Browsing by Subject "self-assembly"
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Item A Computational Study of the Role of Hydration in the Assembly of Collagen and Other Bio laments(2012-10-19) Mayuram Ravikumar, KrishnakumarHydration is known to be crucial in biomolecular interactions including ligand binding and self-assembly. In our earlier studies we have shown the key role of water in stabilizing the specific parts of the collagen triple helix depending on the imino acid content. We further showed that the primary hydration shell around collagen could act as a lubricating layer aiding in collagen assembly. But key details on the structure and dynamics of water near protein surfaces and its role in protein-protein interactions remain unclear. In the current study we have developed a novel method to analyze hydration maps around peptides at 1-A resolution around three self-assembling lament systems with known structures, that respectively have hydrated (collagen), dry non-polar and dry polar (amyloid) interfaces. Using computer simulations, we calculate local hydration maps and hydration forces. We find that the primary hydration shells are formed all over the surface, regardless of the types of the underlying amino acids. The weakly oscillating hydration force arises from coalescence and depletion of hydration shells as two laments approach, whereas local water diffusion, orientation, or hydrogen bonding events have no direct effect. Hydration forces between hydrated, polar, and non-polar interfaces differ in the amplitude and phase of the oscillation relative to the equilibrium surface separation. Therefore, water-mediated interactions between these protein surfaces ranging in character from ?hydrophobic? to ?hydrophilic,? have a common molecular origin based on the robustly formed hydration shells, which is likely applicable to a broad range of biomolecular assemblies whose interfacial geometry is similar in length scale to those of the present study. In a related study through simulations we show that the rate of tissue optical clearing by chemical agents correlated with the preferential formation of hydrogen bond bridges between agent and collagen. Hydrogen bond bridge formation disrupts the collagen hydration layer and facilitates replacement by a chemical agent to destabilize the tertiary structure of collagens thereby reducing light scattering. This study suggests that the clearing ability of an alcohol not only depends on its molecular size, but also on the position of hydroxyl groups on its backbone.Item Development of Advanced Nanomanufacturing: 3D Integration and High Speed Directed Self-assembly(2011-10-21) Li, HuifengDevelopment of nanoscience and nanotechnology requires rapid and robust nanomanufacturing processes to produce nanoscale materials, structures and devices. The dissertation aims to contribute to two major challenging and attractive topics in nanomanufacturing. Firstly, this research develops fabrication techniques for three dimensional (3D) structures and integrates them into functional devices and systems. Secondly, a novel process is proposed and studied for rapid and efficient manipulation of nanomaterials using a directed self-assembly process. The study begins with the development of nanoimprint lithography for nanopatterning and fabrication of 3D multilayer polymeric structures in the micro- and nano-scale, by optimizing the layer-transfer and transfer-bonding techniques. These techniques allow the integration of microfluidic and photonic systems in a single chip for achieving ultracompact lab-on-a-chip concept. To exemplify the integration capability, a monolithic fluorescence detection system is proposed and the approaches to design and fabricate the components, such as a tunable optical filter and optical antennas are addressed. The nanoimprint lithography can also be employed to prepare nanopatterned polymer structures as a template to guide the self-assembly process of nanomaterials, such as single-walled carbon nanotubes (SWNTs). By introducing the surface functionalization, electric field and ultrasonic agitation into the process, we develop a rapid and robust approach for effective placement and alignment of SWNTs. These nanomanufacturing processes are successfully developed and will provide a pathway to the full realization of the lab-on-a-chip concept and significantly contribute to the applications of nanomaterials.Item Microtubule Patterning and Manipulation Using Electrophoresis and Self-Assembled Monolayers(2010-07-14) Noel, JohnWe developed new methods for controlling and studying microtubules (MTs) outside the complex workings of the living cell. Several surface treatments for preventing MT fouling on surfaces were analyzed and, for the first time, a self-assembled monolayer (SAM) was developed which prevented MT adsorption in the absence of passivating proteins. The morphology and thickness of the SAM was measured to determine the mechanism of formation and origin of the MT-resistant behavior. The SAM was integrated into electron beam lithography for patterning and manipulating MTs using electrophoresis. Reversible MT adsorption and patterning and alignment of single MTs were achieved. We characterized the mechanism for the MT migration under electric field with a focus on the electrodynamics of the flow cell and the forces acting on the MT, along with the time dependence of the process.Item Process Improvements for Gas Barrier Thin Films Deposited Via Layer-By-Layer Assembly(2015-05-04) Hagen, David AustinThin layers of aluminum have provided good oxygen barrier for food packaging for many years, but aluminum coatings can easily crack, are completely opaque, and are not environmentally friendly. One gas barrier solution for food, to flexible electronics, and pressurized bladders is to create polymer nanocomposite thin-films using layer-by-layer (LbL) assembly. These non-metal, water-based thin films contain a tortuous path through which a gas molecule must navigate. The work in this dissertation focuses on improving the process of creating these