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]

Error-free matrix symmetrizers and equivalent symmetric matrices

A symmetrizer of the matrix A is a symmetric solution X that satisfies the matrix equation XA=AprimeX. An exact matrix symmetrizer is computed by obtaining a general algorithm and superimposing a modified multiple modulus residue arithmetic on this algorithm. A procedure based on computing a symmetrizer to obtain a symmetric matrix, called here an equivalent symmetric matrix, whose eigenvalues are the same as those of a given real nonsymmetric matrix is presented.

Characterization of oxygen free radicals generated during vanadate-stimulated NADH oxidation

The oxidation of NADH and accompanying reduction of oxygen to H2O2 stimulated by polyvanadate was markedly inhibited by SOD and cytochrome c. The presence of decavanadate, the polymeric form, is necessary for obtaining the microsomal enzyme-catalyzed activity. The accompanying activity of reduction of cytochrome c was found to be SOD-insensitive and therefore does not represent superoxide formation. The reduction of cytochrome c by vanadyl sulfate was also SOD-insensitive. In the presence of H2O2 all the forms of vanadate were able to oxidize reduced cytochrome c, which was sensitive to mannitol, tris and also catalase, indicating H202-dependent generation of hydroxyl radicals. Using ESR and spin trapping technique only hydroxyl radicals, but not superoxide anion radicals, were detected during polyvanadate-dependent NADH oxidation.

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.

Nonaxisymmetric unsteady motion over a rotating disk in the presence of free convection and magnetic field

The nonaxisymmetric unsteady motion produced by a buoyancy-induced cross-flow of an electrically conducting fluid over an infinite rotating disk in a vertical plane and in the presence of an applied magnetic field normal to the disk has been studied. Both constant wall and constant heat flux conditions have been considered. It has been found that if the angular velocity of the disk and the applied magnetic field squared vary inversely as a linear function of time (i.e. as (1??t*)?1, the governing Navier-Stokes equation and the energy equation admit a locally self-similar solution. The resulting set of ordinary differential equations has been solved using a shooting method with a generalized Newton's correction procedure for guessed boundary conditions. It is observed that in a certain region near the disk the buoyancy induced cross-flow dominates the primary von Karman flow. The shear stresses induced by the cross-flow are found to be more than these of the primary flow and they increase with magnetic parameter or the parameter ? characterizing the unsteadiness. The velocity profiles in the x- and y-directions for the primary flow at any two values of the unsteady parameter ? cross each other towards the edge of the boundary layer. The heat transfer increases with the Prandtl number but reduces with the magnetic parameter.