A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization

We present a new computationally efficient method for large-scale polypeptide folding using coarse-grained elastic networks and gradient-based continuous optimization techniques. The folding is governed by minimization of energy based on Miyazawa–Jernigan contact potentials. Using this method we are able to substantially reduce the computation time on ordinary desktop computers for simulation of polypeptide folding starting from a fully unfolded state. We compare our results with available native state structures from Protein Data Bank (PDB) for a few de-novo proteins and two natural proteins, Ubiquitin and Lysozyme. Based on our simulations we are able to draw the energy landscape for a small de-novo protein, Chignolin. We also use two well known protein structure prediction software, MODELLER and GROMACS to compare our results. In the end, we show how a modification of normal elastic network model can lead to higher accuracy and lower time required for simulation.

Contribution of different physical forces to the disjoining pressure of a thin water film being pressed by an oil droplet

With an objective to understand the nature of forces which contribute to the disjoining pressure of a thin water film on a steel substrate being pressed by an oil droplet, two independent sets of experiments were done. (i) A spherical silica probe approaches the three substrates; mica, PTFE and steel, in a 10 mM electrolyte solution at two different pHs (3 and 10). (ii) The silica probe with and without a smeared oil film approaches the same three substrates in water (pH = 6). The surface potential of the oil film/water was measured using a dynamic light scattering experiment. Assuming the capacity of a substrate for ion exchange the total interaction force for each experiment was estimated to include the Derjaguin-Landau-Verwey-Overbeek (DLVO) force, hydration repulsion, hydrophobic attraction and oil-capillary attraction. The best fit of these estimates to the force-displacement characteristics obtained from the two sets of experiment gives the appropriate surface potentials of the substrates. The procedure allows an assessment of the relevance of a specific physical interaction to an experimental configuration. Two of the principal observations of this work are: (i) The presence of a surface at constant charge, as in the presence of an oil film on the probe, significantly enhances the counterion density over what is achieved when both the surfaces allow ion exchange. This raises the corresponding repulsion barrier greatly. (ii) When the substrate surface is wettable by oil, oil-capillary attraction contributes substantially to the total interaction. If it is not wettable the oil film is deformed and squeezed out. (C) 2010 Elsevier Inc. All rights reserved.

Photocytotoxicity and DNA cleavage activity of L-arg and L-lys Schiff base oxovanadium(IV) complexes having phenanthroline bases

Oxovanadium(IV) complexes [VO(sal-argH)(B)] Cl (1-3) and [VO(sal-lysH)(B)] Cl (4-6), where sal-argH2 and sal-lysH(2) are N-salicylidene-L-arginine and N-salicylidene-L-lysine Schiff bases and B is a phenanthroline base, viz. 1,10-phenanthroline (phen in 1 and 4); dipyrido[3,2-d: 2', 3'-f] quinoxaline (dpq in 2 and 5) and dipyrido[3,2-a: 2', 3'-c] phenazine (dppz in 3 and 6), have been prepared, characterized and their DNA photocleavage activity studied. Complex 1, characterized by X-ray crystallography, shows the presence of a vanadyl group in VIVO3N3 coordination geometry with a tridentate Schiff base having a pendant guanidinium moiety and bidentate phen ligand. The complexes exhibit a d-d band at similar to 715 nm in 20% DMF-Tris-HCl buffer. The complexes are redox active showing cathodic and anodic responses near -1.0 V and 0.85 V (vs. SCE) for the V(IV)-V(III) and V(V)-V(IV) couples, respectively, in DMF-Tris-HCl buffer. The complexes bind to calf thymus DNA giving Kb values in the range of 3.8 x 10(4) to 1.6 x 10(5) M-1. Thermal denaturation and viscosity data suggest DNA groove binding nature of the complexes. The complexes do not show any `chemical nuclease'' activity in dark in the presence of 3-mercaptopropionic acid or H2O2. The dpq and dppz complexes are efficient photocleavers of plasmid DNA in UV-A (365 nm) and red light (676 nm) via singlet oxygen pathway. The dppz complexes exhibit photocytotoxicity in HeLa cancer cells giving IC50 values of 15.4 mu M for 3 and 17.5 mu M for 6 in visible light while being non-toxic in dark giving IC50 values of > 100 mu M.

