Potential energy curve for isomerization of N2H2 and C2H4 using the improved virtual orbital multireference Møller-Plesset perturbation theory

Multireference M?ller-Plesset (MRMP) perturbation theory [K. Hirao, Chem. Phys. Lett. 190, 374 (1992)] is modified to use improved virtual orbitals (IVOs) and is applied to study ground state potential energy curves for isomerization and dissociation of the N2H2 and C2H4 molecules. In contrast to traditional MRMP or multistate multiconfiguration quasidegenerate perturbation theory where the reference functions are obtained from (often difficult to converge) state averaged multiconfiguration self-consistent field methods, our reference functions are represented in terms of computationally efficient IVOs. For convenience in comparisons with other methods, a first order complete active space configuration interaction (CASCI) calculation with the IVOs is followed by the use of the IVOs in MRMP to incorporate residual electron correlation effects. The potential energy curves calculated from the IVO-MRMP method are compared with computations using state-of-the-art coupled cluster singles and doubles (CCSD) methods and variants thereof to assess the efficacy of the IVO-MRMP scheme. The present study clearly demonstrates that unlike the CCSD and its variants, the IVO-MRMP approach provides smooth and reliable ground state potential energy curves for isomerization of these systems. Although the rigorously size-extensive completely renormalized CC theory with noniterative triples corrections (CR-CC(2,3)) likewise provides relatively smooth curves, the CR-CC(2,3) calculations overestimate the cis-trans barrier height for N2H2. The ground state spectroscopic constants predicted by the IVO-CASCI method agree well with experiment and with other highly correlated ab initio methods.     

Identification of Druggable Targets for Acinetobacter baumannii Via Subtractive Genomics and Plausible Inhibitors for MurA and MurB

Emergence of the multidrug-resistant pathogens has rendered the current therapies ineffective thereby, resulting in the need for new drugs and drug targets. The accumulating protein sequence data has initiated a drift from classical drug discovery protocols to structure-based drug designing. In the present study, in silico subtractive genomics approach was implemented to find a set of potential drug targets present in an opportunist bacterial pathogen, Acinetobacter baumannii (A. baumannii). Out of the 43 targets identified, further studies for protein model building and lead-inhibitor identification were carried out on two cell-essential targets, MurA and MurB enzymes (of A. baumannii designated as MurA_Ab and MurB_Ab) involved in the peptidoglycan biosynthesis pathway of bacteria. The homology model built for each of them was further refined and validated using various available programs like PROCHECK, Errat, ProSA energy plots, etc. Compounds showing activity against MurA and MurB enzymes of other organisms were collected from the literature and were docked into the active site of MurA_Ab and MurB_Ab enzymes. Three inhibitors namely, T6361, carbidopa, and aesculin, showed maximum Glide score, hydrogen bonding interactions with the key amino acid residues of both the enzymes and acceptable ADME properties. Furthermore, molecular dynamics simulation studies on MurA_Ab–T6361 and MurB_Ab–T6361 complexes suggested that the ligand has a high binding affinity with both the enzymes and the hydrogen bonding with the key residues were stable in the dynamic condition also. Therefore, these ligands have been propsed as dual inhibitors and promising lead compounds for the drug design against MurA_Ab and MurB_Ab enzymes.     

Universal occurrence of the phase-flip bifurcation in time-delay coupled systems

Recently, the phase-flip bifurcation has been described as a fundamental transition in time-delay coupled, phase-synchronized nonlinear dynamical systems. The bifurcation is characterized by a change of the synchronized dynamics from being in-phase to antiphase, or vice versa; the phase-difference between the oscillators undergoes a jump of pi as a function of the coupling strength or the time delay. This phase-flip is accompanied by discontinuous changes in the frequency of the synchronized oscillators, and in the largest negative Lyapunov exponent or its derivative. Here we illustrate the phenomenology of the bifurcation for several classes of nonlinear oscillators, in the regimes of both periodic and chaotic dynamics. We present extensive numerical simulations and compute the oscillation frequencies and the Lyapunov spectra as a function of the coupling strength. In particular, our simulations provide clear evidence of the phase-flip bifurcation in excitable laser and Fitzhugh-Nagumo neuronal models, and in diffusively coupled predator-prey models with either limit cycle or chaotic dynamics. Our analysis demonstrates marked jumps of the time-delayed and instantaneous fluxes between the two interacting oscillators across the bifurcation; this has strong implications for the performance of the system as well as for practical applications. We further construct an electronic circuit consisting of two coupled Chua oscillators and provide the first formal experimental demonstration of the bifurcation. In totality, our study demonstrates that the phase-flip phenomenon is of broad relevance and importance for a wide range of physical and natural systems.     

