Weak interactions involving organic fluorine: analysis of structural motifs in Flunazirine and Haloperidol

The crystal structure of Flunazirine, an anticonvulsant drug, is analyzed in terms of intermolecular interactions involving fluorine. The structure displays motifs formed by only weak interactions C–H⋯F and C–H⋯π. The motifs thus generated show cavities, which could serve as hosts for complexation. The structure of Flunazirine displays cavities formed by C–H⋯F and C–H⋯π interactions. Haloperidol, an antipsychotic drug, shows F⋯F interactions in the crystalline lattice in lieu of Cl⋯Cl interactions. However, strong O–H⋯N interactions dominate packing. The salient features of the two structures in terms of intermolecular interactions reveal, even though organic fluorine has lower tendency to engage in hydrogen bonding and F⋯F interactions, these interactions could play a significant role in the design of molecular assemblies via crystal engineering.

Structural Variability in the Monofluoroethynylbenzenes Mediated through Interactions Involving ``Organic'' Fluorine

Competition among weak intermolecular interactions can lead to polymorphism, the appearance of various crystalline forms of a substance with comparable cohesive energies. The crystal structures of 2-fluorophenylacetylene (2FPA) and 3-fluorophenylacetylene (3FPA), both of which are liquids at ambient conditions, have been determined by in situ cryocrystallization. Both compounds exhibit dimorphs, with one of the forms observed in common, P2(1), Z = 2 and the other form being Pna2(1), Z = 4 for 2FPA and P2(1)/c, Z = 12 for 3FPA. Variations in the crystal structures of the dimorphs of each of these compounds arise from subtle differences in the way in which weak intermolecular interactions such as C-H center dot center dot center dot pi and C-H center dot center dot center dot F are manifested. The interactions involving ``organic'' fluorine, are entirely different from those in the known structure of 4-fluorophenylacetylene (4FPA), space group P2(1)/c, Z = 4. The commonalities and differences in these polymorphs of 2FPA and 3FPA have been analyzed in terms of supramolecular synthons and extended long-range synthon aufbau module (LSAM) patterns. These structures are compared with the three polymorphs of phenylacetylene, in terms of the T-shaped C-H center dot center dot center dot pi interaction, a feature common to all these structures.

Effects of polarization on study of anomalous VVH interactions at a Linear Collider

We investigate the use of beam polarisation as well as nal state polarisation efects in probing the interaction of the Higgs boson with a pair of heavy vector bosons in the process e+e! ffH, where f is any light fermion. The sensitivity of the International Linear Collider (ILC) operating at ps = 500 GeV, to such V V H(V = W=Z) couplings is examined in a model independent way. The efects of ISR and beamstrahlung are discussed.

Modeling Architecture-OS interactions using Layered Queuing Network Models

The prevalent virtualization technologies provide QoS support within the software layers of the virtual machine monitor(VMM) or the operating system of the virtual machine(VM). The QoS features are mostly provided as extensions to the existing software used for accessing the I/O device because of which the applications sharing the I/O device experience loss of performance due to crosstalk effects or usable bandwidth. In this paper we examine the NIC sharing effects across VMs on a Xen virtualized server and present an alternate paradigm that improves the shared bandwidth and reduces the crosstalk effect on the VMs. We implement the proposed hardwaresoftware changes in a layered queuing network (LQN) model and use simulation techniques to evaluate the architecture. We find that simple changes in the device architecture and associated system software lead to application throughput improvement of up to 60%. The architecture also enables finer QoS controls at device level and increases the scalability of device sharing across multiple virtual machines. We find that the performance improvement derived using LQN model is comparable to that reported by similar but real implementations.

Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies

Single chain fragment variables (ScFvs) have been extensively employed in studying the protein-protein interactions. ScFvs derived from phage display libraries have an additional advantage of being generated against a native antigen, circumventing loss of information on conformational epitopes. In the present study, an attempt has been made to elucidate human chorionic gonadotropin (hCG)-luteinizing hormone (LH) receptor interactions by using a neutral and two inhibitory ScFvs against hCG. The objective was to dock a computationally derived model of these ScFvs onto the crystal structure of hCG and understand the differential roles of the mapped epitopes in hCG-LH receptor interactions. An anti-hCG ScFv, whose epitope was mapped previously using biochemical tools, served as the positive control for assessing the quality of docking analysis. To evaluate the role of specific side chains at the hCG-ScFv interface, binding free energy as well as residue interaction energies of complexes in solution were calculated using molecular mechanics Poisson-Boltzmann/surface area method after performing the molecular dynamic simulations on the selected hCG-ScFv models and validated using biochemical and SPR analysis. The robustness of these calculations was demonstrated by comparing the theoretically determined binding energies with the experimentally obtained kinetic parameters for hCG-ScFv complexes. Superimposition of hCG-ScFv model onto a model of hCG complexed with the 51-266 residues of LH receptor revealed importance of the residues previously thought to be unimportant for hormone binding and response. This analysis provides an alternate tool for understanding the structure-function analysis of ligand-receptor interactions. Proteins 2011;79:3108-3122. (C) 2011 Wiley-Liss, Inc.

Solute solute and solvent solute interactions in solid solutions of Cu+Sn, Au+Sn and Cu+Au+Sn alloys

The chemical potentials of tin in its α-solid solutions with Cu, Au and Cu + Au alloys have been measured using a gas-solid equilibration technique. The variation of the excess chemical potential of tin with its composition in the alloy is related to the solute-solute repulsive interaction, while the excess chemical potential at infinite dilution of the solute is a measure of solvent-solute interaction energies. It is shown that solute-solute interaction is primarily determined by the concentration of (s + p) electrons in the conduction band, although the interaction energies are smaller than those predicted by either the rigid band model or calculation based on Friedel oscillations in the potential function. Finally, the variation of the solvent-solute interaction with solvent composition in the ternary system can be accounted for in terms of a quasi-chemical treatment which takes into account the clustering of the solvent atoms around the solute.

Solute-solute and solute-solvent interactions in transition metal alloys: Pt-Ti system

An isothermal section of the phase diagram for (silver + rhodium + oxygen) at T = 1173 K has been established by equilibration of samples representing twelve different compositions, and phase identification after quenching by optical and scanning electron microscopy (s.e.m.), X-ray diffraction (x.r.d.), and energy dispersive analysis of X-rays (e.d.x.), Only one ternary oxide, AgRhO2, was found to be stable and a three phase region involving Ag, AgRhO2 and Rh2O3 was identified. The thermodynamic properties of AgRhO2 were measured using a galvanic cell in the temperature range 980 K to 1320 K. Yttria-stabilized zirconia was used as the solid electrolyte and pure oxygen gas at a pressure of 0.1 MPa was used as the reference electrode. The Gibbs free energy of formation of the ternary oxide from the elements, ΔfGo (AgRhO2), can be represented by two linear equations that join at the melting temperature of silver. In the temperature range 980 K to 1235 K, ΔfGo(AgRhO2)/(J . mol-1) = -249080 + 179.08 T/K (±120). Above the melting temperature of silver, in the temperature range 1235 K to 1320 K, ΔfGo(AgRhO2)/(J . mol-1) = -260400 + 188.24 T/K (±95). The thermodynamic properties of AgRhO2 at T = 298.15 K were evaluated from the high temperature data. The chemical potential diagram for (silver + rhodium + oxygen) at T = 1200 K was also computed on the basis of the results of this study.

