Kirsi Tappura

A new soft-core potential function for molecular dynamics applied to the prediction of protein loop conformations

We have developed a new soft‐core potential function for the conformational search of complex systems with molecular dynamics. The potential function was designed to maintain the main equilibrium properties of the original force field, which means that the soft‐core potential gives physically realistic performance also without additional restraints, different from most of the previous soft‐core potential functions. The performance of the method was demonstrated by applying it to the problem of finding native conformations for protein loops. Short loops from neocarzinostatin and parvalbumin were used as the first test cases. The use of the new soft‐core potential function was shown to improve significantly the performance of molecular dynamics in the search of the native conformation of protein loops.

Structural and functional characteristics of chimeric avidins physically adsorbed onto functionalized polythiophene thin films.

Stabilized bioreceptor layers are of great importance in the design of novel biosensors. In earlier work, chimeric avidins enabled immobilization of biotinylated antibodies onto gold surfaces with greater stability compared to more conventional avidins (wild-type avidin and streptavidin). In the present study, the applicability of chimeric avidins as a general binding scaffold for biotinylated antibodies on spin-coated functionalized polythiophene thin films has been studied by surface plasmon resonance and atomic force microscopy. Novel chimeric avidins showed remarkably increased binding characteristics compared with other avidins, such as wild-type avidin, streptavidin, and bacterial avidin when merely physically adsorbed onto the polythiophene surface. They gave the highest binding capacities, the highest affinity constant, and the highest stability for biotinylated probe immobilization. Introduction of carboxylic acid groups to polythiophene layer further enhanced the binding level of the avidins. Polythiophene layers functionalized with chimeric avidins thus offered a promising generic platform for biosensor applications.

High-Q micromechanical resonators for mass sensing in dissipative media

Single crystal silicon-based micromechanical resonators are developed for mass sensing in dissipative media. The design aspects and preliminary characterization of the resonators are presented. For the suggested designs, quality factors of about 20 000 are typically measured in air at atmospheric pressure and 1000–2000 in contact with liquid. The performance is based on a wine-glass-type lateral bulk acoustic mode excited in a rectangular resonator plate. The mode essentially eliminates the radiation of acoustic energy into the sample media leaving viscous drag as the dominant fluid-based dissipation mechanism in the system. For a mass loading distributed over the central areas of the resonator a sensitivity of 27 ppm ng−1 is measured exhibiting good agreement with the results of the finite element method-based simulations. It is also shown that the mass sensitivity can be somewhat enhanced, not only by the proper distribution of the loaded mass, but also by introducing shallow barrier structures on the resonator.

Optical and Electrical Characterization of a Large Kinetic Inductance Bolometer Focal Plane Array

Sub-THz imaging techniques are currently emerging with applications especially in security screening requiring higher throughput in mass transit and public areas. In the context of person imagers, the field of view and the spatial resolution set the requirement for the number of image pixels. We perform an experimental feasibility study on a fully staring radiometric camera with one detector per image pixel. The aim is to avoid the shortcomings characteristic of optomechanical scanners with a limited number of detectors. Our approach is based on superconducting kinetic inductance bolometer arrays. We demonstrate successful fabrication and operation of a focal plane array with 2500 nanomembrane-integrated bolometers, and a compatible optical system enabling standoff imaging at the distance of 5 m. We characterize the system in terms of radiometric contrast and spatial resolution.

Influence of Substrate on Plasmon-Induced Absorption Enhancements

A set of periodic plasmonic nanostructures is designed and fabricated as a means to investigate light absorption in single-crystal silicon thin-film structures with silicon-on-insulator (SOI) wafers as a model system. It is shown both computationally and experimentally that plasmon-induced absorption enhancement is remarkably higher for such devices than for thick or semi-infinite structures or for the thin-film amorphous silicon solar cells reported in the literature. Experimental photocurrent enhancements of the orders of 12 and 20 are demonstrated for non-optimized 2200-nm-thick photoconductive and 300-nm-thick photovoltaic test structures, respectively. Theoretical absorption enhancements as high as 80 are predicted to be achievable for the similar structures. The features of the spectral enhancements observed are attributed to several interacting resonance phenomena: not just to the favourable scattering of light by the periodic plasmonic nanoparticle arrays into the SOI device layer and coupling to the waveguide modes interacting with the plasmonic array but also to the Fabry-Pérot type interferences in the layered structure. We show that the latter effect gives a significant contribution to the spectral features of the enhancements, although frequently ignored in the discussions of previous reports.

Vapor-phase self-assembled monolayers for improved MEMS reliability

This paper presents the application of vapor-phase DDMS (dichlorodimethylsilane) self-assembled monolayer (SAM) coating which significantly reduced stiction behavior in optical MEMS components exposed to humidity. Previously SAMs have been deposited in liquid form, making them unsuitable for application in high aspect ratio MEMS/NEMS structures; now vapor-phase SAM deposition is a novel option for improving MEMS in-use reliability. DDMS and ODS (n-octadecyltrimethoxysilane) SAM coatings were tested on surfaces with different pre-treatments and the quality of coatings was assessed through static water contact angle measurements and humidity exposure tests for both test membrane structures (100% stiction on uncoated structures vs. 17% stiction of DDMS SAM coated structures) and optical MEMS FPI components (0% stiction of DDMS SAM coated components). The obtained contact angle of the DDMS SAM coating was ∼ 104°. Both long term stability and thermal stability of the DDMS SAM coatings were found to be good.