Revisiting the ‘cis-effect’ in 1,2-difluoro derivatives of ethylene and diazene using ab initio multireference methods

The relative stabilities of cis- and trans- isomers of 1,2-difluoroethylene and 1,2-difluorodiazene have been studied via the state-specific multireference coupled cluster (SS-MRCC) method and its perturbative counterpart through the computation of the optimised structures and corresponding energies. Despite the existence of several cis-destabilising mechanisms, present calculations reveal the energetic preference of the cis- isomer (the cis-effect) for the systems considered here. Differences in structural parameters and vibrational frequencies among cis- and trans- isomers have been discussed. Very good agreement of our estimates has been found with the benchmark theoretical and experimental results. The SS-MRCC methods produce a smooth and consistent behaviour across the entire torsional surface for the cis–trans isomerisation indicating that the method has sufficient flexibility to model large changes in electronic structure that accompany chemical changes.     

Hybrid spectral finite difference simulations of stratified turbulent flows on distributed memory architectures

A method for efficient implementation of a combined spectral finite difference algorithm for computation of incompressible stratified turbulent flows on distributed memory computers is presented. The solution technique is the fractional step method with a semi-implicit time advancement scheme. A single-programme multiple-data abstraction is used in conjunction with a static data-partitioning scheme. The distributed FFTs required in the explicit step are based on the transpose method and the large sets of independent tridiagonal systems of equations arising in the implicit steps are solved using the pipelined Thomas algorithm. A speed-up analysis of a model problem is presented for three partitioning schemes, namely unipartition, multipartition and transpose partition. It is shown that the unipartitioning scheme is best suited for this algorithm. Performance measurements of the overall as well as individual stages of the algorithm are presented for several different grids and are discussed in the context of associated dependency and communication overheads. An unscaled speed-up efficiency of up to 91% on doubling the number of processors and up to 60% on an eightfold increase in the number of processors was obtained on the Intel Paragon and iPSC/860 Hypercube. Absolute performance of the code was evaluated by comparisons with performance on the Cray-YMP. On 128 Paragon processors, performance up to five times that of a single-processor Cray-YMP was obtained. The validation of the method and results of grid refinement studies in stably stratified turbulent channel flows are presented. © 1997 John Wiley & Sons, Ltd.     

Dynamics of individual single-walled carbon nanotubes in water by real-time visualization

Individual single-walled carbon nanotubes (SWNTs) in aqueous suspension are visualized directly by fluorescence video microscopy. The fluorescent tagging is simple, biocompatible, and does not modify the SWNTs. The dynamics of individual SWNTs in water are observed and quantified for the first time. We measure the confined rotational diffusion coefficient and find it in reasonable agreement with predictions based on confined diffusion of dilute Brownian rods. We determine the critical concentration at which SWNTs in suspensions start interacting. By analyzing the fluctuating shape of SWNTs in the 3 to 5 microm range, we determine that their persistence length ranges between 32 and 174 microm, in agreement with theoretical estimates; thus, commonly available SWNTs in liquids can be considered as rigid Brownian rods in the absence of imposed external fields or self-attractive forces.     

Generalized viscosity implicit scheme with Meir-Keeler contraction for asymptotically nonexpansive mapping in Banach spaces

Numerical Algorithms - Our focus in this paper is on introducing an iterative scheme based on the generalized implicit method and viscosity approximation method with Meir-Keeler contraction for...     

A 1D Cu(II) coordination polymer exhibiting ferromagnetic interactions and a mononuclear Cu(II) complex of substituted pyrazole carboxylic acids: Synthesis, characterization and crystal structure

Reaction of 2 equiv. amount of copper(II) nitrate hexahydrate with 1 equiv. of 5-methyl-1-pyridin-2-yl-1H-pyrazole-3-carboxylic acid (PyPzCA) in presence of triethyl amine base afforded a 1D coordination polymeric compound [Cu₂(PyPzCA)₂(H₂O)₃(NO₃)]NO₃·H₂O (1). Whereas, the same reaction when repeated with 1-(4,6-dimethyl-pyrimidin-2-yl)-5-methyl-1H-pyrazole-3-carboxylic acid (PymPzCA) instead of PyPzCA, a mononuclear compound [Cu(PymPzCA)]·2H₂O·NEt₃ (2) is formed. Both the complexes are crystallographically characterized. In 1, both the copper atoms (Cu1 and Cu2) have distorted square pyramidal geometry with N₂O₃ chromophore while, in 2, the central copper atom has a distorted trigonal bipyramidal geometry with N₄O chromophore. Complex 1, is a 1D coordination polymer where the metal centers being far apart and are involved in a weak ferromagnetic interaction which is quite unexpected.