Melik C. Demirel

Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model

Fluctuations about the native conformation of proteins have proven to be suitably reproduced with a simple elastic network model, which has shown excellent agreement with a number of different properties for a wide variety of proteins. This scalar model simply investigates the magnitudes of motion of individual residues in the structure. To use the elastic model approach further for developing the details of protein mechanisms, it becomes essential to expand this model to include the added details of the directions of individual residue fluctuations. In this paper a new tool is presented for this purpose and applied to the retinol-binding protein, which indicates enhanced flexibility in the region of entry to the ligand binding site and for the portion of the protein binding to its carrier protein.

An engineered anisotropic nanofilm with unidirectional wetting properties

Anisotropic textured surfaces allow water striders to walk on water, butterflies to shed water from their wings and plants to trap insects and pollen. Capturing these natural features in biomimetic surfaces is an active area of research. Here, we report an engineered nanofilm, composed of an array of poly(p-xylylene) nanorods, which demonstrates anisotropic wetting behaviour by means of a pin-release droplet ratchet mechanism. Droplet retention forces in the pin and release directions differ by up to 80 μN, which is over ten times greater than the values reported for other engineered anisotropic surfaces. The nanofilm provides a microscale smooth surface on which to transport microlitre droplets, and is also relatively easy to synthesize by a bottom-up vapour-phase technique. An accompanying comprehensive model successfully describes the films anisotropic wetting behaviour as a function of measurable film morphology parameters.

Nanoparticle-based protein detection by optical shift of a resonant microcavity

We demonstrated a biosensing approach which, for the first time, combines the high sensitivity of whispering gallery modes (WGMs) with a metallic nanoparticle-based assay. We provided a computational model based on generalized Mie theory to explain the higher sensitivity of protein detection. We quantitatively analyzed the binding of a model protein (i.e., Bovine Serum Albumin) to gold nanoparticles from high-Q WGM resonance frequency shifts, and fit the results to an adsorption isotherm, which agrees with the theoretical predictions of a two-component adsorption model. V C 2011 American Institute of Physics. [doi:10.1063/1.3599706]

Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science

Efforts to engineer new materials inspired by biological structures are hampered by the lack of genomic data from many model organisms studied in biomimetic research. Here we show that biomimetic engineering can be accelerated by integrating high-throughput RNA-seq with proteomics and advanced materials characterization. This approach can be applied to a broad range of systems, as we illustrate by investigating diverse high-performance biological materials involved in embryo protection, adhesion and predation. In one example, we rapidly engineer recombinant squid sucker ring teeth proteins into a range of structural and functional materials, including nanopatterned surfaces and photo-cross-linked films that exceed the mechanical properties of most natural and synthetic polymers. Integrating RNA-seq with proteomics and materials science facilitates the molecular characterization of natural materials and the effective translation of their molecular designs into a wide range of bio-inspired materials.

Emerging Technologies for Assembly of Microscale Hydrogels

Assembly of cell encapsulating building blocks (i.e., microscale hydrogels) has significant applications in areas including regenerative medicine, tissue engineering, and cell-based in vitro assays for pharmaceutical research and drug discovery. Inspired by the repeating functional units observed in native tissues and biological systems (e.g., the lobule in liver, the nephron in kidney), assembly technologies aim to generate complex tissue structures by organizing microscale building blocks. Novel assembly technologies enable fabrication of engineered tissue constructs with controlled properties including tunable microarchitectural and predefined compositional features. Recent advances in micro- and nano-scale technologies have enabled engineering of microgel based three dimensional (3D) constructs. There is a need for high-throughput and scalable methods to assemble microscale units with a complex 3D micro-architecture. Emerging assembly methods include novel technologies based on microfluidics, acoustic and magnetic fields, nanotextured surfaces, and surface tension. In this review, we survey emerging microscale hydrogel assembly methods offering rapid, scalable microgel assembly in 3D, and provide future perspectives and discuss potential applications.

