The electrophoresis of transferrins in urea/polyacrylamide gels

The denaturation of transferrin by urea has been studied by (a) electrophoresis in polyacrylamide gels incorporating a urea gradient, (b) measurements of the loss in iron-binding capacity and (c) u.v. difference spectrometry. In human serum transferrin and hen ovotransferrin the N-terminal and C-terminal domains of the iron-free protein were found to denature at different urea concentrations

Studies of the binding of different iron donors to human serum transferrin and isolation of iron-binding fragments from the N- and C-Terminal regions of the protein

1. Trypsin digestion of human serum transferrin partially saturated with iron(III)- nitrilotriacetate at pH5.5 or pH 8.5 produces a carbohydrate-containing iron-binding fragment of mol.wt. 43000. 2. When iron(III) citrate, FeCI3, iron(II) ascorbate and (NH4)2SO4,FeSO4 are used as iron donors to saturate the protein partially, at pH 8.5, proteolytic digestion yields a fragment of mol.wt. 36000 that lacks carbohydrate. 3. The two fragments differ in their antigenic structures, amino acid compositions and peptide 'maps'. 4. The fragment with mol.wt. 36000 was assigned to the N-terminal region of the protein and the other to the C-terminal region. 5. The distribution of iron in human serum transferrin partially saturated with various iron donors was examined by electrophoresis in urea/polyacrylamide gels and the two possible monoferric forms were unequivocally identified. 6. The site designated A on human serum transferrin [Harris (1977) Biochemistry 16, 560-564] was assigned to the C-terminal region of the protein and the B site to the N-terminal region. 7. The distribution of iron on transferrin in human plasma was determined

Signal Propagation, with Application to a Lower Bound on the Depth of Noisy Formulas

We study the decay of an information signal propagating through a series of noisy channels. We obtain exact bounds on such decay, and as a result provide a new lower bound on the depth of formulas with noisy components. This improves upon previous work of N. Pippenger and significantly decreases the gap between his lower bound and the classical upper bound of von Neumann. We also discuss connections between our work and the study of mixing rates of Markov chains

Statistical Mechanics of Time Independent Non-Dissipative Nonequilibrium States

We examine the question of whether the formal expressions of equilibrium statistical mechanics can be applied to time independent non-dissipative systems that are not in true thermodynamic equilibrium and are nonergodic. By assuming the phase space may be divided into time independent, locally ergodic domains, we argue that within such domains the relative probabilities of microstates are given by the standard Boltzmann weights. In contrast to previous energy landscape treatments, that have been developed specifically for the glass transition, we do not impose an a priori knowledge of the inter-domain population distribution. Assuming that these domains are robust with respect to small changes in thermodynamic state variables we derive a variety of fluctuation formulae for these systems. We verify our theoretical results using molecular dynamics simulations on a model glass forming system. Non-equilibrium Transient Fluctuation Relations are derived for the fluctuations resulting from a sudden finite change to the system's temperature or pressure and these are shown to be consistent with the simulation results. The necessary and sufficient conditions for these relations to be valid are that the domains are internally populated by Boltzmann statistics and that the domains are robust. The Transient Fluctuation Relations thus provide an independent quantitative justification for the assumptions used in our statistical mechanical treatment of these systems.Comment: 17 pages, 4 figures, minor amendment

The rheology of solid glass

As the glass transition is approached from the high temperature side, viewed as a liquid, the properties of the ever more viscous supercooled liquid are continuous functions of temperature and pressure. The point at which we decide to classify the fluid as a solid is therefore subjective. This subjective decision does, however, have discontinuous consequences for how we determine the rheological properties of the glass. We apply the recently discovered relaxation theorem to the time independent, nondissipative, nonergodic glassy state to derive an expression for the phase space distribution of an ensemble of glass samples. This distribution is then used to construct a time dependent linear response theory for aged glassysolids. The theory is verified using molecular dynamics simulations of oscillatory shear for a realistic model glass former with excellent agreement being obtained between the response theory calculations and direct nonequilibrium molecular dynamics calculations. Our numerical results confirm that unlike all the fluid states, including supercooled liquids, a solidglass (in common with crystalline states) has a nonzero value for the zero frequency shear modulus. Of all the states of matter, a supercooled fluid approaching the glass transition has the highest value for the limiting zero frequency shear viscosity. Finally, solidglasses like dilute gases and crystals have a positive temperature coefficient for the shear viscosity whereas supercooled and normal liquids have a negative temperature coefficient.We thank the National Computational Infrastructure NCI for computational facilities and the Australian Research Council ARC for funding

Generalized Stochastic Gradient Learning

We study the properties of generalized stochastic gradient (GSG) learning in forwardlooking models. We examine how the conditions for stability of standard stochastic gradient (SG) learning both di1er from and are related to E-stability, which governs stability under least squares learning. SG algorithms are sensitive to units of measurement and we show that there is a transformation of variables for which E-stability governs SG stability. GSG algorithms with constant gain have a deeper justification in terms of parameter drift, robustness and risk sensitivity

Hamiltonians of Spherically Symmetric, Scale-Free Galaxies in Action-Angle Coordinates

We present a simple formula for the Hamiltonian in terms of the actions for spherically symmetric, scale-free potentials. The Hamiltonian is a power-law or logarithmic function of a linear combination of the actions. Our expression reduces to the well-known results for the familiar cases of the harmonic oscillator and the Kepler potential. For other power-laws, as well as for the singular isothermal sphere, it is exact for the radial and circular orbits, and very accurate for general orbits. Numerical tests show that the errors are always small, with mean errors across a grid of actions always less than 1 % and maximum errors less than 2.5 %. Simple first-order corrections can reduce mean errors to less than 0.6 % and maximum errors to less than 1 %. We use our new result to show that :[1] the misalignment angle between debris in a stream and a progenitor is always very nearly zero in spherical scale-free potentials, demonstrating that streams can be sometimes well approximated by orbits, [2] the effects of an adiabatic change in the stellar density profile in the inner regions of a galaxy weaken any existing 1/r density cusp, which is reduced to $1/r^{1/3}$. More generally, we derive the full range of adiabatic cusp transformations and show how to relate the starting cusp index to the final cusp index. It follows that adiabatic transformations can never erase a dark matter cusp.Comment: 6 pages, MNRAS, in pres

Verification of time-reversibility requirementfor systems satisfying the Evans-Searles fluctuation theorem

The Evans-Searles fluctuation theorem (ESFT) has been shown to be applicable in the near- and far-from-equilibrium regimes for systems with both constant and time-dependent external fields. The derivations of the ESFT have assumed that the external field has a definite parity under a time-reversal mapping. In the present paper, we confirm that the time-reversibility of the system dynamics is a necessary condition for the ESFT to hold. The manner in which the ESFT fails for systems that are not time-reversible is presented, and results are shown which demonstrate that systems which fail to satisfy the ESFT may still satisfy the Crooks relation (CR)