Nonlinear stresses and temperatures in transient adiabatic and shear flows via nonequilibrium molecular dynamics: Three definitions of temperature.

We compare nonlinear stresses and temperatures for adiabatic-shear flows, using up to 262, 144 particles, with those from corresponding homogeneous and inhomogeneous flows. Two varieties of kinetic temperature tensors are compared to the configurational temperatures. This comparison of temperatures led us to two findings beyond our original goal of analyzing shear algorithms. First, we found an improved form for local instantaneous velocity fluctuations, as calculated with smooth-particle weighting functions. Second, we came upon the previously unrecognized contribution of rotation to the configurational temperature.

Chaos, ergodic convergence, and fractal instability for a thermostated canonical harmonic oscillator.

The authors thermostat a qp harmonic oscillator using the two additional control variables zeta and xi to simulate Gibbs' canonical distribution. In contrast to the motion of purely Hamiltonian systems, the thermostated oscillator motion is completely ergodic, covering the full four-dimensional [q,p,zeta,xi] phase space. The local Lyapunov spectrum (instantaneous growth rates of a comoving corotating phase-space hypersphere) exhibits singularities like those found earlier for Hamiltonian chaos, reinforcing the notion that chaos requires kinetic-as opposed to statistical-study, both at and away from equilibrium. The exponent singularities appear to have a fractal character.

A rapid and sensitive method for detection and quantification of calcineurin and calmodulin-binding proteins using biotinylated calmodulin.

Purified bovine brain calmodulin was biotinylated with biotinyl-epsilon-aminocaproic acid N-hydroxysuccinimide. Biotinylated calmodulin was used to detect and quantify calmodulin-binding proteins following both protein blotting and slot-blot procedures by using alkaline phosphatase or peroxidase coupled to avidin. When purified bovine brain calcineurin, a calmodulin-dependent protein phosphatase, was immobilized on nitrocellulose slot blots, biotinylated calmodulin bound in a calcium-dependent saturable manner; these blots were then quantified by densitometry. Biotinylated calmodulin was able to detect as little as 10 ng of calcineurin, and the binding was competitively inhibited by addition of either native calmodulin or trifluoperazine. When biotinylated calmodulin was used to probe protein blots of crude brain cytosol and membrane preparations after gel electrophoresis, only protein bands characteristic of known calmodulin-binding proteins (i.e., calmodulin-dependent protein kinase, calcineurin, spectrin) were detected with avidin-peroxidase or avidin-alkaline phosphatase procedures. Purified calcineurin was subjected to one- and two-dimensional gel electrophoresis and protein blotting; as expected, only the 61-kDa calmodulin-binding subunit was detected. When the two-dimensional protein blot was incubated with biotinylated calmodulin and detected with avidin-alkaline phosphatase, several apparent forms of the 61-kDa catalytic subunit were detected, consistent with isozymic species of the enzyme. The results of these studies suggest that biotinylated calmodulin can be used as a simple, sensitive, and quantifiable probe for the study of calmodulin-binding proteins.