Evolution of femtosecond laser-induced damage in doped GaN thin films

Mg- and Si-doped GaN layers deposited by metalorganic chemical vapor deposition method were irradiated with femtosecond pulse duration laser of three different wavelengths 1,030, 515 and 343 nm. Both single and multiple shot laser induced damage thresholds of doped GaN layers were evaluated and discussed. The scanning electron microscopy employed with electron beam induced current and energy dispersive X-ray techniques were used to study laser damage morphology. It was observed that ablated area and laser-induced damage increased with irradiation fluence. The mechanism of damage generation by Gaussian beam profile laser was considered.     

Algebraic approach for the exploration of the onset of chaos in discrete nonlinear dynamical systems

An algebraic approach based on the rank of a sequence is proposed for the exploration of the onset of chaos in discrete nonlinear dynamical systems. The rank of the partial solution is identified and a special technique based on Hankel matrices is used to decompose the solution into algebraic primitives comprising roots of the modified characteristic equation. The distribution of roots describes the dynamical complexity of a solution and is used to explore properties of the nonlinear system and the onset of chaos.     

GPU computing for shallow water flow simulation based on finite volume schemes

This article is a review of the work that we are carrying out to efficiently simulate shallow water flows. In this paper, we focus on the efficient implementation of path-conservative Roe type high-order finite volume schemes to simulate shallow flows that are supposed to be governed by the one-layer or two-layer shallow water systems, formulated under the form of a conservation law with source terms. The implementation of the scheme is carried out on Graphics Processing Units (GPUs), thus achieving a substantial improvement of the speedup with respect to normal CPUs. Finally, some numerical experiments are presented.     

Templating S100A9 amyloids on Aβ fibrillar surfaces revealed by charge detection mass spectrometry,microscopy, kinetic and microfluidic analyses

The mechanism of amyloid co-aggregation and its nucleation process are not fully understood in spite of extensive studies. Deciphering the interactions between proinflammatory S100A9 protein and Aβ₄₂ peptide in Alzheimer''s disease is fundamental since inflammation plays a central role in the disease onset. Here we use innovative charge detection mass spectrometry (CDMS) together with biophysical techniques to provide mechanistic insight into the co-aggregation process and differentiate amyloid complexes at a single particle level. Combination of mass and charge distributions of amyloids together with reconstruction of the differences between them and detailed microscopy reveals that co-aggregation involves templating of S100A9 fibrils on the surface of Aβ₄₂ amyloids. Kinetic analysis further corroborates that the surfaces available for the Aβ₄₂ secondary nucleation are diminished due to the coating by S100A9 amyloids, while the binding of S100A9 to Aβ₄₂ fibrils is validated by a microfluidic assay. We demonstrate that synergy between CDMS, microscopy, kinetic and microfluidic analyses opens new directions in interdisciplinary research.

Templating mechanism of S100A9 amyloids on Aβ fibrillar surfaces during amyloid co-aggregation process was revealed by synergy of biophysical methods including charge detection mass spectrometry, microscopy, kinetic and microfluidic analyses.     

A pseudo-stable structure in a completely invertible bouncer system

It is shown that a pseudo-stable structure of non-asymptotic convergence may exist in a completely invertible bouncing ball model. Visualization of the pattern of H-ranks helps to identify this structure. It appears that this structure is similar to the stable manifold of non-invertible nonlinear maps which govern the non-asymptotic convergence to unstable periodic orbits. But this convergence to the unstable repeller of the bouncing ball problem is only temporary since non-asymptotic convergence cannot exist in completely invertible maps. This nonlinear effect is exploited for temporary stabilization of unstable periodic orbits in completely reversible nonlinear maps.     

In Situ Deprotection and Incorporation of Unnatural Amino Acids during Cell‐Free Protein Synthesis

The S30 extract from E. coli BL21 Star (DE3) used for cell‐free protein synthesis removes a wide range of α‐amino acid protecting groups by cleaving α‐carboxyl hydrazides; methyl, benzyl, tert‐butyl, and adamantyl esters; tert‐butyl and adamantyl carboxamides; α‐amino form‐, acet‐, trifluoroacet‐, and benzamides; and side‐chain hydrazides and esters. The free amino acids are produced and incorporated into a protein under standard conditions. This approach allows the deprotection of amino acids to be carried out in situ to avoid separate processing steps. The advantages of this approach are demonstrated by the efficient incorporation of the chemically intractable (S)‐4‐fluoroleucine, (S)‐4,5‐dehydroleucine, and (2S,3R)‐4‐chlorovaline into a protein through the direct use of their respective precursors, namely, (S)‐4‐fluoroleucine hydrazide, (S)‐4,5‐dehydroleucine hydrazide, and (2S,3R)‐4‐chlorovaline methyl ester. These results also show that the fluoro‐ and dehydroleucine and the chlorovaline are incorporated into a protein by the normal biosynthetic machinery as substitutes for leucine and isoleucine, respectively.     

Screening of antioxidant activity and volatile compounds composition of Chamerion angustifolium (L.) Holub ecotypes grown in Lithuania

Since biological activity of medicinal plants is dependent on cultivation area, climatic conditions, developmental stage, genetic modifications and other factors, it is important to study flora present in different growing sites and geographical zones. This study was focused on screening of antioxidant activity of C. angustifolium harvested in six different locations in Lithuania. The total contents of phenolic compounds, flavonoids and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity were evaluated by spectrophotometric methods. A correlation between radical scavenging activity and total phenolic compounds content was observed (correlation coefficient 0.98). HPLC with online post-column DPPH radical scavenging reaction detection was used for the separation of extracts. Oenothein B, rutin and one unidentified compound were predominant. Volatile compounds were analysed using solid-phase microextraction coupled with gas chromatography–mass spectrometry. Based on the analysis of volatiles, all samples were classified into two chemotypes: (I) with predominant α- and β-caryophyllenes and (II) with predominant anethole.     

Comparative analysis of radical scavenging and antioxidant activity of phenolic compounds present in everyday use spice plants by means of spectrophotometric and chromatographic methods

Comparative analysis of radical scavenging and antioxidant activities of phenolic compounds present in everyday use spice plants was carried out by means of spectrophotometric and chromatographic methods. Six spice plant samples, namely onion (Allium cepa), parsley (Petroselinum crispum) roots and leaves, celery (Apium graveolens) roots and leaves and leaves of dill (Anethum graveolens) were analyzed. Total amount of phenolic compounds and radical scavenging activity (RSA) was the highest in celery leaves and dill extracts and was the lowest in celery roots. Comparing commonly used spectrophotometric analysis of 2,2-diphenyl-1-picrylhydrazyl (DPPH) RSA of extracts with the results obtained using reversed-phase chromatographic separation with on-line post-column radical scavenging reaction detection, good correlation was obtained (R(2)=0.848). Studies using HPLC system with electrochemical detector showed that bioactive phytochemicals can be separated and antioxidant activities of individual compounds evaluated without the need of a complex HPLC system with reaction detector. The results obtained using electrochemical detection correlate with the RSA assayed using spectrophotometric method (R(2)=0.893).