thin films to optimize their performance and achieve lower transmission rates with fewer layers. Excellent gas barrier was achieved in a layer-by-layer thin film with fewer layers by optimizing deposition time of cationic polyethylenimine (PEI) and anionic poly(acrylic acid) [PAA]. Substantial deposition occurs with short deposition times for the first four PEI/PAA bilayers, while thicker deposition occurs with longer deposition times beyond 4 bilayers. Eight bilayers (650 nm) were required to achieve an undetectable oxygen transmission rate (<0.005 cm^3/(m^2?day)) using 1 min deposition steps, but this barrier was obtained with only 6 BL (552 nm) using 1s deposition of the first four bilayers, reducing total deposition time by 73%. Polymer?clay bilayer films show good oxygen barrier properties due to a nanobrick wall structure consisting of clay nanoplatelets within polymeric mortar. Super oxygen barrier trilayer thin films have been deposited using two successive anionic layers of montmorillonite (MMT) clay and polymer (PAA) following every cationic polymer (PEI) layer during layer-by-layer assembly. It is shown here that adding an anionic polymer layer reduces free volume of the film by filling in gaps of the similarly charged clay layer, which increases the barrier performance by at least one order of magnitude. Barrier improvement can also be achieved by reducing the pH of the clay suspension in the PEI/MMT system. The charge of the deposited PEI layer increases in the clay suspension environment as the pH decreases, attracting more clay. This enables a 5? improvement in the gas barrier for a 10 PEI/MMT bilayer thin film (85 nm) made with pH 4 MMT, relative to the same film made with pH 10 MMT (57 nm).Item Region-specific role of water in collagen unwinding and assembly(Texas A&M University, 2008-10-10) Mayuram Ravikumar, KrishnakumarConformational stability of the collagen triple helix affects its turnover and determines tissue homeostasis. Although it is known that the presence of imino acids (prolines or hydroxyprolines) confer stability to the molecule, little is known regarding the stability of the imino-poor region lacking imino acids, which plays a key role in collagen cleavage. In particular, there have been continuing debates about the role of water in collagen stability. We addressed these issues using molecular dynamics simulations on 30-residue long collagen triple helices, including a structure that has a biologically relevant 9-residue imino-poor region from type III collagen (Protein Data Bank ID: 1BKV). We characterized the conformational motion of the molecule that differs between imino-rich and imino-poor regions using a torsional map approach. At temperatures of 300 K and above, unwinding initiates at a common cleavage site, the glycine-isoleucine bond in the imino-poor region. This provides a linkage between previous observations that unwinding of the imino-poor region is a requirement for collagenase cleavage, and that isolated collagen molecules are unstable at body temperature. Unwinding of the imino-poor region is controlled by dynamic water bridges between backbone atoms with average lifetimes on the order of a few picoseconds, as the degree of unwinding strongly correlated with the loss of water bridges, and unwinding could be either prevented or enhanced, respectively by enforcing or forbidding water bridge formation. While individual water bridges were short-lived in the imino-poor region, the hydration shell surrounding the entire molecule was stable even at 330 K. The diameter of the hydrated collagen including the first hydration shell was about 14 ?, in good agreement with the experimentally measured inter-collagen distances. These results elucidate the general role of water in collagen turnover: water not only affects collagen cleavage by controlling its torsional motion, but it also forms a larger-scale lubrication layer mediating collagen self-assembly.Item Studies of block copolypeptide synthesis, self-assembly, and structure-directing ability(Texas A&M University, 2007-04-25) Jan, Jeng-ShiungThe use of organic compounds as templates to assemble inorganic materials with structures over multiple length scales has received much attention due to the potential applications that can be developed from these materials. Many organisms synthesize organic/inorganic composites with exceptional control over morphology, physical properties, and nanoscale organization of these materials. Materials such as bone, nacre, and silica diatoms are excellent examples of the complex yet highly controllable hierarchically structured materials nature can form at ambient conditions. The ability to mimic these organisms through the design of supramolecular assemblies and use them to direct the growth of hierarchically structured materials has increased significantly in recent years. In this dissertation, block copolypeptide templated inorganic materials were synthesized and characterized using a wide range of analytical techniques. There are three major conclusions from this dissertation. First, the conformation of a polypeptide chain can be used to manipulate the porosity of oxide materials obtained. Second, individual supramolecular objects (vesicles) formed by block copolypeptides can be used as templates to form nanostructured hard materials. Third, polypeptide chemistry and solution conditions can be used to control both the morphology and porosity of the hard materials they assemble. This dissertation also describes preliminary work toward designing the block copolypeptides derivatives for biomimetic inorganic synthesis and gene delivery. This work includes the synthesis of these block copolypeptides derivatives and of the templated oxide materials. Some interesting silica materials such as porous silicas and silica nanocapsules were synthesized using double hydrophilic block copolypeptides derivatives as templates. Also, the preliminary work of using these block copolypeptides derivatives for gene delivery is included and shows these copolypeptide derivatives are potential delivery vehicles.