Effect of salt bridges on the energy landscape of a model protein

The effect of introducing salt bridges (gatekeepers) into an off-lattice three-color, 46-bead model protein is investigated in terms of the effect on global optimization statistics. The global minima for all the gatekeepers that exhibited faster folding in previous molecular dynamics studies are located more rapidly than for the original potential, although the global minimum itself may change. Visualization of the underlying potential energy surface using disconnectivity graphs reveals that the gatekeepers exhibit structure intermediate between the original potential and a Go model. Competition between low-lying minima and the global minimum is reduced in the gatekeepers compared to the original potential, and interconversion barriers are generally smaller.     

Lowest-energy structures of (C60)nX (X=Li+,Na+,K+,Cl-) and (C60)nYCl (Y=Li,Na,K) clusters for n</=13

Basin-hopping global optimization is used to find likely candidates for the lowest minima on the potential energy surface of (C(60))(n)X (X=Li(+),Na(+),K(+),Cl(-)) and (C(60))(n)YCl (Y=Li,Na,K) clusters with n相似文献   

Continuation methods applied to the 2D Navier–Stokes equations at high Reynolds numbers

Nonlinearities arise in aerodynamic flows as a function of various parameters, such as angle of attack, Mach number and Reynolds number. These nonlinearities can cause the change from steady to unsteady flow or give rise to static hysteresis. Understanding these nonlinearities is important for safety validation and performance enhancement of modern aircraft. A continuation method has been developed to study nonlinear steady state solutions with respect to changes in parameters for two‐dimensional compressible turbulent flows at high Reynolds numbers. This is the first time that such flows have been analysed with this approach. Continuation methods allow the stable and unstable solutions to be traced as flow parameters are changed. Continuation has been carried out on two‐dimensional aerofoils for several parameters: angle of attack, Mach number, Reynolds number, aerofoil thickness and turbulent inflow as well as levels of dissipation applied to the models. A range of results are presented. Copyright © 2012 John Wiley & Sons, Ltd.     

The Birman-Murakami-Wenzl algebras of type E n

The Birman-Murakami-Wenzl algebras (BMW algebras) of type E _n for n = 6; 7; 8 are shown to be semisimple and free over the integral domain \mathbbZ[ d^±1,l^±1,m ]

Magnetoelectric effect in cobalt ferrite-barium titanate composites and their electrical properties

CoFe₂O₄-BaTiO₃ composites were prepared using conventional ceramic double sintering process with various compositions. Presence of two phases in the composites was confirmed using X-ray diffraction. The dc resistivity and thermoemf as a function of temperature in the temperature range 300 K to 600 K were measured. Variation of dielectric constant (ɛ′) with frequency in the range 100 Hz to 1 MHz and also with temperature at a fixed frequency of 1 kHz was studied. The ac conductivity was derived from dielectric constant (ɛ′) and loss tangent (tan δ). The nature of conduction is discussed on the basis of small polaron hopping model. The static value of magnetoelectric conversion factor has been studied as a function of magnetic field.     

Energy dependence of multiplicity in proton-nucleus collisions and models of multiparticle production

This is a continuation of our earlier investigation (Gurtuet al 1974Phys. Lett. 50 B 391) on multiparticle production in proton-nucleus collisions based on an exposure of emulsion stack to 200 GeV/c beam at the NAL. It is found that the ratioR _em = 〈n _s〉/〈n _ch〉, where 〈n _ch〉 is the charged particle multiplicity in pp-collisions, increases slowly from about 1 at 10 GeV/c to 1·6 at 68 GeV/c and attains a constant value of 1·71 ± 0·04 in the region 200 to 8000 GeV/c. Furthermore,R _em = 1·71 implies an effectiveA-dependence ofR _A =A ^0.18,i.e., a very weak dependence. Predictions ofR _em on various models are discussed and compared with the emulsion data. Data seem to favour models of hadron-nucleon collisions in which production of particles takes place through adouble step mechanism,e.g., diffractive excitation, hydrodynamical and energy flux cascade as opposed to models which envisage instantaneous production.     

A rapid,new and direct method for isolation and measurement of porphyrins in biological samples by high performance liquid chromatography

Reversed-phase high performance liquid chromatography on microparticulate columns of octadecylsilane with elution by a gradient of acetonitrile in phosphate buffer, pH 7.5, separated porphyrin free acids directly in urine for the first time. Interfering fluorescence was removed with a precolumn of large particle size at acid pH. Peak area fluorescence by the method of standard addition was related linearly to amount of a porphyrin from 5 to 60 nanograms. The method was reproducible to ± 13%, able to detect 0.3 nanograms of a porphyrin in a 1 ml urine sample in 45 minutes, and capable of detecting the typical clinical patterns of normal and porphyrinuric urines. Modifications make the method applicable to measurements in other biological samples and to research separations. With the added rapidity of analysis, the method could expand porphyrin analysis in routine clinical medicine.     

Protein structure prediction using basin-hopping

Associative memory Hamiltonian structure prediction potentials are not overly rugged, thereby suggesting their landscapes are like those of actual proteins. In the present contribution we show how basin-hopping global optimization can identify low-lying minima for the corresponding mildly frustrated energy landscapes. For small systems the basin-hopping algorithm succeeds in locating both lower minima and conformations closer to the experimental structure than does molecular dynamics with simulated annealing. For large systems the efficiency of basin-hopping decreases for our initial implementation, where the steps consist of random perturbations to the Cartesian coordinates. We implemented umbrella sampling using basin-hopping to further confirm when the global minima are reached. We have also improved the energy surface by employing bioinformatic techniques for reducing the roughness or variance of the energy surface. Finally, the basin-hopping calculations have guided improvements in the excluded volume of the Hamiltonian, producing better structures. These results suggest a novel and transferable optimization scheme for future energy function development.     

QTAIM and stress tensor interpretation of the (H2O)5 potential energy surface

Using the quantum theory of atoms in molecules a near complete combined directed spanning quantum topology phase diagram (QTPD) was constructed from the nine (H₂O)₅ reaction‐pathways and five unique Poincaré–Hopf solutions that were found after an extensive search of the MP2 potential energy surface. Two new energy minima that were predicted from earlier work are found and include the first (H₂O)₅ conformer with a 3‐D_QT quantum topology. The stress tensor Poincaré–Hopf relation indicated a preference for 2‐D_QT (H₂O)₅ topologies as well as the presence of coupling between shared‐shell O? H BCPs to the hydrogen‐bond BCPs that share an H NCP. The complexity of the near complete combined QTPD was explained in terms of the O…O bonding interactions that were found in six of the nine (H₂O)₅ reaction‐pathways and for all points of the combined QTPD. The stabilizing role of the O…O bonding interactions from the values of the total local energy density was explored. © 2016 Wiley Periodicals, Inc.