Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

Working group report: Quantum chromodynamics

This is the report of the subgroup QCD of Working Group-4 at WHEPP-9. We present the activities that had taken place in the subgroup and report some of the partial results arrived at following the discussion at the working group meetings.     

The Statistical Mechanics of Semiflexible Equilibrium Polymers

We give an overview of studies of models for semiflexible, equilibrium polymers with special emphasis on our work on both lattice and continuum models for such systems. We show, principally by Monte Carlo simulations, that, once monomers self assemble to form polymers, their semiflexibility leads to nematic phases at low temperatures. Attractive wall potentials encourage the adsorption of these equilibrium polymers on surfaces. Rapid cooling leads to the formation of glasses with entangled polymers. Shear promotes nematic ordering, but, at high shear rates, this tendency decreases since the equilibrium polymers are torn apart. A version of our model in which the polymers are directed shows the polymer analog of bosonic Mott-insulating, mass-density-wave, and supersolid phases. We give a brief comparison of our work with other studies and also explore the experimental implications of our study.     

Quark mass corrections to the perturbative thrust and its effect on the determination of αs

We consider the effects of quark masses to the perturbative thrust in e ⁺ e ⁻ annihilation. In particular we show that perturbative power corrections resulting from non-zero quark masses considerably alters the size of the non-perturbative power corrections and consequently, significantly changes the fitted value of α_s.     

Capacity augmentation of a supply chain for a short lifecycle product: A system dynamics framework

For an innovative product characterized by short product lifecycle and high demand uncertainty, investment in capacity buildup has to be done cautiously. Otherwise either the product’s market diffusion is impeded or the manufacturer is left with unutilized capacity. Using the right information for making capacity augmentation decisions is critical in facing this challenge. In this paper, we propose a method for identifying critical information flows using the system dynamics model of a two-echelon supply chain. The fundamental premise of system dynamics methodology is that (system) structure determines (its) behavior. Using loop dominance analysis method we study the feedback loop structure of the supply chain system. The outcome is a set of dominant loops that determine the dynamics of capacity growth. It is revealed that the delivery delay information has little effect while the loop that connects retail sales with production order affects the dynamics significantly. Modifying this loop yields appropriate capacity augmentation decisions resulting in higher performance. What-if analyses bring out effects of modifying other structural elements. In conclusion, we claim that the information feedback based methodology is general enough to be useful in designing decision support systems for capacity augmentation. The limitations of the model are also discussed and possible extensions identified.     

On solving energy-dependent partitioned eigenvalue problem by genetic algorithm: The case of real symmetric Hamiltonian matrices

An energy-dependent partitioning scheme is explored for extracting a small number of eigenvalues of a real symmetric matrix with the help of genetic algorithm. The proposed method is tested with matrices of different sizes (30 × 30 to 1000 × 1000). Comparison is made with Löwdin’s strategy for solving the problem. The relative advantages and disadvantages of the GA-based method are analyzed     

Working group report: Neutrino and astroparticle physics

This is the report of neutrino and astroparticle physics working group at WHEPP-7. Discussions and work on CP violation in long baseline neutrino experiments, ultra high energy neutrinos, supernova neutrinos and water Cerenkov detectors are discussed.     

Thermal Studies on Ionic Derivatives of Hafnium(IV) Involving Maltol Ligand

A number of ionic chelate complexes of maltol(A) and hafnium(IV) the type[(η₅−C₅H₅)₂HfL]⁺[MCl3]⁻ (B) [HL=maltol; M=Zn(II), Cd(II), Hg(II), Cu(II)]have been synthesized and characterized by spectral studies (IR, UV, ¹H NMR and ¹³C NMR). The stoichiometry of the complexes has been confirmed by conductance measurements. Thermogravimetric (TG) and differential thermal analytical (DTA) studies have been carried out for these complexes and from TG curves, the order, apparent activation energy and apparent activation entropy of the thermal decomposition reactions have been elucidated .The order in each case has been determined to be one and the degree of spontaneity and lability have been inferred from the apparent activation energy and entropy, respectively. Thermal parameters have been correlated with some structural aspects of the complexes concerned. From differential thermal analysis curves, the heat of reaction has been calculated. This revised version was published online in August 2006 with corrections to the Cover Date.