Transfer Thermodynamics of Protein in Denaturing and Stabilizing Media

Free energies of transfer (ΔG_t) of RibonucleaseA (RNaseA) from water to aqueous solutions of urea (4 M, 6 M and 8 M), a protein denaturing solvent as well as ΔG_t of RibonucleaseA, β‐Lactoglobulin, α‐Chymotripsin and ChymotrypsinogenA from water to aqueous glycerol (10%, 20%, 30% and 40%), a protein stabilizing solvent has been dissected into cavity term [ΔG_t(cav)] and interaction term [ΔG_t(int)]. The interaction free energy includes all types of interactions like hard‐soft, hydrogen bonding, electrostatic, etc. The cavity forming free energies have been calculated using the standard version of scaled particle theory (SPT) with well‐reported SPT parameters. It has been found that transfer free energies of cavity terms ΔG_t(cav) for native protein from water to urea‐water and water to aqueous glycerol follow almost opposite trends. This primarily indicates there may be some correlation between cavity creation energies and protein denaturing and stabilizing ability of a solvent. The results are in agreement with those obtained from preferential binding coefficient studies in these media.     

A simple mathematical model for seasonal planktonic blooms

We show how the inclusion of the defense strategy by different species can alter the prediction of simple models. One of the defense strategy by the phytoplankton population against their grazer is the release of toxic chemicals. In turn the zooplankton population reduces there predation rate over toxin producing phytoplankton (TPP) to protect themselves from those toxic chemicals. Thus, when the level of toxicity is high, the grazing pressure is low and when the level of toxicity is low or when the toxin is absent, the grazing pressure is high. Here we have considered a TPP–zooplankton system where the rate of toxin liberation and the predation rate vary with zooplankton abundance. We observe that our proposed model has the potential to show different dynamical behaviour that are similar to that seen in real‐world situations. Further, we consider three different functional forms for the distribution of the toxins and compare them using latin hypercube sampling technique and found that the functional forms seem to have no effect in determining the final outcome of the system. Copyright © 2009 John Wiley & Sons, Ltd.     

Continuation of limit cycles near saddle homoclinic points using splines in phase space

We present a new algorithm for continuation of limit cycles of autonomous systems as a system parameter is varied. The algorithm works in phase space with an ordered set of points on the limit cycle, along with spline interpolation. Currently popular algorithms in bifurcation analysis packages compute time-domain approximations of limit cycles using either shooting or collocation. The present approach seems useful for continuation near saddle homoclinic points, where it encounters a corner while time-domain methods essentially encounter a discontinuity (a relatively short period of rapid variation). Other phase space-based algorithms use rescaled arclength in place of time, but subsequently resemble the time-domain methods. Compared to these, we introduce additional freedom through a variable stretching of arclength based on local curvature, through the use of an auxiliary index-based variable. Several numerical examples are presented. Comparisons with results from the popular package, MATCONT, are favorable close to saddle homoclinic points.     

Linked scans of peptides and protein digests: amino acid sequence determination of components of complex mixtures

Two-sector linked-scan analysis of an unpurified proteolytic digest of a pyruvate decarboxylase enzyme (60,000 Da) has allowed the discovery and assignment of an amino-terminal post-translational modification and processing event. A difference in amino acid sequence from that predicted by a recently published nucleotide sequence has also been found. These results illustrate both the use and considerable potential of linked-scan methods for the analysis of complex biopolymer mixtures.     

Alpha particle and deuteron impactL-shell ionization of Ar,Cu, Ge,Br, Zr and Ag

Alpha particle and deuteron impactL-subshell ionization cross-sections of Ar, Cu, Ge, Br, Zr and Ag have been computed using Vriens’ expressions for ionization cross-section of atoms due to impact of heavy charged particles. The effects of Coulomb deflection of the projectile and increase in binding of the target electron in the presence of projectile have been incorporated. Hartree-Fock velocity distributions for the target electrons have been used in the present calculations. The simple binary encounter approximation model is found to give results which are in satisfactory agreement with those obtained from experiments and from other theories.     

Superheated drops of R114—as a neutron spectrometer

The basic principle that has been used in the application of superheated drops in neutron spectrometry is its dependence of threshold energy of nucleation on temperature. In the present work, superheated drops of R114 suspended in a visco-elastic gel were irradiated at different temperatures by neutrons obtained from an ²⁴¹Am–Be source. The temperature of the detector was converted to the energy of the incident neutrons following the method developed by us to unfold the neutron energy spectrum. The threshold energy obtained by us agrees well with other results obtained using monochromatic neutron sources, clearly demonstrating the validity of our principle of spectrometry.     

Characterization of the Hf-NTA complex

Hafnium ion forms a strong complex with nitrilotriacetic acid (NTA). But there is a controversy about the nature of the complex on whether it is a 1:1 or a 1:2 complex. We have carried out an electrophoresis experiment and supplemented data to establish the nature of the complex. Our data indicates that it is a 1:2 complex i.e. [Hf(NTA)₂]^2- in which the coordination number 8 has been satisfied for hafnium.     

Highly stereoselective approach toward the synthesis of the macrolactone core of amphidinolide W

The diastereoselective synthesis of the macrolactone core of amphidinolide W was successfully accomplished using Evans’ asymmetric alkylation, Aldol reaction, Julia-Kocienski olefination, and Kita’s macrocyclization protocol.