Circular dichroic constrained structure optimization of homoalanine peptides

This article describes a new method for peptide structure optimization within a Monte Carlo Simulated Annealing (MCSA) framework, namely the cominimization of potential energies under the constraint of a calculated Circular Dichroism (CD) spectrum. We compute potential energy as well as the CD spectrum of every structure generated within the course of the MCSA run, and cooptimize the mean deviation of this calculated spectrum to a corresponding experimental spectrum together with the potential energies of the respective structures using a modified Metropolis Criterion within the MCSA scheme. We compare the performance of this technique with two other MCSA optimization variants—first, a cominimization of potential energies and free energies of solvation; and second, the standard minimization of potential energy alone. We use homoalanines in lengths of 10 and 15, whose optimized structures are highly α‐helical, and correspondingly give α‐helix characteristic CD signals as the test peptides. This circular dichroic constrained optimization of potential energies is, compared to the other methods, highly efficient in locating α‐helical structures with lowest potential energies in both the 10 alanine and the 15 alanine peptide system, within short MCSA runs. The overall structural information embedded in the CD spectrum efficiently guides the optimization towards the native peptide structure. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 270–281, 2000     

A spectral–finite difference solution of the Navier–Stokes equations in three dimensions

A new computational code for the numerical integration of the three-dimensional Navier–Stokes equations in their non-dimensional velocity–pressure formulation is presented. The system of non-linear partial differential equations governing the time-dependent flow of a viscous incompressible fluid in a channel is managed by means of a mixed spectral–finite difference method, in which different numerical techniques are applied: Fourier decomposition is used along the homogeneous directions, second-order Crank–Nicolson algorithms are employed for the spatial derivatives in the direction orthogonal to the solid walls and a fourth-order Runge–Kutta procedure is implemented for both the calculation of the convective term and the time advancement. The pressure problem, cast in the Helmholtz form, is solved with the use of a cyclic reduction procedure. No-slip boundary conditions are used at the walls of the channel and cyclic conditions are imposed at the other boundaries of the computing domain. Results are provided for different values of the Reynolds number at several time steps of integration and are compared with results obtained by other authors. © 1998 John Wiley & Sons, Ltd.     

Phase and orientational behaviors in liquid crystalline main-chain/side-group block copolymers

The phase and orientational behaviors of a series of liquid crystalline (LC) AB-type diblock copolymers comprising thermotropic main-chain (MC) polyester and side-group (SG) polymethacrylate blocks were investigated by X-ray diffraction. The MC and SG blocks were phase separated and gave rise to their individual mesophases that coexisted at equilibrium. The samples were oriented by using either a magnetic field or a mechanical field. In magnetically aligned samples both the MC and SG microphases were oriented with their smectic planes orthogonal to the magnetic field direction, independent of the copolymer composition. Mechanically aligned, fiber samples showed different orientations of the MC and SG smectic planes for different sample compositions. In this case the disposition of the smectic planes of the MC and SG blocks was driven by the relative length of the two blocks. Some features of the X-ray patterns of the copolymers were compared to those of the MC and SG homopolymers. In addition, the MC smectic domains crystallized on annealing without affecting the orientation that had been achieved by applying a magnetic field. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36 : 21–29, 1998     

A numerical application of the Eshelby theory for geobarometry of non-ideal host-inclusion systems

Meccanica - In the complex geodynamic processes occurring at convergent plate margins, rocks can be subducted at depth into the Earth experiencing metamorphism. A mineral inhomogeneity entrapped...