UCPH NanoScience - a student research journal

Chemical Fabrication and Characterization of Graphene for Water-Based Inks used in Screen-Printing

Mathias Kirkholt Laursen — 2019-01-04

Graphene exhibits a range of interesting properties such as high optical transmittance, good thermal conductivity, high
Young’s modulus, and good electrical conductivity. Graphene can serve as a component in conductive applications and
potentially replace the expensive conductive materials, such as indium tin oxide (ITO), that are used today. In this article
the graphene derivatives graphene oxide (GO) and reduced graphene oxide (rGO) are synthesized. The reduction of GO
is done by either microwave assisted reduction, intense light reduction or chemical reduction with hydrogen iodide. The
structures of the synthesized compounds are characterized and analyzed using X-ray photoelectron spectroscopy (XPS)
and Raman spectroscopy. Based on the synthesized GO, a GO-ink is formulated and screen-printed on a polymer-based
polyethylene terephthalate (PET) substrate, from which a sheet resistance of 0.4 kΩ s−q1 is measured. This work
suggests that the synthesized GO can be used in production of conductive circuits or serve as a precursor for future
scalable conductive films.

Characterization of the formation of magic-sized {Bi38O45} clusters by PDF and SAXS

Andy Anker — 2019-01-04

Bismuth oxido clusters exist in a range of sizes, all built up by octahedral {Bi6O8} units. While the atomic structure of various clusters has been solved by single crystal diffraction, it is much more challenging to study clusters directly in solution. Here, we use in situ X-ray total scattering with Pair Distribution Function (PDF) analysis to study the formation of the {Bi38O45}a cluster from [Bi6O5(OH)3(NO3)5]·(H2O)3 crystals dissolved in DMSO. The implementation of PDF analysis provides a unique insight into the structural rearrangements on the atomic scale. By combining with Small Angle X-ray Scattering (SAXS) we can furthermore investigate the size, morphology and size 10 dispersion of the clusters taking place in the process. Consequently, the combination of these two complementary techniques provides a mean of bridging the local atomic and macroscopic characteristics of the material.
In the presented study, the results obtained show that the reaction goes through several stable intermediates before the magic-sized product {Bi38O45} is reached. Through an associated temperature study, the intermediate was furthermore found to be capable of stabilization of up to days by varying the resulting reaction rate. The present studies show how powerful a tool the Debye Equation is in combination with 15 SAXS and PDF, which in this field is a new development that has a large potential for unravelling important questions in nanochemistry in solution.

Fabrication and measurement of hybrid quantum dot devices featuring Yu-Shiba-Rusinov sub-gap states

Jacob Ovesen — 2019-01-04

The aim of this bachelor project is to fabricate and study hybrid quantum dot (QD) devices featuring Yu-Shiba-Rusinov (YSR) sub-gap
states, made on special InAs nanowires with 7 nm epitaxial aluminum coating on 3 facets. The advantage with these nanowires is the
epitaxial aluminum, which can be etched away in a small window of semiconducting nanowire for creating QDs. These dots can be used for
measuring the sub-gap states in superconducting materials due to the high degree of tunability. A device with a single QD featuring
YSR sub-gap states was fabricated and analyzed, and a double QD system was afterwards made from the device using superconducting
leads in the normal state, but not yet featuring YSR sub-gap states. The device does show the possibility for making an superconductordouble
dot-superconductor device featuring YSR sub-gap states.

Structural dynamics of Cpf1 by FRET

Freja Jacobsen Bohr — 2019-01-04

The RNA-guided endonuclease of class V Cpf1 (Clustered Regularly Interspaced Short Palindromic Repeats from
Prevotella and Francisella) is a central element in prokaryotic immune mechanism, which use a CRISPR-RNA (crRNA) to
locate and cleave viral DNA. Cpf1 allow genome-editing at a specific position specified by synthetic crRNA, hence a
promising therapeutic agent to treat gene deficiencies. Our current understanding of Cpf1 structure and function primarily
10 relies on crystal structures and cryoEM data, providing unique and invariant structures. In contrast to recent methods, the
scope of this project is to expand our understanding of the dynamic structure of Cpf1, and understand how conformational
changes and catalysis are related. To do this I used FRET (Förster Resonance Energy Transfer). Here, the work on this
projects is presented, with the aim of 1) understanding the conformational changes of Cpf1 in free-form, binary complex
(crRNA-bound) and tertiary complex (DNA-bound) in bulk, and correlating the conformational changes to intramolecular
15 distances, thus providing insight to the mechanism of DNA-cleavage and 2) calibrate the distance using dsDNA as a rigid
scaffold, preparing for single molecule FRET measurements on Cpf1. Ensemble measurements revealed conformational
changes of Cpf1 upon binding DNA, however the assay needs to be optimized further to extract distinct distances.
Spectrometric experiments revealed that excess dye in solution was a general problem in ensemble measurements,
interfering with the results. To validate and setup the calibration I did both ensemble and smFRET measurements on dual20
labelled dsDNA to address and eliminate the role of excess dye in solution. The inter-dye distance of dual-labelled dsDNA
was determined to be 62.72 ± 0.93 Å. The simulated distance with Monte Carlo simulations was found to be 61.6 Å. This
illustrates smFRET as a method to probe enzymatic motion, and thus could provide novel information about the mechanism
of DNA-cleavage in Cpf1, paving the way for future genome-editing.

