Browsing by Subject "Nanotechnology."

Now showing 1 - 5 of 5

Open Access
Bioactive porous peg-peptide composite hydrogels with tunable mechanical properties
(2014) Göktaş, Melis
Mimicking the instructive cues of native extracellular matrix (ECM) is fundamental to understand and control the processes regulating cell function and cell fate. Extensive research on the structure and biological complexity of ECM has shown that three types of critical information from the ECM have influence on cellular behaviour: (1) biophysical properties (elasticity, stiffness), (2) biochemical properties (bioactive peptide epitopes of ECM molecules), and (3) nanoarchitecture (nanofibrillar structure, porosity) of ECM. Recent efforts have therefore focused on the construction of ECM mimetic materials to modulate tissue specific cell functions. Advances in biomaterial platforms include artificial ECM mimics of peptide conjugated synthetic polymer hydrogels presenting bioactive ligands produced with covalent chemistry. These materials have already found application in tissue engineering, however, these biomaterial platforms represent oversimplified mimics of cellular microenvironment and lack the complexity and multifunctional aspects of native ECM. In this work, we developed a novel polyethylene glycol (PEG)-peptide nanofiber composite hydrogel system with independently tunable biochemical, mechanical and physical cues that does not require any chemical modification of polymer backbone to create synthetic ECM analogues. This approach allows noninteracting modification of multifactorial niche properties (i.e. bioactive ligands, stiffness, porosity), since no covalent conjugation method was used to modify PEG monomers for the incorporation of bioactivity and porosity. Combining the self-assembled peptide nanofibers with crosslinked polymer network simply by facile mixing followed by photo-polymerization resulted in the formation of porous hydrogel systems. Resulting porous network can be functionalized with desired bioactive signalling epitopes by simply altering the amino acid sequence of peptide amphiphile molecules. In addition, the mechanical properties of the composite system can be precisely controlled by changing the PEG concentration. Ultimately, multifunctional PEG-peptide composite scaffolds reported in this work, can fill a critical gap in the available biomaterials as versatile synthetic mimics of ECM with independently tunable properties. Such a system could provide a useful tool allowing the investigation of how complex niche cues interplay to influence cellular behaviour and tissue formation both in 2D and 3D platforms.
Open Access
Biophotonic applications of ultrafast fiber lasers: from biomaterial surface modification to sub-cellular nanosurgery
(2014) Erdoğan, Mutlu
Just a year after the invention of the LASER in 1960, it was demonstrated that lasers could be used for the treatment of certain skin abnormalities. At present, lasers are extensively used in a broad range of medical treatments. After the development of femtosecond pulse lasers in the 1980s, even more exciting possibilities in a diverse range of fields have been realized. Accordingly, ultrashort pulse lasers are widely used in biological applications in recent years. In parallel to these, fiber laser systems have increasingly been utilized in a wide range of scientific and biomedical applications, since they are highly compatible systems for being employed for industrial and biomedical applications. Consequently, the aim of this Ph.D. thesis proposal is to develop compact, simpler to operate, and cost-efficient ultrafast fiber lasers with different repetition rates and pulse energies. By using such systems, we demonstrate the biophotonic applications of these lasers on two different biological research fields. As a part of this thesis study, we develop ultrafast fiber lasers and apply them in biomaterial surface modification. We demonstrate that different surfaces with micro- and nano-scale topographies can be generated at high speed, precision and repeatability. The outcomes of biomaterial surface modification with different laser parameters are compared in terms of topographical uniformity and repeatability. Additionally, a variety of topographical modifications are assessed with respect to the efficiency on cell attachment and proliferation on metal implants.As the second part of this thesis, we develop a custom-built ultrafast fiber laser-integrated microscope system for nanosurgery and tissue ablation experiments. Subsequently, we employ this system in order to make high-precision cuts onto different biological specimens ranging from the tissue level to subcellular level, such as a part of an axon or a single organelle. Finally, we improve this integrated system in a way that it becomes capable of generating optical pulses in any desired sequence possible. This is achieved by using acousto-optic modulators (AOM) and custom-developed field-programmable gate arrays (FPGA).
