane buckling deformation. The thin film is sandwiched between two flexible electrodes and the mechanism is implemented in a microfluidic device to pump the fluid into a micro channel. We show that the critical buckling voltage at which the thin film buckles out of the plane is mainly a function of voltage while the shape of deformation and so the functionality of this mechanism depend considerably on the applied boundary conditions. Finally, we enhance the fluid-soft structure response of the actuating mechanism by substituting flexible electrodes with fluid electrodes, resulting in a significant increase in the actuation frequency as well as a reduction in the critical buckling voltage. / Ph. D.

京都大学 / 新制・課程博士 / 博士(工学) / 甲第23926号 / 工博第5013号 / 新制||工||1782(附属図書館) / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 古川 修平, 教授 生越 友樹, 教授 浜地 格 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

The influence of vocal fold (VF) vibration on perfused flow through VF vasculature is an area of research that has previously received limited attention. The aim of the research presented in this thesis was to contribute towards an improved understanding of the effects vibration on perfusion through vasculature within the VFs. This was done using a series of computational simulations of geometric changes to, and perfusion through, microchannels embedded in VF models. A computational structural model based on synthetic VF models used in previous experimental studies was first developed. The model and its embedded microchannel were initially studied under static pressure loads applied to the inner surfaces of the channel as well as to the VF inferior and medial surfaces. It was shown that the channel volume decreased linearly and the channel length increased quadratically with increasing pressure on the external VF surfaces. Changes in Poisson's ratio and its influence on the embedded channel's maximum deflection, volume, and length were also studied. Across the range of Poisson's ratios that has been studied for silicone used in synthetic VF models (0.4 to 0.495) there was shown to be limited change in microchannel maximum deflection, channel length, and volume for equivalent pressure loads. The model was then modified to include an external oscillating pressure load on the VF surface that caused the model to vibrate. Two separate studies were conducted to determine how frequency and deflection amplitude affected the predicted perfusion flow rate through the embedded microchannel by accounting for the changes in microchannel geometry during vibration. These studies showed that frequency had little effect on predicted flow rate, while increased deflection amplitude led to greater reductions in predicted flow rate. These reductions in flow rate were attributed to channel lengthening and cross section deformation during vibration, with the latter playing a much larger role. Reductions in flow rate results were found to favorably agree with measured experimental flow rate reductions reported previously. Computational fluid dynamics simulations of water flowing through the inflated embedded microchannel during vibration were also conducted. These simulations were used to explore how changes in vibration length, amplitude, and frequency affected the fluid dynamics in the microchannel whilst minimizing geometric changes to the microchannel. The flow rates from each of the simulation cases were compared to determine which of the vibration parameters contributed the most to flow losses. Vibration length and amplitude were shown to be statistically significant. An investigation was undertaken to further elucidate the mechanisms behind the flow losses induced by vibration. The effects of channel elongation, increased channel curvature, pressure rises, and pressure gradients during vibration were analyzed. Changes in channel elongation and pressure were shown to significantly contribute to flow losses and flow rate reduction. The results from these simulations were compared with the structural simulations which analyzed how changes in microchannel geometry affected flow rate reductions. Changes in the microchannel geometry were shown to contribute much more significantly to reductions in perfusion flow rate compared to changes in vibration parameters (i.e., vibration length, amplitude, and frequency).

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