Synergistic use of thermogravimetric and electrochemical techniques for thermodynamic study of TiOx (1.67 <= x <= 2.0) at 1573 K

A thermodynamic study of the Ti-O system at 1573 K has been conducted using a combination of thermogravimetric and emf techniques. The results indicate that the variation of oxygen potential with the nonstoichiometric parameter delta in stability domain of TiO2-delta with rutile structure can be represented by the relation, Delta mu o(2) = -6RT In delta - 711970(+/-1600) J/mol. The corresponding relation between non-stoichiometric parameter delta and partial pressure of oxygen across the whole stability range of TiO2-delta at 1573 K is delta proportional to P-O2(-1/6). It is therefore evident that the oxygen deficient behavior of nonstoichiometric TiO2-delta is dominated by the presence of doubly charged oxygen vacancies and free electrons. The high-precision measurements enabled the resolution of oxygen potential steps corresponding to the different Magneli phases (Ti-n O2n-1) up to n = 15. Beyond this value of n, the oxygen potential steps were too small to be resolved. Based on composition of the Magneli phase in equilibrium with TiO2-delta, the maximum value of n is estimated to be 28. The chemical potential of titanium was derived as a function of composition using the Gibbs-Duhem relation. Gibbs energies of formation of the Magneli phases were derived from the chemical potentials of oxygen and titanium. The values of -2441.8(+/-5.8) kJ/mol for Ti4O7 and -1775.4(+/-4.3) kJ/mol for Ti3O5 Obtained in this study refine values of -2436.2(+/-26.1) kJ/mol and-1771.3(+/-6.9) kJ/mol, respectively, given in the JANAF thermochemical tables.

Spin and mass content of linearized Poincaré gauge theories

A unified gauge theory of massless and massive spin-2 fields is of considerable current interest. The Poincaré gauge theories with quadratic Lagrangian are linearized, and the conditions on the parameters are found which will lead to viable linear theories with massive gauge particles. As well as the 2+ massless gravitons coming from the translational gauge potential, the rotational gauge potentials, in the linearized limit, give rise to 2+ and 2− particles of equal mass, as well as a massive pseudoscalar.

Use of the Nasicon/Na2SO4 couple in a solid state sensor for SOx (x=2,3)

The e.m.f. of a concentration cell for SO x (x=2,3)-O2 incorporating Nasicon as the main solid electrolyte has been measured in the temperature range 720 to 1080 K. The cell arrangement can be represented as,$$Pt, O'_2 + SO'_2 + SO'_3 \left| {Na_2 SO_4 \left\| {\left. {Nasicon} \right\|} \right.} \right.\left. {Na_2 SO_4 } \right|SO''_3 + SO''_2 + O''_2 , Pt$$ The Na2SO4 acts both as an auxiliary electrode, converting chemical potentials of SO x and O2 to equivalent sodium potentials, and as an electrolyte. The presence of Na2SO4 provides partial protection of Nasicon from chemical reaction with gas mixtures containing SO x . The open circuit e.m.f. of the cell is in close agreement with values given by the Nernst equation. For certain fixed inlet gas compositions of SO2+O2, the e.m.f. varies non-linearly with temperature. The intrinsic response time of the cell to step changes in gas composition is estimated to vary from sim2.0 ksec at 723K to sim 0.2 ksec at 1077K. The cell functions well for large differences in partial pressures of SO3(pPrimeSO 3/pprimeSO 3ap104) at the electrodes.