A numerical study on the design trade-offs of a thin-film thermoelectric generator for large-area applications

Thin-film thermoelectric generators with a novel folding scheme are proposed for large-area, low energy density applications. Both the electrical current and heat transfer are in the plane of the thermoelectric thin-film, yet the heat transfer is across the plane of the thermoelectric module - similar to a conventional bulk thermoelectric module. With such a design, the heat leakage through the module itself can be minimized and the available temperature gradient maximized. Different from the previously reported corrugated thermoelectric generators, the proposed folding scheme enables high packing densities without compromising the thermal contact area to the heat source and sink. The very thin thermoelectric films (400 nm) and modest temperature gradients applied are shown to set some unconventional prerequisite for the design: the performance cannot be optimized by concentrating on maximizing the output power. Instead, specific attention has to be paid to the current production properties to enable practical applications. Various design aspects and their influence on the thermal transport mechanisms under heat sink limited conditions are analyzed and their (complex) impact on the performance highlighted. Further, it is shown that ZT describing the material properties is not always a good measure for predicting the power production of such thin-film devices.

van der Waals interactions are critical in Car–Parrinello molecular dynamics simulations of porphyrin–fullerene dyads

The interplay between electrostatic and van der Waals (vdW) interactions in porphyrin‐C60 dyads is still under debate despite its importance in influencing the structural characteristics of such complexes considered for various applications in molecular photovoltaics. In this article, we sample the conformational space of a porphyrin‐C60 dyad using Car–Parrinello molecular dynamics simulations with and without empirical vdW corrections. Long‐range vdW interactions, which are poorly described by the commonly used density functional theory functionals, prove to be essential for a proper dynamics of the dyad moieties. Inclusion of vdW corrections brings porphyrin and C60 close together in an orientation that is in agreement with experimental observations. The structural differences arising from the vdW corrections are shown to be significant for several properties and potentially less important for others. Additionally, our Mulliken population analysis reveals that contrary to the common belief, porphyrin is not the primary electron donating moiety for C60. In the considered dyad, fullerenes affinity for electrons is primarily satisfied by charge transfer from the amide group of the linker. However, we show that in the absence of another suitable bound donor, C60 can withdraw electrons from porphyrin if it is sufficiently close.

Fluorescence-based fast diagnostics platform for the direct and indirect immunodiagnostic analysis methods

VTT Technical Research Centre of Finland has developed two reader prototypes for immunodiagnostic tests. VTT has also developed a one-step, homogeneous noncompetitive immunoassay for small analytes using recombinant antibodies and morphine as the model analyte. VTT developed reader for lateral flow test. Lateral flow test is a strip, which has a sample area and a detection area. In the sample area there are antibodies attached to gold or fluorescence particles, which are captured into the detection area, if a sample has a desired analyte. The concentration of the measured sample is then calculated from the fluorescence detection or color change. The second developed prototype reader is based on Time Resolved Fluorescence Resonance Energy Transfer (TR-FRET). In this reader samples are put on microwell array. There are two fluorophores in each of the wells and emission of both fluorophores is measured. The sample concentration is calculated from these emission signals. The optimization of homogenous FRET assays for morphine was included to this project. The first results obtained with the TR-FRET reader prototype show that the sensitivity of the current morphine test is clearly adequate.

Self-Assembly of Pyridine-Modified Lipoic Acid Derivatives on Gold and Their Interaction with Thyroxine (T4)

Pyridyl derivatives of lipoic acid were prepared as ligands for the study of the interaction with thyroxine (T4). Thin self-assembled films of the ligands were prepared in 70% ethanol on gold and their interaction with T4 was studied by titration experiments in an aqueous buffer solution using Surface Plasmon Resonance (SPR). The thickness and refractive index of the ligand layers were calculated from SPR spectra recorded in two media, also allowing for surface coverage and the density of the layers to be estimated. Two ligands, a 4-pyridyl and a bis(2-hydroxyethyl) derivative of lipoic acid, were selected to investigate the feasibility for producing molecularly imprinted self-assembled layers on gold for T4. The methodology was to co-assemble T4 and the ligand onto the gold surface, elute the T4 from the layer under alkaline conditions, and study the rebinding of T4 to the layer. Multiple elution/rebinding cycles were conducted in different buffer solutions, and rebinding of T4 could be observed, with a moderate binding affinity that depended greatly on the solvent used. More optimal binding was observed in HBS buffer, and the affinity of the interaction could be slightly increased when the 4-pyridyl and bis(2-hydroxy-ethyl) derivatives of lipoic acid were combined in the imprinted layer.