Vortex Dynamics within the BCS Theory

We outline a conventional path integral derivation of the transverse force and the friction for a vortex in a superconductor based on the BCS theory. The derivation is valid in both clean and dirty limits at both zero and finite temperatures. The transverse force is found to be precisely as what has been obtained by Ao and Thouless using the Berry's phase method. The friction is essentially the same as the Bardeen and Stephen's result. Errors in some previous representive microscopic derivations are discussed.Comment: Revtex. the Invited Talk in M2S-HTSC-V conference in Beijing, Feb. 28-March 4, 1997. to appear in Physica

Effects of Geometric Phases in Josephson Junction Arrays

We show that the en route vortex velocity dependent part of the Magnus force in a Josephson junction array is effectively zero, and predict zero Hall effect in the classical limit. However, geometric phases due to the finite superfluid density at superconductor grains have a profound influence on the quantum dynamics of vortices. Subsequently we find rich and complex Hall behaviors analogous to the Thouless-Kohmoto-Nightingale-den Nijs effect in the quantum regime.Comment: Latex, 11 pages, appeared in Phys. Rev. Lett. v.77, 562 (1996) with minor change

Nonlinear Schr\"odinger Equation for Superconductors

Using the Hartree-Fock-Bogoliubov factorization of the density matrix and the Born-Oppenheimer approximation we show that the motion of the condensate satisfies a nonlinear Schr\"odinger equation in the zero temperature limit. The Galilean invariance of the equation is explicitly manifested. {}From this equation some general properties of a superconductor, such as Josephson effects, the Magnus force, and the Bogoliubov-Anderson mode can be obtained readily.Comment: Latex, 12 page

Calculating Biological Behaviors of Epigenetic States in Phage lambda Life Cycle

Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function. However, its stability and robustness for both wild type and mutants has been a notorious theoretical/mathematical problem. In this paper we report our successful calculation on the properties of this gene regulatory network. We believe it is of its first kind. Our success is of course built upon numerous previous theoretical attempts, but following 3 features make our modeling uniqu: 1) A new modeling method particular suitable for stability and robustness study; 2) Paying a close attention to the well-known difference of in vivo and in vitro; 3) Allowing more important role for noise and stochastic effect to play. The last two points have been discussed by two of us (Ao and Yin, cond-mat/0307747), which we believe would be enough to make some of previous theoretical attempts successful, too. We hope the present work would stimulate a further interest in the emerging field of gene regulatory network.Comment: 16 pages, 3 figures, 1 tabl