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This is the first report, to our knowledge, on a systematic method for constructing a large scale kinetic metabolic model with incomplete information on kinetic parametersr, and its initial application to the modeling of central metabolism of Methylobacterium extorquens AM1, a methylotrophic and environmental important bacterium, with all necessary constraints. Through a systematic and consistent procedure of finding a set of parameters in the physiological range we overcome an outstanding difficulty in large scale kinetic modeling: the requirement for a massive number of enzymatic reaction parameters. We are able to construct the kinetic model based on general biological considerations and incomplete experimental kinetic parameters. The success of our approach with incompletely input information is guaranteed by two known principles in biology, the robustness of the system and the cooperation among its various parts. (Will be pleased to be informed on other methodologies dealing with same type of problems: aoping@u.washington.edu), Comment: 15 pages, pdf format

Based on our experience in kinetic modeling of coupled multiple metabolic pathways we propose a generic rate equation for the dynamical modeling of metabolic kinetics. Its symmetric form makes the kinetic parameters (or functions) easy to relate to values in database and to use in computation. In addition, such form is workable to arbitrary number of substrates and products with different stoichiometry. We explicitly show how to obtain such rate equation exactly for various binding mechanisms. Hence the proposed rate equation is formally rigorous. Various features of such a generic rate equation are discussed. For irreversible reactions, the product inhibition which directly arise from enzymatic reaction is eliminated in a natural way. We also discuss how to include the effects of modifiers and cooperativity., Comment: Accepted by Journal of Biological Systems (8 Sep 2007)

We calculate the effective mass of a single quantized vortex in the BCS superconductor at finite temperature. Using the effective action for a vortex, we arrive at the mass formula as the integral of the spectral function $J(\omega)/\omega^3$ over frequency. The spectral function is given in terms of the transition elements of the gradient of the Hamiltonian between Bogoliubov-deGennes eigenstates. We show that core-core, and core-extended transitions yield the vortex mass, near T=0, of order of electron mass displaced by the normal core. The extended-extended states contributions are linearly divergent with the low frequency cutoff $\omega_c$, in accordance with the Ohmic character of the spectral function at low energies. We argue that the mass and friction are closely related in this system and arise from the same mechanism - interaction with the surrounding fermionic degrees of freedom.

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��dinger 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., Latex, 12 pages

In order to explore the existence of SARS coronavirus (Co-V) and/or its RNA in sewage of hospitals administered SARS patients.A novel electropositive filter was used to concentrate the SARS-CoV from the sewage of two hospitals administered SARS patients in Beijing, including twelve 2,500 ml sewage samples from the hospitals before disinfection, and ten 25,000 ml samples after disinfection; as well as cell culture, RT-PCR and sequencing of gene to detect and identify the viruses from sewage.There was no live SARS-CoV detected in the sewage in this study. The nucleic acid of SARS-CoV had been found in the 12 sewage samples before disinfection from both hospitals by semi-nested PCR. After disinfection, SARS-CoV RNA could only be detected from the samples from the 309th Hospital, and the others were negative.It provides evidence that there is no live SARS-Cov in the sewage from hospitals with SARS patients though SARS-CoV RNA can be detected.