Multi-scale interactions and predictability of the Indian summer monsoon

Following the seminal work of Charney and Shukla (198 1), the tropical climate is recognised to be more predictable than extra tropical climate as it is largely forced by 'external' slowly varying forcing and less sensitive to initial conditions. However, the Indian summer monsoon is an exception within the tropics where 'internal' low frequency (LF) oscillations seem to make significant contribution to its interannual variability (IAV) and makes it sensitive to initial conditions. Quantitative estimate of contribution of 'internal' dynamics to IAV of Indian monsoon is made using long experiments with an atmospheric general circulation model (AGCM) and through analysis of long daily observations. Both AGCM experiments and observations indicate that more than 50% of IAV of the monsoon is contributed by 'internal' dynamics making the predictable signal (external component) burried in unpredictable noise (internal component) of comparable amplitude. Better understanding of the nature of the 'internal' LF variability is crucial for any improvement in predicition of seasonal mean monsoon. Nature of 'internal' LF variability of the monsoon and mechanism responsible for it are investigated and shown that vigorous monsoon intraseasonal oscillations (ISO's) with time scale between 10-70 days are primarily responsible for generating the 'internal' IAV. The monsoon ISO's do this through scale interactions with synoptic disturbances (1-7 day time scale) on one hand and the annual cycle on the other. The spatial structure of the monsoon ISO's is similar to that of the seasonal mean. It is shown that frequency of occurance of strong (weak) phases of the ISO is different in different seasons giving rise to stronger (weaker) than normal monsoon. Change in the large scale circulation during strong (weak) phases of the ISO make it favourable (inhibiting) for cyclogenesis and gives rise to space time clustering of synoptic activity. This process leads to enhanced (reduced) rainfall in seasons of higher frequency of occurence strong (weak) phases of monsoon ISO.

Some mechanisms of tribofilm formation in metal/metal and ceramic/metal sliding interactions

Tribological interaction often generates new structures and materials which form the interface between the sliding pair. The new material designated tribofilm here may be protective or tribologically deleterious. The tribofilm plays a major role in determining the friction and wear of the interaction. Here, we give three examples: mechanically mixed, chemically generated and thermally activated, of tribofilms formed in three different tribological systems and speculate on the mechanism of their formation.

Exact entanglement studies of strongly correlated systems: role of long-range interactions and symmetries of the system

We study the bipartite entanglement of strongly correlated systems using exact diagonalization techniques. In particular, we examine how the entanglement changes in the presence of long-range interactions by studying the Pariser-Parr-Pople model with long-range interactions. We compare the results for this model with those obtained for the Hubbard and Heisenberg models with short-range interactions. This study helps us to understand why the density matrix renormalization group (DMRG) technique is so successful even in the presence of long-range interactions. To better understand the behavior of long-range interactions and why the DMRG works well with it, we study the entanglement spectrum of the ground state and a few excited states of finite chains. We also investigate if the symmetry properties of a state vector have any significance in relation to its entanglement. Finally, we make an interesting observation on the entanglement profiles of different states (across the energy spectrum) in comparison with the corresponding profile of the density of states. We use isotropic chains and a molecule with non-Abelian symmetry for these numerical investigations.

A model investigation of vegetation-atmosphere interactions on a millennial timescale

A terrestrial biosphere model with dynamic vegetation capability, Integrated Biosphere Simulator (IBIS2), coupled to the NCAR Community Atmosphere Model (CAM2) is used to investigate the multiple climate-forest equilibrium states of the climate system. A 1000-year control simulation and another 1000-year land cover change simulation that consisted of global deforestation for 100 years followed by re-growth of forests for the subsequent 900 years were performed. After several centuries of interactive climate-vegetation dynamics, the land cover change simulation converged to essentially the same climate state as the control simulation. However, the climate system takes about a millennium to reach the control forest state. In the absence of deep ocean feedbacks in our model, the millennial time scale for converging to the original climate state is dictated by long time scales of the vegetation dynamics in the northern high latitudes. Our idealized modeling study suggests that the equilibrium state reached after complete global deforestation followed by re-growth of forests is unlikely to be distinguishable from the control climate. The real world, however, could have multiple climate-forest states since our modeling study is unlikely to have represented all the essential ecological processes (e. g. altered fire regimes, seed sources and seedling establishment dynamics) for the reestablishment of major biomes.