Open Access
Design and development of novel large scale applications in micro/nanophotonics and nanobiotechnology
(2014) Özgür, Erol
Developments in micro/nanophotonics and nanobiotechnology creates new opportunities regarding development of devices with unprecedented capabilities, which could improve human civilization substantially. On the other hand, a certain level of maturity in transforming these possibilities into reality still requires considerable efforts. One of the main problems of these novel technologies is that their practical know-how is so scarce that they could only be utilized within strictly determined laboratory conditions, and by highly sophisticated scientists. This thesis focuses on large scale applications at the intersection of microphotonics and nanobiotechnology, and also in nanophotonics. On microphotonics side, optical microresonators with toroidal shape were successfully fabricated and optically integrated. Having an extremely high sensitivity towards perturbations in their environments, these microcavities could be used as biological sensors; however, they are also very sensitive for nonspecific interactions. Thus, a novel surface chemistry enabling bioconjugation of molecular probes without compromising their sensitivity and enhancing their selectivity was developed, based on methylphosphonate containing silane modification of the microtoroid surface. After this functionalization, microtoroids were used in biodetection in complex media. Also, a macroscopic photodetection device composed on intrinsically aligned semiconducting selenium nanowires were demonstrated. This device could be considered as a novel and efficient demonstration of nanowire integration to the macroscopic world. Together with the research on biosensors, these are important large scale applications of emergent science of our age.
Open Access
Peptide nanofibers for engineering tissues and immune system
(2014) Mammadov, Rashad
Interdisciplinary work at the interface of biology and materials science is important for finding cures to complex diseases. Achievements in materials science allow us to control materials at nanoscale and design them according to specific therapeutic purposes. This includes incorporating biophysical and biochemical signals into materials to make them biologically functional. These signals are sensed by cells in normal or pathological cases and influence their decision-making process, which eventually alters cellular behavior. However, cellular environment is so complex in terms of these signals that recapitulating it with synthetic materials is unattainable considering our limited resources. Therefore, we need to distinguish those signals that are structurally simple, but at the same time biologically critical, that would drive cellular behavior to desired outcome. In this thesis, I will describe peptide nanofiber systems for tissue engineering and vaccinology applications. First system is inspired from heparan sulfate (HS) – a natural polymer in extracellular matrix – that bind to growth factors and regulate their functioning, therefore central for induction of various physiological processes. Peptide nanofibers with right composition of bioactive chemical functional groups from HS showed specific interaction with growth factors and induced endothelial cells to form blood vessels similar to natural matrices carrying HS. Considering mentioned features, these peptide nanofibers could be useful for effective regeneration of tissues. Secondly, the peptide nanofiber system carrying pathogenic DNA motives, which is an infection signal, was developed. While non-immunogenic by itself, these nanofibers shifted immune response against pathogenic DNA towards a context that is useful for fighting intracellular pathogens and cancer. Overall, this thesis demonstrates that structurally simple but appropriate biophysical and biochemical signals could be synergistic for inducing desired biological processes at the nanoscale.
Open Access
Three dimensional nanoplasmonic surfaces : modeling, fabrication and characterization
(2013) Güngör, Kıvanç
Today designing functional nanoplasmonic structures specific to a variety of applications attracts great interest from various fields ranging from optoelectronics to life sciences. There are numerous ways of making nanoplasmonic structures. Among them, nanopatterning of a thin-film metal layer is one of the most common approaches, which allows for finely controlled fabrication of a plasmonic unit and their repeating layout in the plane of the starting metal film. Although there are many examples of such nanopatterned plasmonic structures reported to date, they are typically designed and implemented on a planar surface. In these architectures, plasmonic layout commonly covers significantly less than 100% of the substrate surface and can provide field localization most strongly around the sharp corners and small gaps between the patterns. In the case of using a periodic layout, which is commonly employed for experimental realization (although periodicity is not necessary), the plasmonic array inherently yields a duty cycle substantially less than unity (usually close to 0.5). As a result, the surface coverage of nanopatterned plasmonic structures on a planar surface has intrinsically been limited and the field enhancement across their nanoplasmonic layout has been possible mostly in the plane and slightly above it. To address these limitations, this thesis proposed and demonstrated three-dimensional (3D) nanoplasmonic arrayed structures designed and implemented on a non-planar surface that allows for strong field enhancement in the out-of-plane direction and enables a very large surface coverage of the substrate close to unity. The thesis work included both numerical modeling and experimental characterizations. As a proof-of-concept demonstration, we fabricated non-planar arrays of checkerboard nanostructures, each with two-fold rotational symmetry, laid out in a volumetric fashion as two interlocked square lattice arrays at two different levels, facilitating strong field localization vertically between these two complementary planes. The resulting nanofabricated samples exhibited a maximum surface coverage of 100% in plan view. With full electromagnetic solution of such 3D nanoplasmonic surfaces, we showed that the out-of-plane field localization is 7.2-fold stronger than the inplane localization, in comparison to their two-dimensional (2D) components alone. These numerical results agree well with the experimental observations including far-field optical transmission and reflection measurements. The absorption spectroscopy further revealed that the resulting spectrum of the 3D checkerboard features a unique signature arising from the out-of-plane localization, which does not exist in the case of the 2D counterparts. These results indicate that 3D nanoplasmonics of such non-planar surfaces provides us with the ability to generate and better utilize the plasmonic volume, possibly useful for increased plasmonic coupling and interactions.