Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study

Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G7) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the 06 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. These quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 A from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Na+ counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. In the absence of any coordinated ion, due to strong mutual repulsion, 06 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures

Temperature dependent free energy surface of polymer folding from equilibrium and quench studies

Langevin dynamics simulation studies have been employed to calculate the temperature dependent free energy surface and folding characteristics of a 500 monomer long linear alkane (polyethylene) chain with a realistic interaction potential. Both equilibrium and temperature quench simulation studies have been carried out. Using the shape anisotropy parameter (S) of the folded molecule as the order parameter, we find a weakly first order phase transition between the high-temperature molten globule and low-temperature rodlike crystalline states separated by a small barrier of the order of k(B)T. Near the melting temperature (580 K), we observe an intriguing intermittent fluctuation with pronounced ``1/f noise characteristics'' between these two states with large difference in shape and structure. We have also studied the possibilities of different pathways of folding to states much below the melting point. At 300 K starting from the all-trans linear configuration, the chain folds stepwise into a very regular fourfold crystallite with very high shape anisotropy. Whereas, when quenched from a high temperature (900 K) random coil regime, we identify a two step transition from the random coiled state to a molten globulelike state and, further, to a anisotropic rodlike state. The trajectory reveals an interesting coupling between the two order parameters, namely, radius of gyration (R-g) and the shape anisotropy parameter (S). The rodlike final state of the quench trajectory is characterized by lower shape anisotropy parameter and significantly larger number of gauche defects as compared to the final state obtained through equilibrium simulation starting from all-trans linear chain. The quench study shows indication of a nucleationlike pathway from the molten globule to the rodlike state involving an underlying rugged energy landscape. (C) 2010 American Institute of Physics. doi:10.1063/1.3509398]

Energy for the Developing World

Described are methods which can be used by developing countries to affordably obtain the energy without ruining the environment. The approaches mix efficient end-use technologies with modest increases in generating capacity. (CW).

Electron energy loss spectroscopic study of Cr(CO)6, Mo(CO)6 and W(CO)6 in the vapour phase

Electron energy loss spectra (EELS) of Cr, Mo and W hexacarbonyls in the vapour phase are reported. Most of the bands observed are similar to those in optical spectra, but the two high energy transitions in the 9·8–11·2 eV region are reported here for the first time. Based on the orbital energies from the ultraviolet photoelectron spectra and the electronic transition energies from EELS and earlier optical studies, the molecular energy level schemes of these molecules are constructed.

Energy efficiencies of end-use devices in an electro-metallurgical industry: A critical study

The inefficient use of energy in a large number of industries is slowly developing into a major energy crisis in the already power-starved Karnataka State, India. This study attempts to bring out the present inefficient pattern of energy use in an electro-metallurgical industry. It also brings out the considerable scope for energy conservation, especially by increasing the efficiency of the end-use devices used. This concept, when extended to other industries, wherein increasing efficiency of the end-use devices would provide the desired end results with small energy input. This, in turn, would result in a slower rate of energy growth as well as saving in energy use.

A fault-tolerant multi-transputer architecture

A new fault-tolerant multi-transputer architecture capable of tolerating failure of any one component in the system is described. In the proposed architecture the processing nodes are automatically reconfigured in the event of a fault and the computations continue from the stage where the fault occurred. The process of reconfiguration is transparent to the user, and the identity of the failed component is communicated to the user along with the results of computations. Parallel solution of a typical engineering problem involving solution of Laplace's equation by the boundary element method has been implemented. The performance of the architecture in the event of faults has been investigated.

Analysis of energy utilization in the grain mill sector in Karnataka

Energy is a major constituent of a small-scale industry such as grain mills. Based on a sample survey of several mills spread over Karnataka, a state in India, a number of energy analyses were conducted primarily to establish relationships and secondarily to look at them in more detail. Initially specific energy consumption (SEC) was computed for all industries so as to compare their efficiencies of energy use. A wide disparity exists in SEC among various grain mills. In order to understand the disparities better, regression analyses were performed on the variables energy and production, SEC and production, and energy/SEC with percentage production capacity utilization. The studies show that smaller range industries have lower capacity utilization. This paper also examines the energy savings possible by shifting industries from the lower production ranges to the next higher range (thereby utilizing installed production capacity optimally). This leads to an overall energy capacity saving of 23.12% for the foodgrain sector and 18.67% for the paddy dehusking subgroup. If this is extrapolated to the whole state, we obtain a saving of 55 million kWh.

A structure-preserving energy function for stability analysis of AC/DC systems

Direct stability analysis ofAC/DC power systems using a structure-preserving energy function (SPEF) is proposed in this paper. The system model considered retains the load buses thereby enabling the representation of nonlinear voltage dependent loads. TheHVDC system is represented with the same degree of detail as is normally done in transient stability simulation. The converter controllers can be represented by simplified or detailed models. Two or multi-terminalDC systems can be considered. The stability analysis is illustrated with a 3-machine system example and encouraging results have been obtained.

Critical phenomena in polymer solutions: Scaling of the free energy

The thermodynamics of monodisperse solutions of polymers in the neighborhood of the phase separation temperature is studied by means of Wilson’s recursion relation approach, starting from an effective ϕ4 Hamiltonian derived from a continuum model of a many‐chain system in poor solvents. Details of the chain statistics are contained in the coefficients of the field variables ϕ, so that the parameter space of the Hamiltonian includes the temperature, coupling constant, molecular weight, and excluded volume interaction. The recursion relations are solved under a series of simplifying assumptions, providing the scaling forms of the relevant parameters, which are then used to determine the scaling form of the free energy. The free energy, in turn, is used to calculate the other singular thermodynamic properties of the solution. These are characteristically power laws in the reduced temperature and molecular weight, with the temperature exponents being the same as those of the 3d Ising model. The molecular weight exponents are unique to polymer solutions, and the calculated values compare well with the available experimental data.

Excitation energy transfer in covalently linked pheophorbied—porphyrin systems

Steady-state fluorescence, lifetime measurements and time-resolved absorption spectra of the covalently linked hetero dimers consisting of pheophorbide and porphyrin revealed rapid (1011–1012s−1) and efficient singlet—singlet excitation energy transfer from porphyrin unit to pheophorbide.

Ferrous-iron induces lipid peroxidation with little damage to energy transduction in mitochondria

Addition of ferrous sulfate, but not ferric chloride, in micromolar concentrations to rat liver mitochondria induced high rates of consumption of oxygen. The oxygen consumed was several times in excess of the reducing capacity of ferrous-iron (O: Fe ratios 5�8). This occurred in the absence of NADPH or any exogenous oxidizable substrate. The reaction terminated on oxidation of ferrous ions. Malondialdehyde (MDA), measured as thiobarbituric acid-reacting material, was produced indicating peroxidation of lipids. The ratio of O2: MDA was about 4: 1. Pretreatment of mitochondria with ferrous sulfate decreased the rate of oxidation (state 3) with glutamate (+malate) as the substrate by about 40% but caused little damage to energy tranduction process as represented by ratios of ADP: O and respiratory control, as well as calcium-stimulated oxygen uptake and energy-dependent uptake of [45Ca]-calcium. Addition of succinate or ubiquinone decreased ferrous iron-induced lipid peroxidation in intact mitochondria. In frozen-thawed mitochondria, addition of succinate enhanced lipid peroxidation whereas ubiquinone had little effect. These results suggest that ferrous-iron can cause peroxidation of mitochondrial lipids without affecting the energy transduction systems, and that succinate and ubiquinone can offer protection from damage due to such ferrous-iron released from the stores within the cells.