In Hybrid Monte Carlo simulations for full QCD, the gauge fields evolve smoothly as a function of Molecular Dynamics time. Here we investigate improved methods of estimating the trial or starting solutions for the Dirac matrix inversion as superpositions of a chronological sequence of solutions in the recent past. By taking as the trial solution the vector which minimizes the residual in the linear space spanned by the past solutions, the number of conjugate gradient iterations per unit MD time is decreased by at least a factor of 2. Extensions of this basic approach to precondition the conjugate gradient iterations are also discussed.

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To elucidate the role in hadron structure of quark zero modes associated with instantons, the lowest eigenfunctions of the Dirac operator have been calculated in quenched QCD, full QCD, and full QCD with cooling. Eigenmodes associated with a single instanton and an instanton-anti-instanton pair were studied to understand the role of lattice artifacts for Wilson Fermions. By truncating the spectral representation of the quark propagator, we show that the rho and pion contributions to the vector and pseudoscalar correlation functions are dominated by the zero-mode contributions.

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In order to optimize cooling as a technique to study the instanton content of the QCD vacuum, we have studied the effects of alternative algorithms, improved actions and boundary conditions on the evolution of single instantons and instanton anti-instanton pairs. Using these results, we have extracted and compared the instanton content of quenched and full QCD.