A new measure for functional similarity of gene products based on Gene Ontology

BACKGROUND: Gene Ontology (GO) is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role. RESULTS: We present a new method for comparing sets of GO terms and for assessing the functional similarity of gene products. The method relies on two semantic similarity measures; sim(Rel )and funSim. One measure (sim(Rel)) is applied in the comparison of the biological processes found in different groups of organisms. The other measure (funSim) is used to find functionally related gene products within the same or between different genomes. Results indicate that the method, in addition to being in good agreement with established sequence similarity approaches, also provides a means for the identification of functionally related proteins independent of evolutionary relationships. The method is also applied to estimating functional similarity between all proteins in Saccharomyces cerevisiae and to visualizing the molecular function space of yeast in a map of the functional space. A similar approach is used to visualize the functional relationships between protein families. CONCLUSION: The approach enables the comparison of the underlying molecular biology of different taxonomic groups and provides a new comparative genomics tool identifying functionally related gene products independent of homology. The proposed map of the functional space provides a new global view on the functional relationships between gene products or protein families

How to Create Trusted Tribological Characterization Data of Soft Polymers as Input for FEM Simulations?

Soft polymers such as the investigated polyurethane, characterized by low Young’s moduli and prone to high shear deflection, are frequently applied in pneumatic cylinders. Their performance and lifetime without external lubrication are highly determined by the friction between seal and shaft and the wear rate. FEM simulation has established itself as a tool in seal design processes but requires input values for friction and wear depending on material, load, and velocity. This paper presents a tribological test configuration for long stroke, reciprocating movement, allowing the generation of data which meet the requirements of input parameters for FEM simulations without the geometrical influences of specific seal profiles. A numerical parameter study, performed with an FEM model, revealed the most eligible sample geometry as a flat, disc-shaped sample of the polymer glued on a stiff sample holder. At the same time, the study illustrates that the sensitivity of the contact pressure distribution to Poisson’s ratio and CoF can be minimized by the developed and verified setup. It ensures robust, reliable, and repeatable experimental results with uniform contact pressures and constant contact areas to be used in databases and FEM simulations of seals, enabling upscaling from generically shaped samples to complex seal profiles

Bioinspired morphologies generated on steel surfaces by ultrashort laser pulse irradiation mimicking the fluid transport of bugs

Conferencia invitada. -- Strasbourg (France), from May 22 to 26, 2017. -- https://www.european-mrs.com/meetings/archives/2017-spring-meetingNature provides countless examples of surface structures featuring extraordinary properties such as directional fluid transport. In order to mimic the morphology and outstanding wetting behaviour of bark bugs, ultrashort laser pulses with durations in the fs- to ps-range were employed for large area surface processing of steel. By scanning the laser beam across the surface of initially polished flat sample surfaces and systematically varying the laser processing parameters (peak fluence, scan velocity, line overlap), different regimes associated with characteristic surface morphologies (laser-induced periodic surface structures (LIPSS), grooves, spikes, etc.) could be identified. Additionally, different laser processing strategies were applied, varying laser wavelength, pulse duration and repetition rates, which allowed to achieve a range of morphologies that resemble different structures found on bark bugs. For identifying the ideal combination of parameters for mimicking such bug-like structures, the surfaces were inspected by means of optical and scanning electron microscopy. Complementary to the morphology study, the wetting behaviour of the surface structures for water and oil was examined intensively in terms of fluid transport and philic/-phobic nature. Additionally, with these results in hand, tribological tests investigating the wear resistance of the laser-induced nano- and microstructures were carried out. Our results demonstrate that the functionality of surface structures found in nature could be transferred to technologically relevant materials, such as steel, providing a huge potential for industrial applications for instance in friction and wear reduction.Peer Reviewe