Minimum dissipative relaxed states in toroidal plasmas

Relaxation of toroidal discharges is described by the principle of minimum energy dissipation together with the constraint of conserved global helicity. The resulting Euler-Lagrange equation is solved in toroidal coordinates for an axisymmetric torus by expressing the solutions in terms of Chandrasekhar-Kendall (C-K) eigenfunctions analytically continued in the complex domain. The C-K eigenfunctions are obtained as hypergeometric functions that are solutions of scalar Helmholtz equation in toroidal coordinates in the large aspect-ratio approximation. Equilibria are constructed by assuming the current to vanish at the edge of plasma. For the m=0, n=0 (m and n are the poloidal and toroidal mode numbers respectively) relaxed states, the magnetic field, current, q (safety factor) and pressure profiles are calculated for a given value of aspect-ratio of the torus and for different values of the eigenvalue λ _{r 0}. The new feature of the present model is that solutions allow for both tokamak as well as RFP-like behaviour with increase in the values of λ _{r 0}, which is related directly to volt-sec in the experiment.     

Effects of Bubbles on the Hydraulic Conductivity of Porous Materials – Theoretical Results

In a porous material, both the pressure drop across a bubble and its speed are nonlinear functions of the fluid velocity. Nonlinear dynamics of bubbles in turn affect the macroscopic hydraulic conductivity, and thus the fluid velocity. We treat a porous medium as a network of tubes and combine critical path analysis with pore-scale results to predict the effects of bubble dynamics on the macroscopic hydraulic conductivity and bubble density. Critical path analysis uses percolation theory to find the dominant (approximately) one-dimensional flow paths. We find that in steady state, along percolating pathways, bubble density decreases with increasing fluid velocity, and bubble density is thus smallest in the smallest (critical) tubes. We find that the hydraulic conductivity increases monotonically with increasing capillary number up to Ca 10^–2, but may decrease for larger capillary numbers due to the relative decrease of bubble density in the critical pores. We also identify processes that can provide a positive feedback between bubble density and fluid flow along the critical paths. The feedback amplifies statistical fluctuations in the density of bubbles, producing fluctuations in the hydraulic conductivity.     

An atomic scale characterization of coupled grain boundary motion in silicon bicrystals

The mechanical response of symmetric tilt grain boundaries (GBs) in silicon bicrystals under shear loading are characterized using molecular dynamics simulations. It is seen that under shear, high-angle GBs namely Σ5 and Σ13 having a rotation axis [0 0 1] demonstrate coupled GB motion, such that the displacement of grains parallel to the GB interface is accompanied by normal GB motion. An atomic-scale characterization revealed that concerted rotations of silicon tetrahedra within the GB are the primary mechanisms leading to the coupled GB motion. Interestingly, so far, this phenomenon has only been examined in detail for metallic systems. A distinguishing feature of the coupled GB motion observed for the silicon symmetric tilt bicrystals as compared to metallic bicrystals is the fact that in the absence of shear, spontaneous coupled motion is not observed at high temperatures.     

Discovery and design of new PI3K inhibitors through pharmacophore-based virtual screening,molecular docking,and binding free energy analysis

Phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/the mammalian target of rapamycin (mTOR) signaling pathway is one of the sought after therapeutic target for treating human cancers. This pathway is often hyper activated in cancers. In the present study, pharmacophore-based virtual screening, molecular docking, and binding free energy calculations were performed on a series of quinoline derivatives which were reported to be effective against PI3Kα. A five-point pharmacophore hypothesis with one hydrogen bond acceptor (A), one hydrogen bond donor (D), one hydrophobic group (H), and two aromatic rings (R) was developed with acceptable R² and Q² values of 0.93 and 0.60 respectively. Eventually, common pharmacophore hypothesis-based screening was conducted against TOSLab, CPP, and ASINEX macrocylce databases, and potential hits were identified which were further subjected to rigorous docking process in order to screen out drug like molecules having crucial interactions with the target PI3Kα. Finally, binding free energy analysis was carried out for the top hits obtained from docking process. We also designed new 1, 3, 4-oxadiazole-based cyclic peptides by incorporating the structural features of the hits obtained from the above databases. Among the designed cyclic peptides, the cyclic peptide with tryptophan moiety showed good interactions and free binding energy values. On the whole, this study helped us in identifying new promising molecules as PI3Kα inhibitors which can be explored further to generate greater number of compounds with better pharmacokinetic properties.     

Metal-sensitive and thermostable trypsin from the crevalle jack (<Emphasis Type="Italic">Caranx hippos</Emphasis>) pyloric caeca: purification and characterization

Background

Over the past decades, the economic development and world population growth has led to increased for food demand. Increasing the fish production is considered one of the alternatives to meet the increased food demand, but the processing of fish leads to by-products such as skin, bones and viscera, a source of environmental contamination. Fish viscera have been reported as an important source of digestive proteases with interesting characteristics for biotechnological processes. Thus, the aim of this study was to purify and to characterize a trypsin from the processing by-products of crevalle jack (Caranx hippos) fish.

Results

A 27.5 kDa trypsin with N-terminal amino acid sequence IVGGFECTPHVFAYQ was easily purified from the pyloric caeca of the crevalle jack. Its physicochemical and kinetic properties were evaluated using N-α-benzoyl-_DL-arginine-p-nitroanilide (BApNA) as substrate. In addition, the effects of various metal ions and specific protease inhibitors on trypsin activity were determined. Optimum pH and temperature were 8.0 and 50°C, respectively. After incubation at 50°C for 30 min the enzyme lost only 20% of its activity. K _m , k_cat, and k _cat /K _m values using BApNA as substrate were 0.689 mM, 6.9 s^-1, and 10 s^-1 mM^-1, respectively. High inhibition of trypsin activity was observed after incubation with Cd²⁺, Al³⁺, Zn²⁺, Cu²⁺, Pb²⁺, and Hg²⁺ at 1 mM, revealing high sensitivity of the enzyme to metal ions.

Conclusions

Extraction of a thermostable trypsin from by-products of the fishery industry confirms the potential of these materials as an alternative source of these biomolecules. Furthermore, the results suggest that this trypsin-like enzyme presents interesting biotechnological properties for industrial applications.

     

Computational design of novel cyclic urea as HIV-1 protease inhibitor

A series of novel cyclic urea molecules 5,6-dihydroxy-1,3-diazepane-2,4,7-trione as HIV-1 protease inhibitors were designed using computational techniques. The designed molecules were compared with the known cyclic urea molecules by performing docking studies, calculating their ADME (Absorption, Distribution, Metabolism, and Excretion) properties and protein ligand interaction energy. These novel molecules were designed by substituting the P ₁/P′ ₁ positions (4 ^th and 7 ^th position of 1, 3-diazepan-2-one) with double bonded oxygens. This reduces the molecular weight and increases the bioavailability, indicating better ADME properties. The docking studies showed good binding affinity towards HIV-1 protease. The biological activity of these inhibitors were predicted by a model equation generated by the regression analysis between biological activity (log 1/K ⁱ ) of known inhibitors and their protein ligand interaction energy. The synthetic studies are in progress.