arXiv subjects
Publications and source records attributed to P. Ao.
The present author has long argued, with concrete predictions, that both longitudinal and transverse (Hall) resistivities in the mixed state of superconductors are dominated by vortex many-body effect. Hence there is no need to introduce various ad hoc vortex dynamics theories. It is interesting to note this point of view is now slowly creeping into the work of his most fierce opponents.
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.
Here we postulate three laws which form a mathematical framework to capture the essence of Darwinian evolutionary dynamics. The second law is most quantitative and is explicitly expressed by a unique form of stochastic differential equation. A precise definition of Wright's adaptive landscape is given and a new and consistent interpretation of Fisher's fundamental theorem of natural selection is provided. Based on a recently discovered theorem the generality of the proposed laws is illustrated by an explicit demonstration of their equivalence to a general conventional non-equilibrium dynamics formulation. The proposed laws provide a coherence framework to discuss several current evolutionary problems, such as speciation and stability, and gives a firm base for the application of statistical physics tools in Darwinian dynamics.
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.
With the excitement generated by this year's Nobel Prize in physics, here I give a brief critical review of current vortex dynamics research activity, using a recent book as the background material. Two directions in which major progresses can be expected are selected: the role of vortex-phonon interaction in low temperature superfluid turbulence and the complete integration of topological method into vortex dynamics. In addition, I would like to call attention to 3 important experiments which have not been fully appreciated in the past: 1) the measurement of vorticity quantization via Magnus force done in Britain; 2) the extensive study of Josephson-Anderson relation carried out in USA; and 3) the direct measurement of Magnus force in superconductors performed in Sweden. They will play an important role in the further development of the field.
We discuss two aspects, the in vivo and in vitro difference and the modeling of noise, of integrative modeling of network dynamics in biology, using phage lambda as an example. We believe those two aspects have not been seriously considered, and the including of them may be enough to solve the outstanding stability and robustness puzzle of in gene regulatory network dynamics.
Dynamics near and far away from thermal equilibrium is studied within the framework of Langevin equations. A stochasticity-dissipation relation is proposed to emphasize the equal importance of the stochastic and deterministic forces in describing the system's evolution and destination. It is a generalization of the fluctuation-dissipation theorem. Close to a stationary state an explicit construction of the potential energy is given through a gauged singular decomposition. Possible directions to extend the present study into generic situations are pointed out.
Vortex dynamics in fermionic superfluids is carefully considered from the microscopic point of view. Finite temperatures, as well as impurities, are explicitly incorporated. To enable readers understand the physical implications, macroscopic demonstrations based on thermodynamics and fluctuations- dissipation theorems are constructed. For the first time a clear summary and a critical review of previous results are given.
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.
We study a vortex in a two-dimensional, harmonically trapped Bose-Einstein condensate at zero temperature. Through a variational calculation using a trial condensate wave function and a nonlinear Schroedinger Lagrangian, we obtain the effective potential experienced by a vortex at an arbitrary position in the condensate, and find that an off-center vortex will move in a circular trajectory around the trap center. We find the frequency of this precession to be smaller than the elementary excitation frequencies in the cloud. We also study the radiation of sound from a moving vortex in an infinite, uniform system, and discuss the validity of this as an approximation for the trapped case. Furthermore, we estimate the lifetime of a vortex due to imperfections in the trapping potential.
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.
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 $J(ω)/ω^3$ 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 $ω_c$, 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 investigate analytically the non-equilibrium spatial phase segregation process of a mixture of alkali Bose-Einstein condensates. Two stages (I and II) are found in analogy to the classical spinodal decomposition. The coupled non-linear Schrödinger equations enable us to give a quantitative picture of the present dynamical process in a square well trap. Both time and length scales in the stage I are obtained. We further propose that the stage II is dominated by the Josephson effect between different domains of same condensate different from scenarios in the classical spinodal decomposition. Its time scale is estimated.
We perform a mean-field study of the binary Bose-Einstein condensate mixtures as a function of the mutual repulsive interaction strength. In the phase segregated regime, we find that there are two distinct phases: the weakly segregated phase characterized by a `penetration depth' and the strongly segregated phase characterized by a healing length. In the weakly segregated phase the symmetry of the shape of each condensate will not take that of the trap because of the finite surface tension, but its total density profile still does. In the strongly segregated phase even the total density profile takes a different symmetry from that of the trap because of the mutual exclusion of the condensates. The lower critical condensate-atom number to observe the complete phase segregation is discussed. A comparison to recent experimental data suggests that the weakly segregated phase has been observed.
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.
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.
Physical arguments are presented to show that the Hall anomaly is an effect of the vortex many-body correlation rather than that of an individual vortex. Quantitatively, the characteristic energy scale in the problem, the vortex vacancy formation energy, is obtained for thin films. At low temperatures a scaling relation between the Hall and longitudinal resistivities is found, with the power depending on sample details. Near the superconducting transition temperature and for small magnetic fields the Hall conductivity is found to be proportional to the inverse of the magnetic field and to the quadratic of the difference between the measured and the transition temperatures.
Starting from the microscopic theory of Bardeen-Cooper-Schrieffer (BCS) for the fermionic superfluids, we show that the vortex dynamics can be followed naturally by extending Feynman's influence functional approach to incorporate the transverse force. There is a striking mutual independence of the transverse and longitudinal influences: The former has the topological origin and is insensitive to details, while the latter corresponds to the well-known damping kernel depending on details.