An SOx (x = 2, 3) sensor using ?-alumina/Na2SO4 couple

A solid-state sensor for SOx (x = 2, 3) species has been designed using ?-alumina as the solid electrolyte and Na2SO4 as the auxiliary electrode. The measured e.m.f. of the cell Pt, O?2 + SO?2 + SO?3|Na2SO4short parallel?-aluminashort parallelNa2SO4|SO?3 + SO?2 + O?2, PT in the temperature range 700 K to 1150 K agrees well with values calculated using the Nernst equation. The sodium sulphate acts both as a protective covering, preventing direct access of the gaseous SOx species to the ?-alumina electrolyte, and as an auxiliary electrode, converting chemical potentials of SOx species and O2 into an equivalent sodium potential. The open-circuit e.m.f. varies non-linearly with temperature for fixed composition of inlet gas mixtures containing SO2, O2 and Ar. The response time (t0.99) of the cell varies between 1.9 ks at 750 K and 0.06 ks at 1100 K. The e.m.f. response is faster when the partial pressure of SOx at the electrode is increased than when it is decreased.

Electrochemical reduction of Cu(II)-CyDTA complex at dropping mercury electrode. An impedance approach

The electrochemical reduction of Cu(II)-CyDTA (CyDTA — trans 1,2-cyclohexanediamine N, N, N′, N′ tetraacetic acid) by impedance method reveals the unusual behaviour of complex plane polarograms owing to potential dependence of double layer capacitance. The impedance plane plots by frequency variation method indicates the quasi-reversible nature of the system. From these plots the chargetransfer resistance at various potentials was evaluated. The standard rate constant was evaluated which complements the prediction of impedance plots for the quasireversible behaviour of the system.

A note on transient photocurrents at semiconductor electrodes

The imprint of the changing surface concentration of minority carriers in photocurrent transients is marginalized in “switch off” transients as compared to “switch on” transients. When the surface level is situated close to either one of the band edges, it is shown that in principle it must be possible to obtain the energy of the surface level from “switch off” transients.The time constants for the “switch on” and “switch off” cases behave differently with potential. While in “switch off”, transient plots, the magnitude of the slope decreases monotonically with increasing band bending potentials; for the “switch on” however, though it decreases and is identical to “switch off” initially, beyond a certain increase in potential the magnitude of the slope shows an increase.

Weber-Fechner type nonlinear behavior in zigzag edge graphene nanoribbons

Using a continuum Dirac theory, we study the density and spin response of zigzag edge-terminated graphene ribbons subjected to edge potentials and Zeeman fields. Our analytical calculations of the density and spin responses of the closed system (fixed particle number) to the static edge fields, show a highly nonlinear Weber-Fechner type behavior where the response depends logarithmically on the edge potential. The dependence of the response on the size of the system (e.g., width of a nanoribbon) is also uncovered. Zigzag edge graphene nanoribbons, therefore, provide a realization of response of organs such as the eye and ear that obey Weber-Fechner law. We validate our analytical results with tight-binding calculations. These results are crucial in understanding important effects of electron-electron interactions in graphene nanoribbons such as edge magnetism, etc., and also suggest possibilities for device applications of graphene nanoribbons.

Maturation of a transient outward potassium current in mouse fetal hypothalamic neurons in culture

The whole-cell voltage clamp technique was used to record potassium currents in mouse fetal hypothalamic neurons developing in culture medium from days 1 to 17. The neurons were derived from fetuses of IOPS/OF1 mice on the 14th day of gestation. The mature neurons (>six days in culture) showed both a transient potassium current and a non-inactivating delayed rectifier potassium current. These were identified pharmacologically by using the potassium channel blockers tetraethyl ammonium chloride and 4-aminopyridine, and on the basis of their kinetics and voltage sensitivities. The delayed rectifier potassium current had a threshold of −20 mV, a slow time-course of activation, and was sustained during the voltage pulse. The 4-aminopyridine-sensitive current was transient, and was activated from a holding potential more negative (−80 mV) than that required for evoking the delayed rectifier potassium current (−40 mV). The delayed rectifier potassium current was detectable from day 1 onwards, while the transient potassium current showed a distinct developmental trend. The time-constant of inactivation became faster with age in culture. The half steady-state inactivation potential showed a shift towards less negative membrane potentials with age, and the relationship was best described by a logarithmic regression equation.The developmental trend of the transient potassium current may relate functionally to the progressive morphological changes, and the appearance of synaptic connections during ontogenesis.

