On dynamics of velocity vector potential in incompressible fluids

An elegant quaternionic formulation is given for the Lagrangian advection equation for velocity vector potential in fluid dynamics. At first we study the topological significance of a restricted conserved quantity viz., stream-helicity and later more realistic configuration of open streamlines is figured out. Also, using Clebsch parameterisation of the velocity vector potential yet another physical significance for the stream-helicity is provided. Finally we give a Nambu-Poisson formalism of the Lagrangian advection equation for velocity vector potential.     

Accelerating molecular dynamic simulation on the cell processor and Playstation 3

Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing on implicit solvation models. We conclude with a comparison of improved performance on the PS3's Cell processor over more traditional processors.     

On the Jacobi Last Multiplier, integrating factors and the Lagrangian formulation of differential equations of the Painlevé–Gambier classification

We use a formula derived almost seventy years ago by Madhav Rao connecting the Jacobi Last Multiplier of a second-order ordinary differential equation and its Lagrangian and determine the Lagrangians of the Painlevé equations. Indeed this method yields the Lagrangians of many of the equations of the Painlevé–Gambier classification. Using the standard Legendre transformation we deduce the corresponding Hamiltonian functions. While such Hamiltonians are generally of non-standard form, they are found to be constants of motion. On the other hand for second-order equations of the Liénard class we employ a novel transformation to deduce their corresponding Lagrangians. We illustrate some particular cases and determine the conserved quantity (first integral) resulting from the associated Noetherian symmetry. Finally we consider a few systems of second-order ordinary differential equations and deduce their Lagrangians by exploiting again the relation between the Jacobi Last Multiplier and the Lagrangian.     

Adsorption behavior of rhodamine B on Rhizopus oryzae biomass

The removal of a carcinogenic dye rhodamine B (C. I. 45170) from wastewater by biomass of different moulds and yeasts is described. Among all of the fungal species tested, the biomass of Rhizopus oryzae MTCC 262 is found to be the most effective. Dye adsorption reaches maximum with the biomass harvested from the early stationary phase of growth. The optimum temperature and pH for adsorption are observed to be 40 degrees C and 7.0, respectively. The adsorption rate is very fast initially and attains equilibrium after 5 h. The adsorption isotherm follows the Langmuir isotherm model satisfactorily within the studied dye concentration range. Of the different metabolic inhibitors tested, 2,4-ditrophenol (DNP) and N,N'-dicyclohexylcarbodiimide (DCCD) decrease dye adsorption by approximately 30% suggesting the role of energy metabolism in the process. Spectrophotometric study indicates that the removal of rhodamine B by R. oryzae biomass involves an adsorption process. Scanning (SEM) and transmission (TEM) electron microscopic investigations have been carried out to understand the probable mechanism of the dye-biomass interaction.     

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics

We present a technique for biomolecular free energy calculations that exploits highly parallelized sampling to significantly reduce the time to results. The technique combines free energies for multiple, nonoverlapping configurational macrostates and is naturally suited to distributed computing. We describe a methodology that uses this technique with docking, molecular dynamics, and free energy perturbation to compute absolute free energies of binding quickly compared to previous methods. The method does not require a priori knowledge of the binding pose as long as the docking technique used can generate reasonable binding modes. We demonstrate the method on the protein FKBP12 and eight of its inhibitors.     

A theoretical study of antioxidant activity of some Schiff bases derived from biologically important phenolic aldehydes and phenylenediamines

Because of their numerous biological as well as industrial importance, the study of Schiff bases is an emerging field for the researchers, in recent time. In this study, we have designed some Schiff bases derived from biologically important precursors. The antioxidant activities of the designed compounds are thoroughly studied theoretically using density functional theory taking various parameters like bond dissociation enthalpy, ionization enthalpy, proton dissociation enthalpy, and electron transfer enthalpy followed by the study of effects of solvent, spin density, and molecular orbital on antioxidant activity of the compounds. The comparison of antioxidant activity of the compounds with that of phenol and their parent aldehydes reveals the superior antioxidant activity of the designed compounds. This study contributes towards the information of an important bridge between bioorganic and computational chemistry.     

Inhomogeneous Heisenberg spin chain and quantum vortex filament as non-holonomically deformed NLS systems

Through the Hasimoto map, various dynamical systems can be mapped to different integrodifferential generalizations of Nonlinear Schrödinger (NLS) family of equations some of which are known to be integrable. Two such continuum limits, corresponding to the inhomogeneous XXX Heisenberg spin chain [J. Phys. C 15, L1305 (1982)] and that of a thin vortex filament moving in a superfluid with drag [Eur. Phys. J. B 86, 275 (2013) 86; Phys. Rev. E 91, 053201 (2015)], are shown to be particular non-holonomic deformations (NHDs) of the standard NLS system involving generalized parameterizations. Crucially, such NHDs of the NLS system are restricted to specific spectral orders that exactly complements NHDs of the original physical systems. The specific non-holonomic constraints associated with these integrodifferential generalizations additionally posses distinct semi-classical signature.     

Boundaries of Anion/Naphthalenediimide Interactions: From Anion-π Interactions to Anion-Induced Charge-Transfer and Electron-Transfer Phenomena

The recent emergence of anion-π interactions has added a new dimension to supramolecular chemistry of anions. Yet, after a decade since its inception, actual mechanisms of anion-π interactions remain highly debated. To elicit a complete and accurate understanding of how different anions interact with π-electron-deficient 1,4,5,8-naphthalenediimides (NDIs) under different conditions, we have extensively studied these interactions using powerful experimental techniques. Herein, we demonstrate that, depending on the electron-donating abilities (Lewis basicity) of anions and electron-accepting abilities (π-acidity) of NDIs, modes of anion-NDI interactions vary from extremely weak non-chromogenic anion-π interactions to chromogenic anion-induced charge-transfer (CT) and electron-transfer (ET) phenomena. In aprotic solvents, electron-donating abilities of anions generally follow their Lewis basicity order, whereas π-acidity of NDIs can be fine-tuned by installing different electron-rich and electron-deficient substituents. While strongly Lewis basic anions (OH(-) and F(-)) undergo thermal ET with most NDIs, generating NDI(?-) radical anions and NDI(2-) dianions in aprotic solvents, weaker Lewis bases (AcO(-), H(2)PO(4)(-), Cl(-), etc.) often require the photoexcitation of moderately π-acidic NDIs to generate the corresponding NDI(?-) radical anions via photoinduced ET (PET). Poorly Lewis basic I(-) does not participate in thermal ET or PET with most NDIs (except with strongly π-acidic core-substituted dicyano-NDI) but forms anion/NDI CT or anion-π complexes. We have looked for experimental evidence that could indicate alternative mechanisms, such as a Meisenheimer complex or CH···anion hydrogen-bond formation, but none was found to support these possibilities.     

Cd(ii)-triggered excimer-monomer conversion of a pyrene derivative: time dependent red-shift of monomer emission with cell staining application

An efficient fluorescent probe (E)-N1-((E)-2-((pyren-7-yl)methyleneamino)ethyl)-N2-((pyren-7-yl)methylene)ethane-1,2-diamine (L) has been synthesized by a facile one-step condensation reaction. L can selectively detect Cd(2+) in presence of other common metal ions in 0.1 M HEPES buffered DMSO-water (4?:?1, v/v) medium. The detection limit of Cd(2+) is 1.8 × 10(-8) M. Cd(2+) can effectively convert the excimer emission of L into its monomer emission which in turn exhibits a time-dependent red-shift.