Publications by authors named "Dawid Maciazek"
The algorithms commonly used to select the best stable reference gene in RT-qPCR data analysis have their limitations. We showed that simple selection of the reference gene or pair of genes with the lowest stability value from the pool of potential reference genes-a commonly used approach-is not sufficient to accurately and reliably normalize the target gene transcript and can lead to biologically incorrect conclusions. For reliable assessment of changes in a target gene expression level, we propose our innovative GenExpA software, which works in a manner independent of the experimental model and the normalizer used.
View Article and Find Full Text PDFA gas cluster ion beam (GCIB) source, consisting of CO clusters and operating with kinetic energies of up to 60 keV, has been developed for the high resolution and high sensitivity imaging of intact biomolecules. The CO molecule is an excellent molecule to employ in a GCIB source due to its relative stability and improved focusing capabilities, especially when compared to the conventionally employed Ar cluster source. Here we report on experiments aimed to examine the behavior of CO clusters as they impact a surface under a variety of conditions.
View Article and Find Full Text PDFMolecular dynamics (MD) simulations continue to make important contributions to understanding chemical and physical processes. Concomitant with the growth of MD simulations is the need to have interaction potentials that both represent the chemistry of the system and are computationally efficient. We propose a modification to the ReaxFF potential for carbon and hydrogen that eliminates the time-consuming charge equilibration, eliminates the acknowledged flaws of the electronegativity equalization method, includes an expanded training set for condensed phases, has a repulsive wall for simulations of energetic particle bombardment, and is compatible with the LAMMPS code.
View Article and Find Full Text PDFCO2 Cluster Ion Beam, an Alternative Projectile for Secondary Ion Mass Spectrometry.
J Am Soc Mass Spectrom
September 2016
Article Synopsis
- The use of argon-based gas cluster ion beams in SIMS (Secondary Ion Mass Spectrometry) enhances molecular depth profiling and 3D chemical imaging by reducing surface damage and maintaining better mass spectra quality.
- Despite these benefits, challenges like low sensitivity and beam focusing in nanoscale bioimaging persist, which may be addressed by using CO2 as an alternative projectile.
- Results show CO2 cluster projectiles perform comparably to argon, with improved imaging resolution and greater stability, allowing for more effective operation at lower pressures.
Article Synopsis
- Strengthening one chemical bond can weaken adjacent bonds, but little research has explored how this effect impacts the entire molecular structure.
- By forming self-assembled monolayers on a surface, researchers can selectively change the strength of primary bonds in molecules.
- Using advanced techniques like secondary-ion mass spectrometry and computational simulations, the study reveals detectable fluctuations in bond stability along the molecule, which decrease with distance from the surface, indicating a fundamental characteristic of chemical bonding.