Effects of Hydrogenphosphate Quenching on Fluorescent Lifetime of Hydroxyphenyl Substituted Diazaoxatriangulenium

Stine Grønfeldt Stenspil — 2019-01-04

Fluorophores are used in many research applications such as cell staining and as probes for ions, DNA, proteins or membranes. By
designing and synthesising the fluorophore to have specific photophysical properties it is possible to probe the surrounding
environment of the fluorophore. For example, by utilising the property of photoinduced electron transfer (PET) which quenches the
fluorescence of the fluorophore. A hydroxyphenyl substituted diazaoxatriangulenium (DAOTA+) designed to have the properties
as a pH probe using photoinduced electron transfer showed another pH dependency in addition to the expected quenching. Results
show that hydrogenphosphate is the reason for the additional quenching and other ions is also shown to have quenching abilities.
Further understanding of this mechanism could result in a new triangulenium derivative that is able to detect hydrogenphosphate or
other ions in solution. The detection of hydrogenphosphate is especially interesting as it is a key component in physiological
solutions and cells.

From Breast Cancer to Computational Science

Catalina Cocan — 2019-01-04

Computational science focuses on the development of predictive computer models of the world around us.
Scientific computing methods have become more accurate in the discovering of tumor treatment
possibilities, than laboratory experiments have ever proven. This thesis will provide the mathematical
modeling of breast tumor growth, including different aspects of how the immune system together
with cycle-phase-specific chemotherapy can defeat the disease. The delay differential equations
representing the tumor environment are solved using the Runge Kutta fourth method, taking in
consideration different phases of the cell-cycle.

“Turing mechanisms under pressure”: Mesenchymal condensations could be involved in digit patterning of mice.

Henrik Pinholt — 2019-01-04

In recent years, some attention has been directed towards the possibility that mechanical forces could play a role in creating the expression patterns observed in vertebrate body parts. By compressing regions of cultured embryonic mesenchymal stem cells from mouse autopods, this study provides a novel way of testing effects of mechanochemical stimulation of the Turing mechanism responsible for digit patterning in mice. The study found important features to be included in these compression systems for mesenchymal cells: Com- pressing a small area of the culture, using transparent pistons, and maintaining a stable environment from vibrations and disturbances. The results suggest that mechanical forces upregulates Sox9 in the boundary between compressed and uncompressed regions, but doesn’t seem to change the compressed pattern in comparison to uncompressed cells. However incomplete, these results suggest that both chemical and mechanochemical regulation of Sox9 might be involved in patterning the digits in mice.

Multilayer Reflection Tomography from Monte Carlo Simulations

Rasmus Buus Nielsen — 2019-01-04

X-ray Reflection Tomography (XRT) is a tool for imaging of buried layers and interfaces in multilayer thin-films. The
method combines X-ray reflectivity and computerized tomography to determine spatially dependent reflectivity curves.
Simulations of X-ray reflection tomography experiments make it possible to asses to which accuracy properties can be determined
and evaluate various reconstruction methods.2 It is thus important that such simulations mimic real experiments.
In this paper it is shown that a Monte Carlo approach can be used to simulate XRT experiments and test reconstruction
techniques. This approach takes into account the statistical properties of an experimental X-ray setup and allows for
simulation of diverse experimental configurations. The currently used analytical simulations based on projections do not
include such statistics and are limited in scope. The Monte Carlo approach will facilitate further development of the
applications of XRT.

Full Issue

Thomas Just Sørensen — 2019-01-04

Full Issue

Editorial

Thomas Just Sørensen — 2019-01-04

Editorial