Sonochemical synthesis of Ce1-xFexO2-delta (0 <= x <= 0.45) and Ce0.65Fe0.33Pd0.02O2-delta nanocrystallites: oxygen storage material, CO oxidation and water gas shift catalyst

Nanocrystalline Ce1-xFexO2-delta (0 <= x <= 0.45) and Ce0.65Fe0.33Pd0.02O2-delta of similar to 4 nm sizes were synthesized by a sonochemical method using diethyletriamine (DETA) as a complexing agent. Compounds were characterized by powder X-ray diffraction (XRD), X-ray photo-electron spectroscopy (XPS) and transmission electron microscopy (TEM). Ce1-xFexO2-delta (0 <= x <= 0.45) and Ce0.65Fe0.33Pd0.02O2-delta crystallize in fluorite structure where Fe is in +3, Ce is in +4 and Pd is in +2 oxidation state. Due to substitution of smaller Fe3+ ion in CeO2, lattice oxygen is activated and 33% Fe substituted CeO2 i.e. Ce0.67Fe0.33O1.835 reversibly releases 0.31O] up to 600 degrees C which is higher or comparable to the oxygen storage capacity of CeO2-ZrO2 based solid solutions (Catal. Today 2002, 74, 225-234). Due to interaction of redox potentials of Pd2+/0(0.89 V) and Fe3+/2+ (0.77 V) with Ce4+/3+ (1.61 V), Pd ion accelerates the electron transfer from Fe2+ to Ce4+ in Ce0.65Fe0.33Pd0.02O1.815, making it a high oxygen storage material as well as a highly active catalyst for CO oxidation and water gas shift reaction. The activation energy for CO oxidation with Ce0.65Fe0.33Pd0.02O1.815 is found to be as low as 38 kJ mol(-1). Ce0.67Fe0.33O1.835 and Ce0.65Fe0.33Pd0.02O1.815 have also shown high activity for the water gas shift reaction. CO conversion to CO2 is 100% H-2 specific with these catalysts and conversion rate was found to be as high 27.2 mu moles g(-1) s(-1) and the activation energy was found to be 46.4 kJ mol(-1) for Ce0.65Fe0.33Pd0.02O1.815.

Multicomponent multiphase equilibria

A method has been developed for the computation of multicomponent multiphase equilibrium. This method is essentially a modification of White’s element potentials method. It has been found that if the search for equilibrium is confined to a physically significant zone, a solution of the equilibrium problem can be obtained even with a poor initial guess.

Cross-field gas breakdown in a coaxial cylinder geometry

Sparking potentials in a coaxial cylinder geometry in oxygen and dry air were measured in crossed electric and magnetic fields. From the data effective collision frequencies were calculated using the equivalent pressure concept. It is shown that the equivalent pressure concept holds good for deriving the effective collision frequencies in non-uniform electric fields.

Platinum particles supported on titanium nitride: an efficient electrode material for the oxidation of methanol in alkaline media

In the present study, titanium nitride which shows exceptional stability, extreme corrosion resistance, good electronic conductivity and adhesion behaviour is used to support platinum particles and then used for methanol oxidation in an alkaline medium. The catalyst shows very good CO tolerance for the electrochemical oxidation of methanol. In situ infrared spectroelectrochemical data show the remarkable ability of TiN to decompose water at low over potentials leading to -OH type functional groups on its surface which in turn help in alleviating the carbon monoxide poisoning associated with methanol oxidation. TiN supported catalysts are found to be very good in terms of long term stability, exchange current density and stable currents at low over voltages. Supporting evidence from X-ray photoelectron spectroscopic data and cyclic voltammetry clearly demonstrates the usefulness of TiN supported Pt catalysts for efficient methanol oxidation in alkaline media.