Parallel‐ProBiS: Fast parallel algorithm for local structural comparison of protein structures and binding sites

The ProBiS algorithm performs a local structural comparison of the query protein surface against the nonredundant database of protein structures. It finds proteins that have binding sites in common with the query protein. Here, we present a new parallelized algorithm, Parallel‐ProBiS, for detecting similar binding sites on clusters of computers. The obtained speedups of the parallel ProBiS scale almost ideally with the number of computing cores up to about 64 computing cores. Scaling is better for larger than for smaller query proteins. For a protein with almost 600 amino acids, the maximum speedup of 180 was achieved on two interconnected clusters with 248 computing cores. Source code of Parallel‐ProBiS is available for download free for academic users at http://probis.cmm.ki.si/download . © 2012 Wiley Periodicals, Inc.     

NQR investigation and characterization of cocrystals and crystal polymorphs

The application of ¹⁴N NQR to the study of cocrystals and crystal polymorphs is reviewed. In ferroelectric and antiferroelectric organic cocrystals ¹⁴N NQR is used to determine proton position in an N-H...O hydrogen bond and proton displacement below T_C. In cocrystal isonicitinamide – oxalic acid (2:1) ¹⁴N NQR is used to distinguish between two polymorphs and to determine the type of the hydrogen bond (N^?...H-O). The difference in the ¹⁴N NQR spectra of cocrystal formers and cocrystal is investigated in case of carbamazepine, saccharin and carbamazepine - saccharin (1:1). The experimental resolution allows an unambiguous distinction between the ¹⁴N NQR spectrum of the cocrystal and the ¹⁴N NQR spectra of the cocrystal formers. The possibility of application of NQR and double resonance for the determination of the inhomogeneity of the sample and for the study of the life time of an unstable polymorph is discussed.     

Two-dimensional measurements of laser-induced breakdown in air by high-speed two-frame shadowgraphy

We present two-dimensional measurements of the laser-induced plasma development and shock wave evolution in air. The breakdown is induced by a Q-switched Nd:YAG laser (λ=1064 nm) with a pulse duration of 4 ns. To study these fast laser-induced phenomena, we have developed a high-speed, two frame shadowgraph method. It enables 2D visualization of a laser-induced event in two time instances, which are delayed by an arbitrary time interval in the range from 300 ps to 30 ns. The established method is based on 30 ps, green (λ=532 nm), and linearly polarized laser pulse, which is split into two orthogonally polarized illumination pulses for direct and delayed illumination of the breakdown area. Exploiting polarization of the probe pulses, we capture two temporally and spatially separated frames with two CCD cameras. Special attention is given to the subsequent data processing, especially to the minimization of the systematic error due to alignment of both images, and to the determination of 2D velocity distribution from the captured image pairs.     

Interferometric determination of the high-intensity laser-pulse-material interaction site

We developed a method that accurately determines an unknown position of the high-intensity laser-pulse-material interaction site on the front side of a plate. It is based on interferometric measurements of a normal displacement at known positions on the plate’s rear side. The displacement is caused by reflections of various pulsed-laser-induced mechanical waves. We have superseded the long-established time-of-flight approach with the improved, triple-echo method. To accurately locate the origin of the laser-induced ultrasound on the plate with a known thickness, we only need to detect the arrivals of the first three consecutive mode unconverted waves. Our method works without knowing the propagation velocities of various ultrasonic waves and additionally solves some time-related drawbacks of the conventional time-of-flight approach. The relative uncertainty of the measured source-receiver separations obtained with the presented method is less than 0.01.     

Unique structural features of interconverting monomeric and dimeric G-quadruplexes adopted by a sequence from the intron of the N-myc gene

A multidimensional heteronuclear NMR study has demonstrated that a guanine-rich DNA oligonucleotide originating from the N-myc gene folds into G-quadruplex structures in the presence of K(+), NH(4)(+), and Na(+) ions. A monomeric G-quadruplex formed in K(+) ion containing solution exhibits three G-quartets and flexible propeller-type loops. The 3D structure with three single nucleotide loops represents a missing element in structures of parallel G-quadruplexes. The structural features together with the high temperature stability are suggestive of the specific biological role of G-quadruplex formation within the intron of the N-myc gene. An increase in K(+) ion and oligonucleotide concentrations resulted in transformation of the monomeric G-quadruplex into a dimeric form. The dimeric G-quadruplex exhibits six stacked G-quartets, parallel strand orientations, and propeller-type loops. A link between the third and the fourth G-quartets consists of two adenine residues that are flipped out to facilitate consecutive stacking of six G-quartets.     

