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

Universal Tomonaga-Luttinger liquid phases in one-dimensional strongly attractive SU(N) fermionic cold atoms

A simple set of algebraic equations is derived for the exact low-temperature thermodynamics of one-dimensional multi-component strongly attractive fermionic atoms with enlarged SU(N) spin symmetry and Zeeman splitting. Universal multi-component Tomonaga-Luttinger liquid (TLL) phases are thus determined. For linear Zeeman splitting, the physics of the gapless phase at low temperatures belongs to the universality class of a two-component asymmetric TLL corresponding to spin-neutral N-atom composites and spin-(N-1)/2 single atoms. The equation of states is also obtained to open up the study of multi-component TLL phases in 1D systems of N-component Fermi gases with population imbalance.Comment: 12 pages, 3 figure

Universal local pair correlations of Lieb-Liniger bosons at quantum criticality

The one-dimensional Lieb-Liniger Bose gas is a prototypical many-body system featuring universal Tomonaga-Luttinger liquid (TLL) physics and free fermion quantum criticality. We analytically calculate finite temperature local pair correlations for the strong coupling Bose gas at quantum criticality using the polylog function in the framework of the Yang-Yang thermodynamic equations. We show that the local pair correlation has the universal value $g^{(2)}(0)\approx 2 p/(n\varepsilon)$ in the quantum critical regime, the TLL phase and the quasi-classical region, where $p$ is the pressure per unit length rescaled by the interaction energy $\varepsilon=\frac{\hbar^2}{2m} c^2$ with interaction strength $c$ and linear density $n$. This suggests the possibility to test finite temperature local pair correlations for the TLL in the relativistic dispersion regime and to probe quantum criticality with the local correlations beyond the TLL phase. Furthermore, thermodynamic properties at high temperatures are obtained by both high temperature and virial expansion of the Yang-Yang thermodynamic equation.Comment: 8 pages, 6 figures, additional text and reference

Exactly solvable models and ultracold Fermi gases

Exactly solvable models of ultracold Fermi gases are reviewed via their thermodynamic Bethe Ansatz solution. Analytical and numerical results are obtained for the thermodynamics and ground state properties of two- and three-component one-dimensional attractive fermions with population imbalance. New results for the universal finite temperature corrections are given for the two-component model. For the three-component model, numerical solution of the dressed energy equations confirm that the analytical expressions for the critical fields and the resulting phase diagrams at zero temperature are highly accurate in the strong coupling regime. The results provide a precise description of the quantum phases and universal thermodynamics which are applicable to experiments with cold fermionic atoms confined to one-dimensional tubes.Comment: based on an invited talk at Statphys24, Cairns (Australia) 2010. 16 pages, 6 figure

Quantum correlations in a cluster-like system

We discuss a cluster-like 1D system with triplet interaction. We study the topological properties of this system. We find that the degeneracy depends on the topology of the system, and well protected against external local perturbations. All these facts show that the system is topologically ordered. We also find a string order parameter to characterize the quantum phase transition. Besides, we investigate two-site correlations including entanglement, quantum discord and mutual information. We study the different divergency behaviour of the correlations. The quantum correlation decays exponentially in both topological and magnetic phases, and diverges in reversed power law at the critical point. And we find that in TQPT systems, the global difference of topology induced by dimension can be reflected in local quantum correlations.Comment: 7 pages, 6 figure

The correlations between the twin kHz QPO frequencies of LMXBs

We analyzed the recently published kHz QPO data in the neutron star low-mass X-ray binaries (LMXBs), in order to investigate the different correlations of the twin peak kilohertz quasi-eriodic oscillations (kHz QPOs) in bright Z sources and in the less luminous Atoll sources. We find that a power-law relation \no\sim\nt^{b} between the upper and the lower kHz QPOs with different indices: $b\simeq$1.5 for the Atoll source 4U 1728-34 and $b\simeq$1.9 for the Z source Sco X-1. The implications of our results for the theoretical models for kHz QPOs are discussed.Comment: 6 pages, accepted by MNRA

Wilson ratio of Fermi gases in one dimension

We calculate the Wilson ratio of the one-dimensional Fermi gas with spin imbalance. The Wilson ratio of attractively interacting fermions is solely determined by the density stiffness and sound velocity of pairs and of excess fermions for the two-component Tomonaga-Luttinger liquid (TLL) phase. The ratio exhibits anomalous enhancement at the two critical points due to the sudden change in the density of states. Despite a breakdown of the quasiparticle description in one dimension, two important features of the Fermi liquid are retained, namely the specific heat is linearly proportional to temperature whereas the susceptibility is independent of temperature. In contrast to the phenomenological TLL parameter, the Wilson ratio provides a powerful parameter for testing universal quantum liquids of interacting fermions in one, two and three dimensions.Comment: 5+2 pages, 4+1 figures, Eq. (4) is proved, figures were refine