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The surface of an annealed Cu plate was processed by a high pressure surface rolling (HPSR) process. It is found that the deformed surface layer in the Cu plate after HPSR can be as thick as 2 mm and is characterized by a gradient microstructure, with grain sizes varying from the nanoscale in the topmost surface to the microscale in the bulk. The hardness varies from 1.37 GPa at the topmost surface to about 0.6 GPa in the coarse-grained matrix. The results of the investigation demonstrate that the HPSR process shows good potential for the generation of thick gradient microstructures on the surface of bulk metallic materials.

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

An endogenous molecular-cellular network for both normal and abnormal functions is assumed to exist. This endogenous network forms a nonlinear stochastic dynamical system, with many stable attractors in its functional landscape. Normal or abnormal robust states can be decided by this network in a manner similar to the neural network. In this context cancer is hypothesized as one of its robust intrinsic states. This hypothesis implies that a nonlinear stochastic mathematical cancer model is constructible based on available experimental data and its quantitative prediction is directly testable. Within such model the genesis and progression of cancer may be viewed as stochastic transitions between different attractors. Thus it further suggests that progressions are not arbitrary. Other important issues on cancer, such as genetic vs epigenetics, double-edge effect, dormancy, are discussed in the light of present hypothesis. A different set of strategies for cancer prevention, cure, and care, is therefore suggested., 13 pages

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)

Based on our physical and biological studies we have recently developed a mathematical framework for the analysis of nonlnear dynamics. We call this framework the dynamical structure analysis. It has four dynamical elements: potential landscape, transverse matrix, descendant matrix, and stochastic drive. In particular, the importance and the existence of the potential landscape is emphasized. The dynamical structure analysis is illustrated in detail by the study of stability, robustness, and efficiency of the simplest gene regulatory network of phage lambda., 31 pages

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., 16 pages, 3 figures, 1 table

Using the random matrix theory we demonstrate explicitly the insensitivity of the transverse force on a moving vortex to non-intrinsic and non-magnetic impurities in a superconductor., revtex

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.

We present a microscopic calculation of core states contribution to vortex friction in a type II superconductor at zero temperature. In weak impurity limit, a perturbative calculation leads to a vortex friction proportional to the normal state resistivity. With the aid of random matrix theory, vortex friction due to core states is determined only by the Fermi energy and the energy gap in dirty limit, similar to the phenomenological results of Bardeen and Stephen, but disagrees with the results obtained under the relaxation time approximation. In addition, an explicit demonstration is given on the the insensitivity of transverse force to impurities., revtex, 4 pages

The coexistence of the universal transverse force and the non-universal friction force on a topological singularity in a superfluid is shown here. Based on the BCS type microscopic theory, we explicitly evaluate the quasiparticle contribution to the friction coefficient in a clean fermionic superfluid, showing a new feature of logarithmic divergence., Latex, 4 pages

We investigate the problem of forces on moving vortex in a superfluid or superconductor. The main purpose is to locate the source which leads to the contradictory results in the literature. We establish the connection between this problem to the difficult but well studied subject of resistivity formula in transport theory. The relaxation time approximation used in the force calculation via force-force correlation function is shown to be invalid. The roles of Berry's phase and fluctuation-dissipation theorems are discussed., final verion. appeared in Chinese J. of Physics v.36, 197 (1998)

The vortex motion in a superfluid or a type II superconductor is similar to the electron motion in a magnetic field, because they both feel a transverse force. The vortex dynamics in a superconductor is a basic property of the superconductivity which remains controversial. It is also responsible for a large class of observed physical phenomena. We will examine this issue from the experimental point of view. In particular, we will compare the experiments which have set the stage to the Lorentz force and the experiments influencing our understanding of the Magnus force on vortices in superconductors., To appear in Journal of Korean Physical Society

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

Physical review / B 37(12), 7157 - 7160 (1988). doi:10.1103/PhysRevB.37.7157, We report the results of a grazing-incidence x-ray study on the order-disorder phase transition of a (111)-oriented $Cu_3Au$ film (0.7 μm) epitaxially grown on an $Al_2O_3$ substrate with a Nb buffer layer. By varying the incident beam angles to the surface, penetration depths between 22 and 650 Å were probed. While the bulk disorders at Tb$_c$=665 K through a first-order transition, the surface region appears to exhibit an enhanced ordering with a slightly higher transition temperature. Close to Tb$_c$ pronounced short-range-order scattering is seen in the deeper layers, whereas this effect is much reduced closer to the surface., Published by Inst., Woodbury, NY

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.