<Superscript>14</Superscript>N Nuclear Quadrupole Resonance Study of Polymorphism in Trinitrotoluene Samples Obtained from Old Ordnances

The field application of a ¹⁴N nuclear quadrupole resonance (NQR) detector needed for the detection of different explosives, including trinitrotoluene (TNT), requires the examination of the distribution of ¹⁴N NQR lines stemming from the monoclinic and/or orthorhombic modifications of TNT, as well as from a mixture of both. In this work, 30 different TNT samples up to 70 years old were measured. The main result of this study is that the measured ¹⁴N NQR spectrum is strongly influenced by the environmental conditions to which the explosive was subject during its history.     

A new glucosamine-containing amphiphilic spin probe

A new, nonionic amphiphilic spin probe for investigating the extracellular matrix close to the cell membrane by EPR spectroscopy has been synthesized and characterized. A pyrrolidine type nitroxide spin-label has been introduced to the third position of a nonionic sugar polar head (glucosamine) bonded to a lipophilic stearic acid acyl chain anchor. The compound is soluble in polar organic solvents such as ethanol and chloroform, but is sparingly soluble in water.     

Optodynamic study of multiple pulses micro drilling

This paper describes an analysis of pulsed lasers micro-drilling of different metals. Study focuses to an optodynamic phenomenon which appears as thermal effects induced by laser light pulses and leads to dynamic process manifested as ultrasonic shock waves propagating into the sample material. The shock waves are detected by a non-contact optical method by using arm compensated Michelson. Monitoring of the main parameters of the micro drilling such as material ablation rate and efficiency was realized by analysis of the optodynamic signals. The process is characterized by decreasing ablation rate that leads to the finite hole depth. The experimental part of study comprehends a comparison between various metals. In order to describe decreasing ablation rate a theoretical model based on the energy balance is proposed. It considers the energy/heat transfer from the laser beam to the material and predicts a decreasing drilling rate with an increasing number of successive laser pulses. According to the proposed model, the finite depth of the hole appears as a consequence of the increasing surface area through which the energy of the laser beam is conducted away to the material around the processed area. Decreasing ablation rate and the finite hole depth predicted by model were in good agreement with the experimental results.     

Optodynamic monitoring of laser micro-drilling of glass by using a laser probe

We present a new method for monitoring of the laser micro-drilling process. The method is based on detection of acoustic waves in air above the processed sample using a laser beam deflection probe (LBDP). We present an augmentation of the experimental set-up by means of a digital micrographic system which enables the acquisition of images of the plasma plume and of the hole cross-section during a drilling sequence. Comparing the acquired images with the detected LBDP signals, we examine the drilling process from a new perspective.     

Synthesis and Evaluation of Antioxidant Properties of 2-Substituted Quinazolin-4(3H)-ones

Quinazolinones represent an important scaffold in medicinal chemistry with diverse biological activities. Here, two series of 2-substituted quinazolin-4(3H)-ones were synthesized and evaluated for their antioxidant properties using three different methods, namely DPPH, ABTS and TEAC_CUPRAC, to obtain key information about the structure–antioxidant activity relationships of a diverse set of substituents at position 2 of the main quinazolinone scaffold. Regarding the antioxidant activity, ABTS and TEAC_CUPRAC assays were more sensitive and gave more reliable results than the DPPH assay. To obtain antioxidant activity of 2-phenylquinazolin-4(3H)-one, the presence of at least one hydroxyl group in addition to the methoxy substituent or the second hydroxyl on the phenyl ring in the ortho or para positions is required. An additional ethylene linker between quinazolinone ring and phenolic substituent, present in the second series (compounds 25a and 25b), leads to increased antioxidant activity. Furthermore, in addition to antioxidant activity, the derivatives with two hydroxyl groups in the ortho position on the phenyl ring exhibited metal-chelating properties. Our study represents a successful use of three different antioxidant activity evaluation methods to define 2-(2,3-dihydroxyphenyl)quinazolin-4(3H)-one 21e as a potent antioxidant with promising metal-chelating properties.