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

Tunneling with the Lorentz Force and the Friction

We present a semiclassical study of a transport process, the tunneling, in the presence of a magnetic field and a dissipative environment. We have found that the problem can be mapped onto an effective one-dimensional one, and the tunneling rate is strongly affected by the magnetic field, such as a complete suppression by a large parallel magnetic field, an example of the dynamical localization. In such case a small perpendicular component of the field, or the dissipation, can enhance the tunneling rate. In the small parallel field and finite temperatures the tunneling rate is finite. Explicit expressions will be presented in those cases. If viewing the tunneling in the presence of a magnetic field as a dissipative tunneling process, by varying the magnetic field and the potential one can obtain the dissipative spectral function between the subohmic $s =0$ and the superohmic $s = \infty$. In combination with a real dissipative spectral function, the effect of the magnetic field can map the spectral function from $s$ to $2-s$, with $s>2$ mapping to $s = 0$, revealing a dual symmetry between the friction and the Lorentz force. Two cases relevant to experiments, the edge state tunneling in a Hall bar and the tunneling near the dynamical localization will be discussed in detail.Comment: Late

Power-Aware Speed Scaling in Processor Sharing Systems

Energy use of computer communication systems has quickly become a vital design consideration. One effective method for reducing energy consumption is dynamic speed scaling, which adapts the processing speed to the current load. This paper studies how to optimally scale speed to balance mean response time and mean energy consumption under processor sharing scheduling. Both bounds and asymptotics for the optimal speed scaling scheme are provided. These results show that a simple scheme that halts when the system is idle and uses a static rate while the system is busy provides nearly the same performance as the optimal dynamic speed scaling. However, the results also highlight that dynamic speed scaling provides at least one key benefit - significantly improved robustness to bursty traffic and mis-estimation of workload parameters

Stochastic Analysis of Power-Aware Scheduling

Energy consumption in a computer system can be reduced by dynamic speed scaling, which adapts the processing speed to the current load. This paper studies the optimal way to adjust speed to balance mean response time and mean energy consumption, when jobs arrive as a Poisson process and processor sharing scheduling is used. Both bounds and asymptotics for the optimal speeds are provided. Interestingly, a simple scheme that halts when the system is idle and uses a static rate while the system is busy provides nearly the same performance as the optimal dynamic speed scaling. However, dynamic speed scaling which allocates a higher speed when more jobs are present significantly improves robustness to bursty traffic and mis-estimation of workload parameters

Invalidity of Classes of Approximated Hall Effect Calculations

In this comment, I point out a number of approximated derivations for the effective equation of motion, now been applied to d-wave superconductors by Kopnin and Volovik are invalid. The major error in those approximated derivations is the inappropriate use of the relaxation time approximation in force-force correlation functions, or in force balance equations, or in similar variations. This approximation is wrong and unnecessary.Comment: final version, minor changes, to appear in Phys. Rev. Let

Two Stages in the evolution of binary alkali Bose-Einstein condensate mixtures towards phase segregation

Two stages of quantum spinodal decomposition is proposed and analyzed for this highly non-equilibrium process. Both time and spatial scales for the process are found. Qualitative agreement with existing data is found. Some cases the agreements are quantitative. Further experimental verifications are indicated.Comment: late

Dissipative Tunneling in 2 DEG: Effect of Magnetic Field, Impurity and Temperature

We have studied the transport process in the two dimensional electron gas (2DEG) in presence of a magnetic field and a dissipative environment at temperature T. By means of imaginary time series functional integral method we calculate the decay rates at finite temperature and in the presence of dissipation. We have studied decay rates for wide range of temperatures -- from the thermally activated region to very low temperature region where the system decays by quantum tunneling. We have shown that dissipation and impurity helps the tunneling. We have also shown that tunneling is strongly affected by the magnetic field. We have demonstrated analytical results for all the cases mentioned above.Comment: 8 pages, 2 figure