PRESSURE-VELOCITY EQUILIBRIUM HYDRODYNAMIC MODELS

This article describes mathematical models for phase separated mixtures of materials that are in pressure and velocity equilibrium but not necessarily temperature equilibrium. General conditions for constitutive models for such mixtures that exhibit a single mixture sound speed are discussed and specific examples are described.     

Software news and updates. Carma: a molecular dynamics analysis program

A computer program has been developed to aid the analysis of molecular dynamics trajectories. The program is tuned for macromolecular large-scale problems and supports features such as removal of global translations-rotations of the solute, calculation of average distance maps and their corresponding standard deviations, calculation of the variance-covariance and cross-correlation matrices, and principal component analysis of trajectories with the added ability to create artificial trajectories based on selected eigenvectors. Limited graphics (trajectory viewing) capabilities are also available.     

Grcarma: A fully automated task‐oriented interface for the analysis of molecular dynamics trajectories

We report the availability of grcarma, a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules. It is a cross‐platform, Perl/Tk‐based front‐end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user‐friendly and intuitive design. Particular emphasis was given to the automation of several tedious tasks, such as extraction of clusters of structures based on dihedral and Cartesian principal component analysis, secondary structure analysis, calculation and display of root‐mean‐square deviation (RMSD) matrices, calculation of entropy, calculation and analysis of variance–covariance matrices, calculation of the fraction of native contacts, etc. The program is free‐open source software available immediately for download. © 2013 Wiley Periodicals, Inc.     

Correlation between biological activity and energies of electronic transitions in benzodiazepines. Negative ion mass spectrometry and ultraviolet absorption spectroscopy study of some derivatives

A correlation between the energies of electronic singlet transitions in benzodiazepines and their biological activity, which was revealed earlier by means of negative ion mass spectrometry with resonance electron capture, has been verified with a UV absorption spectroscopy investigation. Also, it has been noted that the energies of electronic singlet transitions in benzodiazepines are close in value to the ionization energies of atoms Cs, Rb, K, Na, Li and Tl, the cations of which are known to play an important role in nerve cell excitation processes. Copyright 1999 John Wiley & Sons, Ltd.     

Gas-phase deprotonation of arylalkylamines. A collision-induced dissociation study

The collision-induced dissociation (CID) of deprotonated arylalkylamines of general formula R(1)C(6)H(4)CHR(2)CH(2)NR(3)(2) (where R(1) = H, OH, F or NO(2); R(2) = H or OH; R(3) = H or CH(3)) generated by negative chemical ionization with H(2)O and D(2)O as ionizing reagents, is discussed. The negative chemical ionization mass spectra show that, in the absence of a hydroxy group in the aromatic ring, deprotonation takes place at the benzylic position whereas the proton is lost from the OH group when present. The nitro compound forms only M(-.) ions. The CID spectra of the deprotonated molecules show that fragmentations are strongly dependent on the structural features of the molecules, namely the presence or absence of substituents in the aromatic ring or aliphatic chain. Copyright 1999 John Wiley & Sons, Ltd.     

Purification and Characterization of Agarase from Marine Bacteria <Emphasis Type="Italic">Acinetobacter</Emphasis> sp. PS12B and Its Use for Preparing Bioactive Hydrolysate from Agarophyte Red Seaweed <Emphasis Type="Italic">Gracilaria verrucosa</Emphasis>

Acinetobacter strain PS12B was isolated from marine sediment and was found to be a good candidate to degrade agar and produce agarase enzyme. The extracellular agarase enzyme from strain PS12B was purified by ammonium sulfate precipitation followed by DEAE-cellulose ion-exchange chromatography. The specific activity of the crude enzyme which was 1.52 U increased to 45.76 U, after two-stage purification, with an enzyme yield of 9.76%. Purified enzyme had a molecular mass of 24 kDa. The optimum pH and temperature for activity of purified agarase were found to be 8.0 and 40 °C, respectively. The K_m and V_max values for agarase were 4.69 mg/ml and 0.5 μmol/min, respectively. Treatment with EDTA reduced the agarase activity by 58% at 5 mM concentration. The enzyme activity was stimulated by the presence of Fe²⁺, Mn²⁺, and Ca2⁺ ions while reducing reagents (β-mercaptoethanol and dithiothreitol, DTT) enhanced its activity by 30–40%. The purified agarase exhibited tolerance to both detergents and organic solvents. Major hydrolysis products of agar were DP4 and also a mixture of longer oligosaccharides DP6 and DP7. The enzyme hydrolysed seaweed (Gracilaria verrucosa) exhibited strong antioxidant activity in vitro. Successful hydrolysis of seaweed indicates the potential use of the enzyme to produce seaweed hydrolysate having health benefits as well as the industrial application like the production of biofuels.     

The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide

The correct balance between attractive, repulsive and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors, we sought a comparison of the folding between two 25-residues peptides, the influenza A M2 protein transmembrane domain (M2TM) and the 25-Ala (Ala₂₅). M2TM forms a stable α-helix as is shown by circular dichroism (CD) experiments. Molecular dynamics (MD) simulations with adaptive tempering show that M2TM monomer is more dynamic in nature and quickly interconverts between an ensemble of various α-helical structures, and less frequently turns and coils, compared to one α-helix for Ala₂₅. DFT calculations suggest that folding from the extended structure to the α-helical structure is favored for M2TM compared with Ala₂₅. This is due to CH⋯O attractive interactions which favor folding to the M2TM α-helix, and cannot be described accurately with a force field. Using natural bond orbital (NBO) analysis and quantum theory atoms in molecules (QTAIM) calculations, 26 CH⋯O interactions and 22 NH⋯O hydrogen bonds are calculated for M2TM. The calculations show that CH⋯O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total hydrogen bonding energy, when compared to NH⋯O, to the stabilization of the α-helix in M2TM. Further, a strengthening of NH⋯O hydrogen bonding interactions is calculated for M2TM compared to Ala₂₅. Additionally, these weak CH⋯O interactions can dissociate and associate easily leading to the ensemble of folded structures for M2TM observed in folding MD simulations.     

Computer extended series solution for unsteady flow in a contracting or expanding pipe

Unsteady flow in a semi-infinite contracting or expanding pipeis reinvestigated using long series analysis. The proposed seriesmethod is useful in analysing the problem for a moderately largeconstant ( = aa/, where a = a(t), the radius of the pipe isa function of time, a(t) is the velocity of the wall, and iskinematic viscosity). For positive values of (expansion ofthe pipe) accuracy of the series representing shear stress andpressure gradient is increased from = 2.89 to = 6.0 by extractingthe singularity followed by completion of the series. For negativevalues of (contraction of the pipe), we revert the series whichresults into the increase of the region of validity of the transposedseries from = -25.0 to = -2.89. Later we use Padé approximantsfor summing them. Also, the asymptotic solution for large valuesof is obtained and it agrees closely with pure numerical valuesof shear stress at the wall and pressure gradient.