Responsive Microgrooves for the Formation of Harvestable Tissue Constructs

Given its biocompatibility, elasticity, and gas permeability, poly(dimethylsiloxane) (PDMS) is widely used to fabricate microgrooves and microfluidic devices for three-dimensional (3D) cell culture studies. However, conformal coating of complex PDMS devices prepared by standard microfabrication techniques with desired chemical functionality is challenging. This study describes the conformal coating of PDMS microgrooves with poly(N-isopropylacrylamide) (PNIPAAm) by using initiated chemical vapor deposition (iCVD). These microgrooves guided the formation of tissue constructs from NIH-3T3 fibroblasts that could be retrieved by the temperature-dependent swelling property and hydrophilicity change of the PNIPAAm. The thickness of swollen PNIPAAm films at 24 °C was approximately 3 times greater than at 37 °C. Furthermore, PNIPAAm-coated microgroove surfaces exhibit increased hydrophilicity at 24 °C (contact angle θ = 30° ± 2) compared to 37 °C (θ = 50° ± 1). Thus PNIPAAm film on the microgrooves exhibits responsive swelling with higher hydrophilicity at room temperature, which could be used to retrieve tissue constructs. The resulting tissue constructs were the same size as the grooves and could be used as modules in tissue fabrication. Given its ability to form and retrieve cell aggregates and its integration with standard microfabrication, PNIPAAm-coated PDMS templates may become useful for 3D cell culture applications in tissue engineering and drug discovery.

Transport of a soft cargo on a nanoscale ratchet

Surface ratchets can guide droplet transport for microfluidic systems. Here, we demonstrated the actuation of microgels encapsulated in droplets using a unidirectional nanotextured surface, which moves droplets with low vibration amplitudes by a ratcheting mechanism. The nanofilm carries droplets along the ratchets with minimal drop shape deformation to move the encapsulated soft cargo, i.e., microscale hydrogels. The tilted nanorods of the nanofilm produce unidirectional wetting, thereby enabling droplet motion in a single direction. Maximum droplet translation speed on the nanofilm was determined to be 3.5 mm∕s, which offers a pathway towards high throughput microgel assembly applications to build complex constructs.

Highly swellable free-standing hydrogel nanotube forests

Well-ordered arrays of high aspect ratio nanotubes display structural anisotropy, high surface area, and functionalizable surface morphology. We demonstrated, for the first time, the vapor deposition synthesis of well-ordered arrays of hydrogel nanotubes (i.e. nanotube forest structures) with controllable swelling properties using anodic aluminium oxide (AAO) membranes. Initiated chemical vapor deposition (iCVD) enabled templating of hydrogel nanotubes from 2-hydroxyethyl methacrylate (HEMA) monomers with systematically tuned crosslinking ratios. Water uptake and the swelling ratios of the nanotubes monotonically decreased with the crosslink density. For a given crosslinked hydrogel composition, the degree of swelling for the nanotubes was observed to be significantly higher than for the planar films. Furthermore, protein adsorption is systematically moderated through the crosslinking density on nanotube samples, making them potential templates for biomaterials.

Bio-organism sensing via surface enhanced Raman spectroscopy on controlled metal/polymer nanostructured substrates

A new class of nonlithographically prepared surface enhanced Raman spectroscopy (SERS) substrates based on metalized, nanostructured poly(p-xylylene) films has been developed and optimized for surface plasmon response with a view to applications of SERS detection of microbial pathogens, specifically, bacteria and viruses. The main emphasis has been on achieving high spot to spot, sample to sample reproducibility of the SERS signals while maintaining useful enhancement factors. The use of these surfaces, metalized with either Ag or Au, provides a noninvasive and nondestructive method for spectral fingerprint analyses of both bacteria and viruses. Examples are given for the detection of bacteria (E. coli and B. cereus) and viruses (respiratory syncytial virus and Coxsackievirus). Our method is able to distinguish Gram positive from Gram negative bacterial strains as well as enveloped and nonenveloped viruses. The results demonstrate the development of a new class of SERS substrates which can provide rapid, selective identification of infectious agents without amplification of cultures.

Quantitative analysis of creatinine in urine by metalized nanostructured parylene.

A highly accurate, real-time multisensor agent monitor for biomarker detection is required for early detection of kidney diseases. Urine creatinine level can provide useful information on the status of the kidney. We prepare nanostructured surface-enhanced Raman spectroscopy (SERS) substrates without template or lithography, which provides controllable, well-organized nanostructures on the surface, for the quantitative analysis of creatinine concentration in urine. We present our work on sensitivity of the SERS substrate to urine samples collected from diabetic patients and healthy persons. We report the preparation of a new type of SERS substrate, which provides fast (<10 s), highly sensitive (creatinine concentration <0.5 microg/mL) and reproducible (<5% variation) detection of urine. Our method to analyze the creatinine level in urine is in good agreement with the enzymatic method.