Melik C. Demirel

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A single-parameter harmonic Hamiltonian based on local packing density and contact topology is proposed for studying residue fluctuations in native proteins. The internal energy obeys an equipartition law, and free energy changes result from entropy fluctuations only. Frequency–wave-number maps show communication between residues involved in slow and fast(More)
We performed a 40 ns simulation of 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI-C18(3)) in a 1,2-dipalmitoyl-sn-glycero-3-phosphatidyl choline (DPPC) bilayer in order to facilitate interpretation of lipid dynamics and membrane structure from fluorescence lifetime, anisotropy, and fluorescence correlations spectroscopy (FCS).(More)
Microcavity and whispering gallery mode (WGM) biosensors derive their sensitivity from monitoring frequency shifts induced by protein binding at sites of highly confined field intensities, where field strengths can be further amplified by excitation of plasmon resonances in nanoparticle layers. Here, we propose a mechanism based on optical trapping of a(More)
Many globular and structural proteins have repetitions in their sequences or structures. However, a clear relationship between these repeats and their contribution to the mechanical properties remains elusive. We propose a new approach for the design and production of synthetic polypeptides that comprise one or more tandem copies of a single unit with(More)
Thin films of poly(chloro-p-xylylene) (PPXC) grown by the pyrolysis and evaporation of chloro-[2.2]paracyclophane in an evacuated chamber contain free-standing, slanted, parallel columns that are 50 mum long and are assemblies of 50- to 100-nm-diameter nanowires, which thus can have an unprecedented aspect ratio as high as 1000:1. The nanostructured thin(More)
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(More)
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.(More)
Nanoengineered parylene-C sculptured thin films (STFs) are deposited on glass and silicon substrates using a direct one-step growth technique. The deposited STFs support fibroblast cell attachment and proliferation in vitro, which is an early indication of biocompatibility and bioactivity of this emerging class of biomaterials. Surface modification of(More)
A set of protein conformations are analyzed by normal mode analysis. An elastic network model is used to obtain fluctuation and cooperativity of residues with low amplitude fluctuations across different species. Slow modes that are associated with the function of proteins have common features among different protein structures. We show that the degree of(More)
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(More)